Merge branch 'lammps:develop' into compute-pace-update
This commit is contained in:
jmgoff
@ -2,7 +2,7 @@
|
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|
||||
units lj
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atom_style tri
|
||||
atom_modify first big
|
||||
atom_modify first big map yes
|
||||
|
||||
read_data data.tri.srd
|
||||
|
||||
@ -52,12 +52,12 @@ pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip
|
||||
overlap yes collision noslip inside ignore
|
||||
|
||||
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
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fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
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|
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# diagnostics
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||||
|
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@ -73,8 +73,8 @@ compute 2 all ke
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compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
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|
||||
thermo 1000
|
||||
thermo_style custom step f_1 c_tsmall f_2[9] temp press
|
||||
thermo 100
|
||||
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
|
||||
thermo_modify temp tbig
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||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z &
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@ -93,9 +93,9 @@ unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
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||||
overlap yes collision noslip tstat yes
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overlap yes collision noslip tstat yes inside ignore
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||||
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#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
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#dump 2 all custom 500 dump2.tri.srd id type &
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|
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812
examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8
Normal file
812
examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8
Normal file
@ -0,0 +1,812 @@
|
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LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537)
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# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
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|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big map yes
|
||||
|
||||
read_data data.tri.srd
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Reading data file ...
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orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
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||||
2 by 2 by 2 MPI processor grid
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reading atoms ...
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||||
1500 atoms
|
||||
1500 triangles
|
||||
read_data CPU = 0.007 seconds
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||||
|
||||
# add small particles as hi density lattice
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||||
|
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lattice sc 0.4
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Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
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region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
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Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
|
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create_atoms 2 region box
|
||||
Created 91125 atoms
|
||||
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
|
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create_atoms CPU = 0.002 seconds
|
||||
|
||||
group big type 1
|
||||
1500 atoms in group big
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||||
group small type 2
|
||||
91125 atoms in group small
|
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set group small mass 0.01
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Setting atom values ...
|
||||
91125 settings made for mass
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 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 = 1.8
|
||||
ghost atom cutoff = 1.8
|
||||
binsize = 0.9, bins = 19 19 19
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:312)
|
||||
Deleted 76354 atoms, new total = 16271
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra big include big
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
|
||||
create bodies CPU = 0.000 seconds
|
||||
125 rigid bodies with 1500 atoms
|
||||
1.8601881 = max distance from body owner to body atom
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
|
||||
|
||||
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute_modify tbig extra/dof -4500
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:527)
|
||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71)
|
||||
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:405)
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 2.9202881 0.87320391
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 17 17 17
|
||||
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
|
||||
SRD per actual grid cell = -3.9971745
|
||||
SRD viscosity = -34.162587
|
||||
big/SRD mass density ratio = -3.3753691
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 19.970837 35.150443
|
||||
ave/max big velocity = 0 0
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 16.874681, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tri/lj, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/newton
|
||||
stencil: half/multi/3d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes
|
||||
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
|
||||
0 0 1.4401779 0 -0.15917996 0 0
|
||||
100 0.36662911 1.1475389 0.24585067 1.0290503 1.1382325 18
|
||||
200 0.73133134 1.0558153 0.49986673 0.73932383 1.049638 34
|
||||
300 1.1229361 1.0218621 0.82641583 0.7589689 1.0205369 40
|
||||
400 1.5826262 0.99541508 1.2201293 0.69171726 0.99190857 52
|
||||
500 1.8834563 0.99351667 1.4778822 1.0147794 1.0005581 63
|
||||
600 2.4225372 0.98954834 1.8740966 1.1362893 0.99760042 61
|
||||
700 3.0172772 0.99153625 2.3351502 1.3284877 0.98731355 39
|
||||
800 3.5307913 1.0012521 2.6477224 1.1404922 0.9846605 52
|
||||
900 3.757064 0.99743944 2.7220653 1.4078087 0.97538456 55
|
||||
1000 4.3165268 1.002214 3.055501 1.2252972 0.99123745 63
|
||||
1100 4.2796945 1.0075233 3.1022956 1.1893685 1.0139864 69
|
||||
1200 4.3719315 1.0037271 3.0054509 1.3886162 1.002661 64
|
||||
1300 4.5628012 0.99368316 3.2690604 1.3621012 0.9810568 56
|
||||
1400 4.6954389 0.99365088 3.1940001 1.8485712 0.99571089 71
|
||||
1500 5.0270163 0.99455258 3.4120396 1.5992539 0.98294263 77
|
||||
1600 5.5897797 1.0021621 3.647347 1.7796904 0.98967622 66
|
||||
1700 5.5330194 1.0130853 3.6407996 1.8005429 1.0068955 62
|
||||
1800 5.3606928 1.0090284 3.5863618 1.3308757 1.0214092 59
|
||||
1900 5.6086195 1.0071865 3.7427101 1.5296314 0.99886937 55
|
||||
2000 5.3726474 1.0064207 3.603621 1.9473142 0.99999816 54
|
||||
2100 5.836183 1.0124553 3.7321841 1.7889397 1.0188986 59
|
||||
2200 5.5090061 1.0113832 3.5884963 1.6617781 1.0071583 59
|
||||
2300 5.4011211 1.0095947 3.520406 1.8937582 0.99689983 61
|
||||
2400 5.2219281 1.0053246 3.3699458 1.7231672 0.99899754 59
|
||||
2500 5.7695275 1.0141459 3.6211469 1.7767598 1.0143133 65
|
||||
2600 5.4206253 1.0182828 3.521774 2.0800518 1.0081603 70
|
||||
2700 5.1401099 1.0085209 3.4200563 2.4019836 1.0107652 59
|
||||
2800 6.5420721 1.0159876 4.1996904 1.863842 1.0160738 61
|
||||
2900 5.9082962 1.0106921 3.7223419 2.0586998 1.0073885 67
|
||||
3000 5.6556123 1.0099021 3.6768976 1.921987 1.0068962 76
|
||||
3100 5.2913762 1.0008567 3.4103831 1.9831969 0.99187526 80
|
||||
3200 5.1032361 0.99756662 3.1967156 2.2448433 0.99743574 93
|
||||
3300 5.2622386 1.0024934 3.3325614 2.0078097 1.0047789 86
|
||||
3400 5.1247527 0.99810102 3.1363556 1.8907269 0.98936508 82
|
||||
3500 4.9424333 1.0009344 3.2153968 1.9002728 0.99161849 71
|
||||
3600 5.1243735 1.0037377 3.3117313 2.1267438 1.0078943 65
|
||||
3700 5.5045819 1.0006119 3.5686193 2.3466538 0.99876164 68
|
||||
3800 5.5355384 1.0022639 3.6701457 2.0383269 1.0008683 76
|
||||
3900 6.4915796 1.0137733 4.3225864 2.6996933 1.0064787 79
|
||||
4000 6.6631737 1.0236248 4.3057163 2.6352666 1.0255232 75
|
||||
4100 6.2999507 1.0263876 4.0101385 2.5479077 1.0168303 79
|
||||
4200 6.7902489 1.0247392 4.4616158 2.4926177 1.0191403 91
|
||||
4300 6.505908 1.0182073 4.0675428 2.168754 1.0177101 74
|
||||
4400 5.9554283 1.0115938 3.5787297 2.9258144 1.0133896 72
|
||||
4500 6.2276609 1.0202416 3.8211204 2.5308249 1.0174385 74
|
||||
4600 6.0485727 1.0195757 3.8217434 2.6421797 1.0201441 78
|
||||
4700 6.511063 1.0220764 3.933486 2.8591093 1.0147269 83
|
||||
4800 6.9478172 1.0106414 4.345402 3.3257663 1.00469 85
|
||||
4900 6.7547045 1.0211842 4.1874576 3.6503845 1.022873 94
|
||||
5000 7.2603949 1.0234313 4.5393985 3.4667806 1.0222306 105
|
||||
5100 7.1899652 1.0256566 4.5421834 3.8137207 1.0317242 99
|
||||
5200 7.1960739 1.026746 4.4288606 3.5523675 1.0242269 97
|
||||
5300 7.1294458 1.017883 4.5799808 3.3917274 1.0145317 99
|
||||
5400 6.2810892 1.0291953 4.0109229 2.8604571 1.0289438 97
|
||||
5500 6.15246 1.0288734 3.8714587 3.2760394 1.0210757 89
|
||||
5600 6.5860526 1.0192882 4.0272883 3.3124298 1.0096258 93
|
||||
5700 7.0296116 1.0097293 4.2652722 3.6049788 1.012463 82
|
||||
5800 6.8372302 1.0140065 4.2205065 4.3686183 1.0088542 93
|
||||
5900 7.8887098 1.0090612 4.9724078 4.457317 1.0045137 92
|
||||
6000 10.120663 1.0312443 6.3025192 4.72018 1.0374722 91
|
||||
6100 9.1318265 1.0304199 5.7084296 4.244548 1.0259056 97
|
||||
6200 8.9758903 1.0295285 5.1842704 4.870955 1.0178851 95
|
||||
6300 9.0088218 1.022484 5.3742805 5.1554352 1.0138365 101
|
||||
6400 10.470322 1.0287848 6.4602103 4.5461489 1.0335978 105
|
||||
6500 11.100779 1.0347405 6.9630121 4.9840664 1.0339044 99
|
||||
6600 10.139333 1.0476079 6.4284839 4.5523893 1.0433517 104
|
||||
6700 8.9706766 1.0386262 5.8387485 4.247024 1.0408151 101
|
||||
6800 7.7799532 1.0362651 4.9946283 4.6093924 1.0274763 102
|
||||
6900 8.0866551 1.0337743 4.9942769 4.1679939 1.0454805 102
|
||||
7000 8.0224277 1.0193598 4.9380527 3.9173115 1.0185001 109
|
||||
7100 7.8361001 1.0211143 4.872673 5.3471479 1.024779 110
|
||||
7200 7.8542147 1.0057183 4.8666653 4.668317 0.99980296 122
|
||||
7300 7.9313852 1.0159181 5.0062527 4.1410294 1.0195705 114
|
||||
7400 7.2769846 1.0155245 4.6349779 4.9138895 1.0005886 119
|
||||
7500 7.5974523 1.0196295 4.7918247 4.2525935 1.0211412 124
|
||||
7600 6.7835063 1.0203187 4.2674694 4.9251624 1.0218296 113
|
||||
7700 6.4039017 1.0119494 4.1086667 5.5240525 1.0078246 118
|
||||
7800 7.0715134 1.0149015 4.2450776 4.8796778 1.0164737 125
|
||||
7900 6.3626535 1.02294 4.202778 4.482164 1.0235878 136
|
||||
8000 6.2423869 1.0212553 4.0460303 5.2753307 1.0124884 132
|
||||
8100 6.550891 1.0223318 4.2993545 5.2634985 1.0163244 143
|
||||
8200 6.9122202 1.008347 4.3551124 5.4108909 1.0084913 142
|
||||
8300 6.9104634 1.0103936 4.4622206 5.6762373 0.99559355 143
|
||||
8400 6.4918879 1.0084381 4.1050732 5.8389788 1.0036021 135
|
||||
8500 7.4377218 1.0216662 4.5229841 5.5431311 1.0260799 123
|
||||
8600 7.572198 1.0228381 4.9058913 7.1028185 1.0015164 116
|
||||
8700 8.204675 1.03457 5.2231696 6.4790244 1.0214635 132
|
||||
8800 8.3118914 1.0381333 5.1795799 6.7437722 1.0290086 132
|
||||
8900 8.2559198 1.0268665 5.218352 7.2191395 1.019804 138
|
||||
9000 8.0403128 1.0339414 4.9310394 6.4942331 1.041527 156
|
||||
9100 7.1773079 1.0397062 4.4993688 7.0272109 1.0388012 167
|
||||
9200 7.1793935 1.0373589 4.3481663 7.4894459 1.0078785 157
|
||||
9300 8.3705146 1.0248112 5.1036971 8.2173072 1.010168 156
|
||||
9400 9.4935002 1.0252907 5.7846951 9.7466018 1.028941 170
|
||||
9500 9.5208037 1.0371093 5.9635099 7.6444933 1.022673 165
|
||||
9600 8.9992217 1.0292895 5.6224192 8.8071452 1.0101362 169
|
||||
9700 8.682661 1.0422224 5.3997636 8.6827834 1.0337928 149
|
||||
9800 7.6191562 1.0350948 4.7198842 8.6125595 1.0300395 151
|
||||
9900 8.0910913 1.0319432 4.8843183 7.9013334 1.0272495 167
|
||||
10000 7.4438347 1.0186098 4.7184985 8.999795 0.99762661 177
|
||||
Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms
|
||||
|
||||
Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 33.647 | 64.106 | 79.639 | 169.5 | 39.49
|
||||
Neigh | 0.30808 | 0.44033 | 0.50863 | 9.8 | 0.27
|
||||
Comm | 26.611 | 43.438 | 74.998 | 215.7 | 26.76
|
||||
Output | 0.0072573 | 0.0087791 | 0.0097993 | 0.9 | 0.01
|
||||
Modify | 53.171 | 54.121 | 55.362 | 12.3 | 33.34
|
||||
Other | | 0.2104 | | | 0.13
|
||||
|
||||
Nlocal: 2033.88 ave 2601 max 1413 min
|
||||
Histogram: 1 2 0 0 0 0 2 1 1 1
|
||||
Nghost: 1647.25 ave 1714 max 1617 min
|
||||
Histogram: 4 0 1 0 0 1 1 0 0 1
|
||||
Neighs: 12482.8 ave 17009 max 8679 min
|
||||
Histogram: 1 1 1 0 1 1 2 0 0 1
|
||||
|
||||
Total # of neighbors = 99862
|
||||
Ave neighs/atom = 6.1374224
|
||||
Neighbor list builds = 562
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
|
||||
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 2.9202881 0.87320391
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 13 13 13
|
||||
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
|
||||
SRD per actual grid cell = -2.775698
|
||||
SRD viscosity = -12.180602
|
||||
big/SRD mass density ratio = -5.5653033
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
|
||||
# of rescaled SRD velocities = 1
|
||||
ave/max small velocity = 16.14994 40
|
||||
ave/max big velocity = 1.6952661 5.2200074
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 13.499745, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tri/lj, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/newton/tri
|
||||
stencil: half/multi/3d/tri
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes
|
||||
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
|
||||
10000 7.4438347 1.0189789 4.7184481 7.9505614 0 0
|
||||
10100 7.0770142 1.0021471 4.4491455 6.606701 1 141
|
||||
10200 6.7628072 1.002308 4.152988 8.5190386 1 125
|
||||
10300 6.5333319 1.0007472 4.1295404 8.2341747 1 109
|
||||
10400 6.3237519 1.0024029 3.8636034 9.4058128 1 95
|
||||
10500 6.6411054 1.0026261 4.2975997 7.6122304 1 82
|
||||
10600 5.7470775 1.0004827 3.7959947 7.3091777 1 67
|
||||
10700 5.9744919 1.0014977 3.6885649 7.5517197 1 59
|
||||
10800 5.8028731 1.0029627 3.7553961 6.2787087 1 49
|
||||
10900 5.3755286 1.0019318 3.5334739 7.1318348 1 41
|
||||
11000 5.3915962 1.001463 3.483172 7.6362496 1 40
|
||||
11100 5.8683672 1.0022459 3.6697589 6.9711866 1 33
|
||||
11200 5.4351801 0.99956703 3.4548447 7.0745257 1 29
|
||||
11300 4.9397513 1.0008287 3.1990325 6.0917337 1 27
|
||||
11400 4.9159845 1.0017862 3.0005677 7.653817 1 26
|
||||
11500 4.9243103 1.0013135 3.1799841 7.744414 1 23
|
||||
11600 5.2036357 1.0017984 3.2963749 7.540477 1 22
|
||||
11700 4.8991892 1.0020757 3.1773032 8.7218471 1 27
|
||||
11800 4.9489399 1.003438 3.1679764 7.1605486 1 26
|
||||
11900 4.82398 1.0019946 3.1939566 7.1397869 1 21
|
||||
12000 4.3531411 1.000532 2.8321416 7.6672501 1 23
|
||||
12100 4.8226081 1.0018898 3.0382137 6.8343432 1 25
|
||||
12200 4.7456418 1.0032116 2.9186038 7.3067818 1 20
|
||||
12300 4.4280468 1.0005857 2.734593 8.0365684 1 22
|
||||
12400 4.7311239 1.0000982 2.8898839 7.9231831 1 22
|
||||
12500 4.7261054 1.0016127 2.9090517 7.6085854 1 24
|
||||
12600 4.7719025 1.0016702 2.9736761 7.6101796 1 26
|
||||
12700 4.386248 1.001394 2.8508378 6.4765102 1 28
|
||||
12800 4.3313538 1.0019737 2.6258221 6.3164681 1 19
|
||||
12900 4.2219861 1.0007469 2.5345699 7.0901077 1 22
|
||||
13000 4.1775643 1.0011891 2.5807017 7.3579938 1 25
|
||||
13100 4.3060837 1.0008671 2.5974066 6.9301328 1 22
|
||||
13200 4.3529062 0.99996469 2.7571632 6.7806287 1 21
|
||||
13300 4.2178709 1.000673 2.7819091 7.6449064 1 18
|
||||
13400 4.2714169 1.0021294 2.7280794 8.0986691 1 18
|
||||
13500 4.3430969 1.0037732 2.6768429 8.1267941 1 18
|
||||
13600 4.3664374 1.0016083 2.6470186 6.2797727 1 20
|
||||
13700 4.4904769 1.0008993 2.7885718 7.7410193 1 22
|
||||
13800 4.2966193 1.001532 2.73862 7.9651302 1 21
|
||||
13900 4.4003185 1.0009984 2.7484129 8.7160439 1 24
|
||||
14000 4.5948292 1.0011748 2.9051777 7.842121 1 22
|
||||
14100 4.6901122 1.0001265 2.9404111 8.9953816 1 20
|
||||
14200 4.8517518 0.99998743 2.9647625 6.6450509 1 22
|
||||
14300 4.889628 1.0018051 3.0891097 7.2671824 1 20
|
||||
14400 4.578862 1.0010629 2.8239776 6.1317183 1 23
|
||||
14500 4.0865406 1.0013917 2.5119661 6.864665 1 19
|
||||
14600 4.30688 1.0009041 2.6817814 6.9007433 1 18
|
||||
14700 4.1295726 1.002342 2.6032093 7.1441648 1 15
|
||||
14800 4.2176021 1.0015157 2.7332903 6.8394683 1 16
|
||||
14900 4.2012664 0.99986345 2.6498409 7.4568241 1 15
|
||||
15000 4.6124269 1.0014751 2.9584178 7.9341875 1 16
|
||||
15100 4.947327 1.0010615 3.0784409 7.6241305 1 21
|
||||
15200 5.253281 1.002095 3.3093754 8.1872718 1 25
|
||||
15300 5.2642369 1.0017799 3.1511136 7.4668389 1 25
|
||||
15400 5.1967916 1.0029407 3.247548 8.0840111 1 23
|
||||
15500 5.7465412 1.001896 3.468834 9.5990471 1 15
|
||||
15600 6.2245772 1.0021086 3.6127689 7.8242016 1 19
|
||||
15700 5.5626191 0.99984979 3.3893723 7.8124588 1 20
|
||||
15800 5.5945727 1.0010291 3.3442448 7.0116922 1 17
|
||||
15900 5.4450219 1.0006248 3.3132381 8.4803413 1 15
|
||||
16000 5.7800459 1.001449 3.5002534 8.7989456 1 19
|
||||
16100 6.1168718 1.0008109 3.8081142 8.0119729 1 18
|
||||
16200 5.4901649 1.0020643 3.3673653 7.3483134 1 17
|
||||
16300 5.4051694 1.0015652 3.3560012 7.4641983 1 19
|
||||
16400 5.4237612 1.0012686 3.3816406 7.3845086 1 14
|
||||
16500 5.1935593 1.001754 3.3340381 7.8607712 1 16
|
||||
16600 5.539343 1.0021073 3.4164309 8.1541097 1 12
|
||||
16700 5.8922923 1.0013792 3.553426 7.5220576 1 14
|
||||
16800 5.956937 1.0005959 3.7630589 8.7417987 1 13
|
||||
16900 5.469721 1.0016219 3.5531223 8.6721994 1 13
|
||||
17000 5.3110154 1.001142 3.4167244 7.4644182 1 15
|
||||
17100 5.9226035 0.99918238 4.0244287 6.5172028 1 16
|
||||
17200 5.4897042 0.99981565 3.4350691 5.6840394 1 20
|
||||
17300 5.4302636 1.0021571 3.421473 6.4317025 1 21
|
||||
17400 5.5559131 1.0013807 3.4951403 6.874191 1 24
|
||||
17500 5.4068006 1.0010448 3.4506835 7.7069504 1 22
|
||||
17600 4.9283792 1.0007628 3.1736308 7.3098058 1 20
|
||||
17700 4.9319722 0.99935896 3.0956257 8.2120111 1 15
|
||||
17800 4.6842391 1.00037 2.9602433 7.4116352 1 17
|
||||
17900 4.7714682 1.0009332 2.9666778 7.5925131 1 17
|
||||
18000 4.7233188 1.0035687 3.0991778 7.1636357 1 10
|
||||
18100 4.6487958 1.0020255 3.10781 6.8468658 1 12
|
||||
18200 4.6284129 1.0012617 3.089724 6.3082275 1 13
|
||||
18300 4.7136404 0.99962415 3.1261978 7.3359556 1 15
|
||||
18400 5.0367681 1.0011016 3.2413493 8.3910633 1 14
|
||||
18500 4.9658104 1.0025407 3.2420827 7.4701216 1 17
|
||||
18600 4.6100059 1.0014508 3.0216884 6.553483 1 17
|
||||
18700 4.3246452 1.0016721 2.7810363 6.7450293 1 19
|
||||
18800 4.9415788 1.0012406 3.1661907 7.5544034 1 18
|
||||
18900 5.3930915 1.000138 3.2557456 7.350955 1 21
|
||||
19000 5.1938599 1.0007364 3.2398733 6.5397956 1 22
|
||||
19100 5.4433048 1.0019191 3.2699245 8.3625772 1 22
|
||||
19200 6.1303261 1.0004005 3.7823203 8.0537369 1 22
|
||||
19300 5.5762518 1.0008117 3.5689121 8.3714373 1 22
|
||||
19400 5.1316743 0.9999834 3.099381 7.405287 1 23
|
||||
19500 5.2064799 1.0012007 3.3059455 7.3499127 1 25
|
||||
19600 5.1650099 1.0023314 3.3759492 7.3637616 1 21
|
||||
19700 5.8316278 1.0023317 3.601564 7.153887 1 19
|
||||
19800 5.6435147 1.0010657 3.4967581 6.8899334 1 21
|
||||
19900 5.4071193 0.99961357 3.4977894 6.1068438 1 20
|
||||
20000 5.5058495 1.000982 3.5185057 8.5657603 1 19
|
||||
20100 5.6551271 1.0025852 3.5672369 7.8242273 1 20
|
||||
20200 5.7196886 1.002283 3.6010925 7.1449072 1 22
|
||||
20300 5.5593553 1.0009987 3.4363398 8.4141755 1 21
|
||||
20400 5.5550247 1.001081 3.3950874 8.0222131 1 20
|
||||
20500 5.4510415 0.99997273 3.5505093 7.5243655 1 18
|
||||
20600 5.8014064 1.0007611 3.8084579 7.6583499 1 18
|
||||
20700 5.7337315 1.0020309 3.7973684 8.7376766 1 17
|
||||
20800 5.2512898 0.99901254 3.5027763 7.8902791 1 14
|
||||
20900 5.3245034 1.0014504 3.3354615 6.7030716 1 17
|
||||
21000 5.2071731 1.0020459 3.3881369 5.8616999 1 20
|
||||
21100 5.3187535 1.0010762 3.2845672 8.1422146 1 21
|
||||
21200 5.5298545 0.99942313 3.4393978 7.1183144 1 22
|
||||
21300 5.8430744 1.0008652 3.719408 7.8522038 1 20
|
||||
21400 5.8190457 1.0017046 3.5624252 7.8150165 1 20
|
||||
21500 6.004585 1.0035276 3.9161914 7.7719377 1 21
|
||||
21600 6.7202635 0.99970072 3.9642141 8.7934294 1 18
|
||||
21700 6.8590346 1.0007883 4.4285217 8.9014638 1 20
|
||||
21800 6.627638 1.0012117 4.1154082 8.3153026 1 22
|
||||
21900 7.8281047 1.0008299 4.8842343 8.4016227 1 20
|
||||
22000 7.200038 1.0014681 4.4141419 9.4091956 1 18
|
||||
22100 7.7442011 1.0018051 4.7850371 8.9885489 1 15
|
||||
22200 7.4770203 1.0033558 4.7512643 8.4898148 1 17
|
||||
22300 8.1080801 1.0000019 5.2725185 9.2314625 1 14
|
||||
22400 7.8068311 1.0020672 4.9055683 8.4064748 1 12
|
||||
22500 7.4594636 1.0008427 4.6586396 8.5102986 1 11
|
||||
22600 6.9380609 1.0024634 4.2435619 10.395118 1 16
|
||||
22700 6.9338066 1.001056 4.3436179 7.9126284 1 18
|
||||
22800 6.8049493 1.0020052 4.1443407 7.8228868 1 18
|
||||
22900 6.2280158 1.0021474 3.7695343 7.3179647 1 20
|
||||
23000 5.649403 1.0017128 3.5941976 7.2964709 1 19
|
||||
23100 5.3203116 1.001912 3.3807399 6.6454551 1 15
|
||||
23200 5.8172882 1.0005742 3.6625896 8.4256312 1 15
|
||||
23300 5.9647182 1.0015466 3.9106019 8.3303303 1 14
|
||||
23400 5.9784055 1.0034542 3.7229235 7.7934273 1 14
|
||||
23500 5.377627 1.00192 3.5481778 6.8195124 1 17
|
||||
23600 5.4807136 1.0014662 3.563123 7.6356376 1 18
|
||||
23700 5.8896329 1.0013553 3.7990694 8.5513408 1 13
|
||||
23800 6.3463707 0.9999403 3.9609397 8.5741923 1 11
|
||||
23900 6.656669 1.0014998 4.1993183 9.0862996 1 13
|
||||
24000 7.583723 1.0025057 4.7628652 7.5007245 1 20
|
||||
24100 6.9868359 1.0014089 4.4369841 7.692833 1 25
|
||||
24200 7.1966062 1.0013149 4.4384528 9.5264821 1 18
|
||||
24300 6.7765706 1.0007065 4.3500477 9.4974154 1 16
|
||||
24400 7.0853466 1.0013246 4.409163 9.2215823 1 17
|
||||
24500 6.9603823 1.0004247 4.4866051 7.7870058 1 20
|
||||
24600 6.9208291 0.99953329 4.2298144 6.5732392 1 21
|
||||
24700 6.5005518 1.0026848 4.0003505 7.8094715 1 22
|
||||
24800 5.8421948 1.0012055 3.6686768 7.6078157 1 26
|
||||
24900 5.8410604 1.0023428 3.746177 6.8971309 1 22
|
||||
25000 5.8728511 1.0001747 3.7170134 7.4456816 1 19
|
||||
25100 6.0217168 1.000624 3.7756108 6.6542452 1 20
|
||||
25200 6.1939015 1.0017861 3.8943084 9.395821 1 25
|
||||
25300 6.161998 1.0010373 3.9255122 6.2228884 1 28
|
||||
25400 5.5850406 1.0018505 3.5129832 7.2551309 1 24
|
||||
25500 6.0286276 1.0009028 3.8580887 6.8065265 1 24
|
||||
25600 5.6262228 1.0005097 3.4574446 7.5061246 1 21
|
||||
25700 6.1348187 1.0009828 3.8073512 7.4818375 1 17
|
||||
25800 6.09781 1.0026426 3.9585383 9.0915939 1 21
|
||||
25900 6.2673667 1.0002269 3.8182813 9.2134822 1 21
|
||||
26000 6.6001776 1.0020444 4.041386 8.0403555 1 18
|
||||
26100 6.3063025 1.0016633 3.8649839 8.8149734 1 19
|
||||
26200 6.0046983 1.002332 3.5380766 8.6145656 1 17
|
||||
26300 5.9627788 1.0005401 3.56864 6.7821213 1 15
|
||||
26400 5.0547314 0.9998295 3.2106781 9.2935351 1 15
|
||||
26500 5.256781 1.0013131 3.2946631 8.8590275 1 15
|
||||
26600 5.6250355 1.0023929 3.5243033 8.8985058 1 17
|
||||
26700 6.0197165 1.0018323 3.7973947 7.3093402 1 17
|
||||
26800 5.4556541 1.0015309 3.4295107 8.2342049 1 18
|
||||
26900 5.420428 1.0024996 3.4374201 7.1444636 1 16
|
||||
27000 6.165624 1.0019174 3.8726016 8.6588275 1 20
|
||||
27100 6.7131697 1.0006541 4.266264 8.7063389 1 24
|
||||
27200 6.4855163 1.0016139 4.2029778 7.667611 1 29
|
||||
27300 6.0525608 1.000478 3.9169723 7.4515279 1 25
|
||||
27400 6.1426194 1.0014522 3.9176108 6.8689671 1 24
|
||||
27500 6.5981349 1.0001143 4.0620686 8.6804552 1 27
|
||||
27600 6.7827138 1.0016694 4.2764286 9.3912843 1 21
|
||||
27700 6.6368902 1.0025149 4.1452128 9.1814523 1 24
|
||||
27800 6.9791025 1.0019486 4.3989933 7.9446882 1 24
|
||||
27900 6.617142 1.0015736 4.360571 9.3732108 1 26
|
||||
28000 7.2818263 1.0014101 4.6041512 8.2398587 1 28
|
||||
28100 7.2543709 1.0007625 4.5724787 7.7373488 1 22
|
||||
28200 7.0631847 1.0023922 4.4021705 8.3290554 1 29
|
||||
28300 7.2999952 1.0012593 4.4655563 8.612666 1 27
|
||||
28400 7.4124538 1.0014043 4.5011335 8.379391 1 29
|
||||
28500 7.0350937 1.0011392 4.3528091 7.8167375 1 24
|
||||
28600 7.9659642 1.0031684 4.8732467 8.0661929 1 30
|
||||
28700 7.2865919 1.0010958 4.6650146 8.0325989 1 32
|
||||
28800 7.7039529 1.0027912 4.8299888 9.5471747 1 30
|
||||
28900 8.3288847 1.0012438 5.0785288 8.8964877 1 31
|
||||
29000 7.9348665 1.0021794 4.9393968 9.5531767 1 31
|
||||
29100 8.2473389 1.0013795 4.9890359 9.7697184 1 29
|
||||
29200 8.6383362 1.0018356 4.9856954 7.6402719 1 25
|
||||
29300 8.2504592 1.0011048 4.9631793 7.9466724 1 24
|
||||
29400 8.0502922 1.0010516 5.2521065 8.4515028 1 26
|
||||
29500 7.9475896 1.0012951 4.8584644 9.1225463 1 19
|
||||
29600 8.5641641 1.0016228 5.4361335 9.2045399 1 23
|
||||
29700 8.9932021 1.0011848 5.5727205 8.6045729 1 23
|
||||
29800 8.0320178 1.0019073 5.2837013 8.9335413 1 22
|
||||
29900 8.2676522 1.0012734 5.2213798 8.8966896 1 24
|
||||
30000 9.1848984 1.001747 5.9147628 12.096129 1 27
|
||||
30100 10.184519 0.99977427 6.4260136 11.140491 1 27
|
||||
30200 9.271472 1.0023983 6.0252189 9.6954338 1 30
|
||||
30300 9.0751572 1.000851 5.6010295 9.734426 1 28
|
||||
30400 9.4581261 1.0018449 5.6987258 9.70456 1 34
|
||||
30500 9.1574751 0.99944001 5.582217 9.300318 1 27
|
||||
30600 8.619312 1.001388 5.3503985 8.2759155 1 26
|
||||
30700 7.9370031 1.0026674 5.0702831 8.5368014 1 28
|
||||
30800 7.9221619 1.0019077 5.1278637 11.046922 1 26
|
||||
30900 9.9722884 1.0025903 6.4055506 10.167311 1 25
|
||||
31000 8.8648667 0.99962676 5.4777514 10.142102 1 21
|
||||
31100 8.576344 1.000906 5.3216342 8.7984921 1 18
|
||||
31200 7.8480974 1.0010341 4.9584917 9.0696437 1 16
|
||||
31300 8.3536183 1.0005758 5.208516 9.7971514 1 15
|
||||
31400 8.5301933 1.0007603 5.2241536 9.0257241 1 17
|
||||
31500 8.5196226 1.0018215 5.0576064 8.8847294 1 19
|
||||
31600 8.1470823 1.0023147 4.9182956 9.0205413 1 20
|
||||
31700 8.1475888 1.0005764 5.1814113 9.0603162 1 16
|
||||
31800 7.8629717 1.0014194 4.9221218 9.366291 1 16
|
||||
31900 7.7206559 1.0021082 4.9167636 7.4136735 1 16
|
||||
32000 7.5152809 1.0004752 4.6330638 8.830959 1 16
|
||||
32100 8.2693974 1.0011751 4.9094804 9.427636 1 13
|
||||
32200 8.3067661 0.9997006 4.9036865 9.0374633 1 17
|
||||
32300 7.2068514 1.0007866 4.3580755 8.6445065 1 17
|
||||
32400 6.885063 1.0011887 4.1528011 8.1199454 1 16
|
||||
32500 6.9147014 1.0020825 4.160405 7.5398034 1 19
|
||||
32600 6.8809668 1.000971 4.3312782 8.2157688 1 16
|
||||
32700 6.4818892 1.0000885 3.9433899 7.309605 1 22
|
||||
32800 6.6875555 1.0018674 4.1017504 7.2327183 1 22
|
||||
32900 7.6118502 0.99975736 4.4498951 8.5072395 1 19
|
||||
33000 7.7576909 1.0022061 4.7239551 9.2132467 1 22
|
||||
33100 7.8616235 1.000482 5.0031322 9.349805 1 20
|
||||
33200 8.2620563 1.0015059 5.2482188 10.286446 1 17
|
||||
33300 8.0217099 1.0015466 5.1166876 9.1381844 1 20
|
||||
33400 7.6565746 1.0024855 4.7594208 9.2646824 1 22
|
||||
33500 7.9633887 1.0010334 4.6754116 9.1085184 1 23
|
||||
33600 7.9566834 1.0024542 4.6712679 9.2046594 1 25
|
||||
33700 8.2639384 1.0003021 5.1326892 8.0930215 1 24
|
||||
33800 8.5648917 1.0000947 5.2099387 8.8127486 1 21
|
||||
33900 8.3593557 1.0002488 5.1291354 8.5938391 1 25
|
||||
34000 8.1922068 1.0030011 5.1441189 7.1529563 1 24
|
||||
34100 8.4260308 1.0004639 5.5876122 9.0450303 1 28
|
||||
34200 8.3014654 1.0002204 5.1964772 8.4920822 1 33
|
||||
34300 7.4736545 1.0010306 4.7932244 7.8442244 1 30
|
||||
34400 7.0023126 1.0024002 4.5665168 8.4702188 1 29
|
||||
34500 7.3797703 1.000813 4.7224014 8.4098954 1 30
|
||||
34600 7.7158761 0.99973161 4.7441628 8.5818592 1 29
|
||||
34700 7.6135895 1.0015768 4.6612844 7.2195952 1 28
|
||||
34800 7.0458078 0.99992638 4.2805357 7.4162305 1 32
|
||||
34900 7.6190708 1.0007146 4.8064968 8.2709405 1 27
|
||||
35000 7.4614294 1.0006051 4.7807207 7.7137359 1 28
|
||||
35100 7.7008336 1.0008263 4.6823621 7.0208513 1 26
|
||||
35200 8.1510766 1.000271 5.1781834 7.3231692 1 24
|
||||
35300 7.5106275 1.0010438 4.6988185 8.9418343 1 25
|
||||
35400 7.8116652 1.0009688 4.8622216 7.4624002 1 17
|
||||
35500 7.2159785 1.0027484 4.543984 8.3177043 1 21
|
||||
35600 7.6978875 1.0004834 4.7021203 8.3706905 1 20
|
||||
35700 7.7827655 1.0019919 4.775879 8.6083292 1 15
|
||||
35800 7.8433537 1.001844 4.7506574 7.3250009 1 15
|
||||
35900 7.9456497 1.0004336 4.7925775 7.9824359 1 18
|
||||
36000 8.1044513 1.0022261 5.1213755 9.211699 1 16
|
||||
36100 7.6657532 1.0025661 4.751804 8.9770412 1 19
|
||||
36200 7.909323 1.0035462 4.8435293 10.232493 1 21
|
||||
36300 8.4188244 1.0016775 5.4337725 9.2060079 1 24
|
||||
36400 8.7352689 1.0011274 5.6313351 8.6202832 1 24
|
||||
36500 8.3459273 1.0005659 5.187336 6.9333716 1 21
|
||||
36600 7.7118105 1.0018769 4.9293347 8.2789615 1 14
|
||||
36700 7.8069879 1.0014021 4.7782709 8.4841233 1 15
|
||||
36800 7.862085 1.0005342 4.8680692 8.1055023 1 16
|
||||
36900 7.9469362 1.0027815 4.9339095 9.157722 1 16
|
||||
37000 7.9085375 1.0024851 5.0921374 8.9374239 1 16
|
||||
37100 8.9464869 1.0005734 5.6837772 8.806998 1 16
|
||||
37200 8.1482632 1.0021175 5.1266453 8.5772094 1 18
|
||||
37300 7.7958072 1.0026336 4.788431 8.3233372 1 19
|
||||
37400 7.3647655 1.0015482 4.4786134 9.6606112 1 23
|
||||
37500 7.3071882 1.0003912 4.681549 8.6319438 1 17
|
||||
37600 7.8672509 1.0000478 4.7981944 8.3051478 1 14
|
||||
37700 7.9306696 0.99923102 4.9316544 9.3672856 1 15
|
||||
37800 7.7397949 0.99948557 5.1168552 8.5978047 1 17
|
||||
37900 7.9121039 1.0020122 4.9866234 7.640888 1 14
|
||||
38000 7.433451 1.0007901 4.6254894 8.0853539 1 14
|
||||
38100 7.4636908 1.0021552 4.8472833 8.1975615 1 10
|
||||
38200 7.4453077 1.0010305 4.6910943 7.8192603 1 13
|
||||
38300 7.0488536 1.0012587 4.5490462 8.190036 1 16
|
||||
38400 8.0686748 1.0016782 5.0747029 7.7242015 1 15
|
||||
38500 7.9575875 1.0007137 4.8361776 8.05268 1 15
|
||||
38600 7.6690498 1.0027522 4.8823286 9.1926516 1 20
|
||||
38700 7.1567 1.002374 4.5600354 10.098089 1 19
|
||||
38800 6.9100518 1.0008695 4.4101446 7.8832032 1 19
|
||||
38900 6.8021882 1.0017647 4.1844125 8.1858761 1 21
|
||||
39000 8.3996464 1.0010263 4.8183813 8.0997387 1 16
|
||||
39100 8.4533834 1.0021643 5.074254 11.291904 1 19
|
||||
39200 8.2406701 1.002062 5.0117425 8.778159 1 24
|
||||
39300 8.3134114 1.0008218 5.0067136 7.9871787 1 22
|
||||
39400 7.4307571 1.0014205 4.5858283 8.8596594 1 25
|
||||
39500 7.1146821 1.0016367 4.5021057 7.4890018 1 22
|
||||
39600 8.0048978 0.99992107 4.9235747 7.8770845 1 24
|
||||
39700 8.070853 1.0029024 5.0842957 9.020664 1 21
|
||||
39800 7.6939108 1.0012543 4.8986595 8.3306129 1 20
|
||||
39900 7.2915444 1.00267 4.5038291 8.3844384 1 20
|
||||
40000 7.3023994 1.0020441 4.4960911 8.1023709 1 18
|
||||
40100 7.0221648 1.0033695 4.6374149 8.3756822 1 24
|
||||
40200 7.4114756 1.0019246 4.6733475 7.6547258 1 23
|
||||
40300 7.5323108 1.0005472 4.8284493 8.2820085 1 26
|
||||
40400 7.3890772 1.0010491 4.6599273 8.9203575 1 19
|
||||
40500 7.5786764 1.0016114 4.8166885 8.6760107 1 25
|
||||
40600 8.165763 1.0006961 5.1488995 7.9321524 1 22
|
||||
40700 8.1277597 0.99933464 5.0441567 10.069551 1 16
|
||||
40800 8.1050904 1.0024705 5.4408599 8.3244459 1 21
|
||||
40900 7.805318 1.0022992 4.9965408 9.7193723 1 21
|
||||
41000 9.0130932 1.0006842 5.7931112 6.1646073 1 20
|
||||
41100 8.0387975 1.0017359 5.3355655 9.6123191 1 21
|
||||
41200 8.4484723 1.0014151 5.4461007 8.5146504 1 27
|
||||
41300 8.6181909 1.0007562 5.2963876 9.1122306 1 30
|
||||
41400 9.6762899 1.0010931 5.950456 9.2851025 1 25
|
||||
41500 9.9414226 1.0016186 6.1433384 10.741453 1 24
|
||||
41600 9.3348435 1.0003483 5.9291766 11.460717 1 20
|
||||
41700 9.6125587 1.0013661 5.8530052 9.2105722 1 19
|
||||
41800 11.383056 1.0032034 7.1988684 10.312945 1 22
|
||||
41900 10.884524 1.0034888 6.9126707 10.775457 1 20
|
||||
42000 11.071218 1.0026753 7.0004189 10.740627 1 20
|
||||
42100 11.054304 1.0008347 6.9602414 8.9885498 1 22
|
||||
42200 22.478691 1.0020466 14.997099 12.72513 1 19
|
||||
42300 18.303508 1.0027626 11.336523 12.638769 1 18
|
||||
42400 15.998712 1.0030312 9.4092725 11.070501 1 24
|
||||
42500 15.034488 1.0024472 9.3543751 11.48052 1 28
|
||||
42600 14.538257 1.0033153 9.2523745 10.909576 1 27
|
||||
42700 13.986613 1.001458 8.5544184 10.765136 1 29
|
||||
42800 13.240256 1.0027899 8.2014429 10.506497 1 32
|
||||
42900 12.784336 1.0001406 8.0823431 12.258209 1 33
|
||||
43000 13.374145 1.0012996 8.4207155 10.32817 1 31
|
||||
43100 13.142334 1.0022503 8.5908808 10.152205 1 32
|
||||
43200 12.669284 1.0018944 7.8511966 10.580104 1 32
|
||||
43300 13.155032 1.001144 8.0337768 10.6652 1 39
|
||||
43400 12.155928 1.0019472 7.5886584 11.234772 1 35
|
||||
43500 12.385603 1.0007639 7.8865245 9.3868914 1 32
|
||||
43600 12.236179 1.0027456 7.7521353 10.456701 1 42
|
||||
43700 11.49535 1.0008758 7.3633144 8.8490079 1 40
|
||||
43800 11.469157 1.0015845 7.0035577 10.594522 1 41
|
||||
43900 11.228266 1.0013014 7.0137223 8.0653711 1 38
|
||||
44000 10.56742 1.0016631 6.6908938 8.1094154 1 35
|
||||
44100 9.8964699 1.0008351 6.3550438 8.6578181 1 36
|
||||
44200 9.041539 1.0019541 5.6721401 8.6518043 1 38
|
||||
44300 9.0767434 1.0034191 5.7446596 8.3838528 1 38
|
||||
44400 9.2299608 1.0019526 5.7117964 8.3106491 1 37
|
||||
44500 9.458981 1.0030409 5.7612138 7.7679755 1 37
|
||||
44600 8.9611997 1.0014848 5.6490756 6.9224078 1 37
|
||||
44700 8.0853184 1.0018894 5.2288749 8.0910912 1 32
|
||||
44800 7.9999755 1.0015853 4.8088312 7.1854304 1 30
|
||||
44900 7.6598023 1.0009751 4.6690664 7.1999858 1 28
|
||||
45000 7.4939315 1.0010307 4.8119666 7.9615769 1 26
|
||||
45100 7.4690079 0.99913423 4.9704428 7.6026835 1 32
|
||||
45200 7.7001199 1.001626 4.9315953 7.4926686 1 25
|
||||
45300 7.8794405 1.0011648 4.8624857 8.0804457 1 26
|
||||
45400 7.493909 1.0016257 4.7631808 8.0330626 1 26
|
||||
45500 7.5963141 1.0005825 4.7220659 7.0971298 1 23
|
||||
45600 7.9028612 1.0017008 4.9561022 8.440428 1 23
|
||||
45700 7.2285584 1.0006033 4.5521456 9.385579 1 23
|
||||
45800 7.5687284 1.0024318 4.8557498 8.3052658 1 23
|
||||
45900 7.8938604 1.0013937 5.1393944 5.5323667 1 26
|
||||
46000 8.318466 1.0020803 5.4761811 8.2227801 1 25
|
||||
46100 7.9169512 1.0024598 5.0406355 8.64365 1 27
|
||||
46200 7.5535458 1.0016318 4.8010133 9.370726 1 26
|
||||
46300 7.8926896 1.0001525 5.18463 7.9830196 1 27
|
||||
46400 7.487145 1.002671 4.7718312 8.300134 1 29
|
||||
46500 7.3564658 1.0006114 4.6762189 7.34947 1 26
|
||||
46600 7.2261291 1.0005569 4.4751221 6.5847138 1 27
|
||||
46700 7.2943203 1.0020164 4.3335327 7.7296507 1 25
|
||||
46800 8.5849411 1.0014634 5.4501531 9.0933014 1 25
|
||||
46900 10.176752 1.0023799 6.0456779 9.4050423 1 16
|
||||
47000 9.1913098 1.0029076 5.7577256 9.1826215 1 22
|
||||
47100 9.5479771 1.0022102 6.1100973 8.9440056 1 28
|
||||
47200 9.9944172 1.0004924 6.3649417 9.1507264 1 25
|
||||
47300 9.3543283 1.0013246 6.0873147 10.41657 1 24
|
||||
47400 8.594101 1.0020068 5.6864295 9.2388304 1 24
|
||||
47500 9.3191964 1.002411 6.0537511 9.3506828 1 23
|
||||
47600 8.1615734 1.001364 5.3757905 10.303962 1 30
|
||||
47700 8.3615046 1.0003075 5.2727936 9.3162209 1 32
|
||||
47800 8.3566467 1.0026031 5.4379524 7.7644422 1 33
|
||||
47900 8.4062556 1.0006471 5.3098736 8.0181121 1 33
|
||||
48000 8.2233307 1.0012304 4.9650027 9.2644288 1 34
|
||||
48100 8.4495256 1.000088 4.9940422 10.01023 1 27
|
||||
48200 8.8068097 1.0014275 5.4732649 8.410093 1 31
|
||||
48300 8.0008187 1.0017459 4.7732764 9.25726 1 27
|
||||
48400 7.7242529 1.0026909 4.9084505 8.7147295 1 30
|
||||
48500 8.3752816 1.001333 5.1071228 8.2267308 1 32
|
||||
48600 9.0777805 1.0019328 5.7331841 9.6679383 1 29
|
||||
48700 9.3623061 1.0001767 5.7117062 8.396895 1 25
|
||||
48800 8.1186637 1.0013185 5.2697427 8.6058372 1 27
|
||||
48900 7.3685497 1.0007173 4.6097553 7.8047228 1 24
|
||||
49000 7.1661421 1.0023152 4.5389038 8.8759552 1 22
|
||||
49100 6.9857144 1.0016394 4.6489319 8.2022359 1 24
|
||||
49200 6.7160336 1.0018413 4.2488082 8.3393245 1 25
|
||||
49300 7.9703755 1.0010628 5.2328567 7.968278 1 28
|
||||
49400 8.2628465 1.0010877 5.2292977 8.0196533 1 27
|
||||
49500 8.1436558 1.0015175 5.0344712 8.0712037 1 30
|
||||
49600 8.5182498 1.0021589 5.1029028 8.6869789 1 28
|
||||
49700 8.3604444 1.0015016 5.0333696 9.4861656 1 25
|
||||
49800 7.336335 1.0020055 4.6365173 8.7210022 1 30
|
||||
49900 7.432996 1.0016415 4.7090587 8.7033033 1 29
|
||||
50000 7.4937053 1.001014 4.7212573 9.0890363 1 29
|
||||
Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms
|
||||
|
||||
Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 293.48 | 403.7 | 545.29 | 357.5 | 40.39
|
||||
Neigh | 2.4176 | 3.2721 | 3.8303 | 25.2 | 0.33
|
||||
Comm | 163.58 | 305.88 | 419.83 | 416.7 | 30.60
|
||||
Output | 0.032483 | 0.034794 | 0.040514 | 1.2 | 0.00
|
||||
Modify | 281.15 | 285.67 | 293.8 | 24.3 | 28.58
|
||||
Other | | 1.023 | | | 0.10
|
||||
|
||||
Nlocal: 2033.88 ave 2657 max 1198 min
|
||||
Histogram: 2 0 0 0 0 2 1 0 1 2
|
||||
Nghost: 1628.12 ave 1719 max 1569 min
|
||||
Histogram: 2 0 1 1 2 1 0 0 0 1
|
||||
Neighs: 13566 ave 18212 max 8488 min
|
||||
Histogram: 1 0 0 1 2 1 2 0 0 1
|
||||
|
||||
Total # of neighbors = 108528
|
||||
Ave neighs/atom = 6.6700264
|
||||
Neighbor list builds = 2447
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:19:22
|
||||
@ -1,243 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
|
||||
|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big
|
||||
|
||||
read_data data.tri.srd
|
||||
orthogonal box = (-8.43734 -8.43734 -8.43734) to (8.43734 8.43734 8.43734)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1500 atoms
|
||||
1500 triangles
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.35721 1.35721 1.35721
|
||||
region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
|
||||
Lattice spacing in x,y,z = 0.368403 0.368403 0.368403
|
||||
create_atoms 2 region box
|
||||
Created 91125 atoms
|
||||
|
||||
group big type 1
|
||||
1500 atoms in group big
|
||||
group small type 2
|
||||
91125 atoms in group small
|
||||
set group small mass 0.01
|
||||
91125 settings made for mass
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
Deleted 76354 atoms, new total = 16271
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule big include big
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
|
||||
125 rigid bodies with 1500 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
|
||||
|
||||
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step f_1 c_tsmall f_2[9] temp press
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
run 10000
|
||||
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 1.46014 0.436602
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 67 67 67
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.251861 0.251861 0.251861
|
||||
SRD per actual grid cell = 0.0647662
|
||||
SRD viscosity = -1.09837
|
||||
big/SRD mass density ratio = 24.668
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 19.9708 35.1504
|
||||
ave/max big velocity = 0 0
|
||||
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
|
||||
Memory usage per processor = 116.135 Mbytes
|
||||
Step 1 tsmall 2[9] Temp Press
|
||||
0 0 1.4405441 0 0 -0.15917996
|
||||
1000 1.0535509 1.1241378 1.1224038 0 0.15526438
|
||||
2000 2.4635987 1.0240667 0.94231519 0 0.011069846
|
||||
3000 3.1093028 1.0070585 1.0176028 0 0.34124888
|
||||
4000 2.9524179 1.0101774 1.0311733 0 -0.22118101
|
||||
5000 2.9175438 1.0109144 1.0284445 0 0.1839507
|
||||
6000 3.3200928 0.99108983 0.95968219 0 1.0229339
|
||||
7000 3.3020156 0.99661428 0.98000621 0 2.3333851
|
||||
8000 4.1500999 0.99129645 0.99723707 0 4.3054414
|
||||
9000 6.537028 1.0074533 1.0251098 0 18.782913
|
||||
10000 16.233245 1.0145766 1.0219787 0 147.83787
|
||||
Loop time of 228.558 on 8 procs for 10000 steps with 16271 atoms
|
||||
|
||||
Pair time (%) = 145.018 (63.4492)
|
||||
Neigh time (%) = 32.6283 (14.2757)
|
||||
Comm time (%) = 43.3283 (18.9572)
|
||||
Outpt time (%) = 0.000848889 (0.00037141)
|
||||
Other time (%) = 7.58254 (3.31755)
|
||||
|
||||
Nlocal: 2033.88 ave 2092 max 1902 min
|
||||
Histogram: 1 0 0 0 1 1 0 1 1 3
|
||||
Nghost: 2805 ave 2855 max 2751 min
|
||||
Histogram: 1 0 2 1 0 0 0 2 1 1
|
||||
Neighs: 30026.5 ave 38700 max 24367 min
|
||||
Histogram: 1 0 2 1 3 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 240212
|
||||
Ave neighs/atom = 14.7632
|
||||
Neighbor list builds = 501
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
triclinic box = (-5.0624 -5.0624 -5.0624) to (5.0624 5.0624 5.0624) with tilt (0 0 0)
|
||||
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 1.46014 0.436602
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 40 40 40
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25312 0.25312 0.25312
|
||||
SRD per actual grid cell = -1.93929
|
||||
SRD viscosity = -0.36972
|
||||
big/SRD mass density ratio = -0.836253
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
|
||||
# of rescaled SRD velocities = 1
|
||||
ave/max small velocity = 16.0639 40
|
||||
ave/max big velocity = 2.05735 6.73052
|
||||
Memory usage per processor = 65.2471 Mbytes
|
||||
Step 1 tsmall 2[9] Temp Press
|
||||
10000 16.233245 1.0144194 0 0 146.27032
|
||||
11000 17.301043 1.0619209 1 0 84.226323
|
||||
12000 13.481177 1.063945 1 0 80.42834
|
||||
13000 12.616615 1.0536125 1 0 68.365053
|
||||
14000 12.16592 1.0581344 1 0 59.709941
|
||||
15000 10.811557 1.0650453 1 0 59.869798
|
||||
16000 9.9303081 1.0641012 1 0 59.289126
|
||||
17000 10.452639 1.0589904 1 0 52.680235
|
||||
18000 9.2488947 1.0556713 1 0 51.044123
|
||||
19000 8.7179788 1.0566791 1 0 50.927924
|
||||
20000 7.8641299 1.0668891 1 0 53.961014
|
||||
21000 8.4333975 1.0628003 1 0 54.677068
|
||||
22000 8.554623 1.0591872 1 0 51.784737
|
||||
23000 7.895462 1.0598512 1 0 53.26885
|
||||
24000 7.7014869 1.055569 1 0 54.236941
|
||||
25000 7.508138 1.0581539 1 0 53.297709
|
||||
26000 8.0707381 1.0586451 1 0 51.411341
|
||||
27000 8.224223 1.0585509 1 0 52.775784
|
||||
28000 8.8720461 1.0648837 1 0 49.681447
|
||||
29000 8.503895 1.0538278 1 0 52.478556
|
||||
30000 8.2272425 1.0625583 1 0 52.795709
|
||||
31000 8.4626161 1.0599557 1 0 52.905343
|
||||
32000 7.7410527 1.0587681 1 0 57.464472
|
||||
33000 7.2765481 1.0677531 1 0 59.46728
|
||||
34000 7.036016 1.0640728 1 0 60.636828
|
||||
35000 8.497203 1.0577458 1 0 55.257312
|
||||
36000 8.9218761 1.0585038 1 0 55.668201
|
||||
37000 8.0469115 1.0561193 1 0 58.711565
|
||||
38000 8.6456966 1.0663818 1 0 53.691658
|
||||
39000 8.566667 1.0616928 1 0 52.866468
|
||||
40000 7.7081259 1.0577046 1 0 54.105829
|
||||
41000 7.4051952 1.0570277 1 0 56.094997
|
||||
42000 7.331432 1.0632261 1 0 55.661067
|
||||
43000 7.5587053 1.0602077 1 0 54.30762
|
||||
44000 7.4521497 1.0594391 1 0 52.993548
|
||||
45000 7.6234559 1.0641992 1 0 53.352202
|
||||
46000 8.0659693 1.0609367 1 0 50.302682
|
||||
47000 7.5227882 1.0563543 1 0 50.43551
|
||||
48000 8.0798684 1.0628968 1 0 48.419201
|
||||
49000 7.130784 1.0594143 1 0 50.656081
|
||||
50000 7.3219268 1.0608236 1 0 54.808358
|
||||
Loop time of 1651.84 on 8 procs for 40000 steps with 16271 atoms
|
||||
|
||||
Pair time (%) = 1232.76 (74.6296)
|
||||
Neigh time (%) = 171.893 (10.4061)
|
||||
Comm time (%) = 193.625 (11.7218)
|
||||
Outpt time (%) = 0.00338289 (0.000204795)
|
||||
Other time (%) = 53.5578 (3.24231)
|
||||
|
||||
Nlocal: 2033.88 ave 2229 max 1953 min
|
||||
Histogram: 2 1 2 2 0 0 0 0 0 1
|
||||
Nghost: 2757.88 ave 2810 max 2692 min
|
||||
Histogram: 1 1 1 0 1 0 0 1 1 2
|
||||
Neighs: 30098.6 ave 37369 max 25592 min
|
||||
Histogram: 1 3 0 1 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 240789
|
||||
Ave neighs/atom = 14.7987
|
||||
Neighbor list builds = 2007
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
@ -1,9 +1,8 @@
|
||||
##########################################
|
||||
# CMake build system for coupling to the LAMMPS library
|
||||
# -*- CMake -*- file for example programs that use the LAMMPS library
|
||||
# where the library is loaded dynamically at runtime.
|
||||
##########################################
|
||||
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
# enforce out-of-source build
|
||||
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
|
||||
@ -23,9 +22,7 @@ endif()
|
||||
# and prints lots of pointless warnings about "unsafe" functions
|
||||
if(MSVC)
|
||||
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
|
||||
if(LAMMPS_EXCEPTIONS)
|
||||
add_compile_options(/EHsc)
|
||||
endif()
|
||||
add_compile_options(/EHsc)
|
||||
endif()
|
||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||
endif()
|
||||
|
||||
@ -239,7 +239,7 @@ struct _liblammpsplugin {
|
||||
|
||||
void (*free)(void *);
|
||||
|
||||
void (*is_running)(void *);
|
||||
int (*is_running)(void *);
|
||||
void (*force_timeout)(void *);
|
||||
|
||||
int (*has_error)(void *);
|
||||
|
||||
@ -1,4 +1,6 @@
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
# -*- CMake -*- file for simple examples using the LAMMPS library interface
|
||||
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
# enforce out-of-source build
|
||||
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
|
||||
@ -18,9 +20,7 @@ endif()
|
||||
# and prints lots of pointless warnings about "unsafe" functions
|
||||
if(MSVC)
|
||||
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
|
||||
if(LAMMPS_EXCEPTIONS)
|
||||
add_compile_options(/EHsc)
|
||||
endif()
|
||||
add_compile_options(/EHsc)
|
||||
endif()
|
||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||
endif()
|
||||
|
||||
@ -39,7 +39,7 @@ fix INT all nve
|
||||
###############################################################################
|
||||
# OUTPUT
|
||||
###############################################################################
|
||||
dump 1 all atom 1 dump.hdnnp
|
||||
# dump 1 all atom 1 dump.hdnnp
|
||||
|
||||
###############################################################################
|
||||
# SIMULATION
|
||||
|
||||
53
examples/PACKAGES/hdnnp/in.hybrid
Normal file
53
examples/PACKAGES/hdnnp/in.hybrid
Normal file
@ -0,0 +1,53 @@
|
||||
###############################################################################
|
||||
# MD simulation for HDNNP water
|
||||
###############################################################################
|
||||
|
||||
###############################################################################
|
||||
# VARIABLES
|
||||
###############################################################################
|
||||
clear
|
||||
# Configuration files
|
||||
variable cfgFile string "data.H2O-360mol"
|
||||
# Timesteps
|
||||
variable numSteps equal 10
|
||||
variable dt equal 0.0005
|
||||
# HDNNP
|
||||
variable hdnnpCutoff equal 6.36
|
||||
variable hdnnpDir string "hdnnp-data"
|
||||
|
||||
###############################################################################
|
||||
# GENERAL SETUP
|
||||
###############################################################################
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
|
||||
create_box 3 box
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
read_data ${cfgFile} add append offset 1 0 0 0 0
|
||||
timestep ${dt}
|
||||
thermo 1
|
||||
|
||||
###############################################################################
|
||||
# HDNNP
|
||||
###############################################################################
|
||||
pair_style hybrid lj/cut 6.0 hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_coeff * * hdnnp NULL H O
|
||||
pair_coeff 1 * lj/cut 0.1 3.0
|
||||
|
||||
###############################################################################
|
||||
# INTEGRATOR
|
||||
###############################################################################
|
||||
fix INT all nve
|
||||
|
||||
###############################################################################
|
||||
# OUTPUT
|
||||
###############################################################################
|
||||
#dump 1 all atom 1 dump.hdnnp
|
||||
|
||||
###############################################################################
|
||||
# SIMULATION
|
||||
###############################################################################
|
||||
run ${numSteps}
|
||||
667
examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.1
Normal file
667
examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.1
Normal file
@ -0,0 +1,667 @@
|
||||
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
###############################################################################
|
||||
# MD simulation for HDNNP water
|
||||
###############################################################################
|
||||
|
||||
###############################################################################
|
||||
# VARIABLES
|
||||
###############################################################################
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Configuration files
|
||||
variable cfgFile string "data.H2O-360mol"
|
||||
# Timesteps
|
||||
variable numSteps equal 10
|
||||
variable dt equal 0.0005
|
||||
# HDNNP
|
||||
variable hdnnpCutoff equal 6.36
|
||||
variable hdnnpDir string "hdnnp-data"
|
||||
|
||||
###############################################################################
|
||||
# GENERAL SETUP
|
||||
###############################################################################
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
read_data ${cfgFile}
|
||||
read_data data.H2O-360mol
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1080 atoms
|
||||
read_data CPU = 0.004 seconds
|
||||
timestep ${dt}
|
||||
timestep 0.0005
|
||||
thermo 1
|
||||
|
||||
###############################################################################
|
||||
# HDNNP
|
||||
###############################################################################
|
||||
pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_style hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_style hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_coeff * * H O
|
||||
|
||||
###############################################################################
|
||||
# INTEGRATOR
|
||||
###############################################################################
|
||||
fix INT all nve
|
||||
|
||||
###############################################################################
|
||||
# OUTPUT
|
||||
###############################################################################
|
||||
# dump 1 all atom 1 dump.hdnnp
|
||||
|
||||
###############################################################################
|
||||
# SIMULATION
|
||||
###############################################################################
|
||||
run ${numSteps}
|
||||
run 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
|
||||
|
||||
@Article{Singraber19,
|
||||
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
|
||||
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
|
||||
Neural Network Potentials},
|
||||
year = {2019},
|
||||
month = mar,
|
||||
volume = {15},
|
||||
pages = {1827--1840},
|
||||
doi = {10.1021/acs.jctc.8b00770},
|
||||
journal = {J.~Chem.\ Theory Comput.},
|
||||
number = {3}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
|
||||
*******************************************************************************
|
||||
|
||||
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
|
||||
------------------------------------------------------------------
|
||||
|
||||
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
|
||||
(version.h): v2.2.0
|
||||
------------------------------------------------------------
|
||||
Git branch : collected-small-changes
|
||||
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
|
||||
Compile date/time : Aug 23 2023 08:43:11
|
||||
------------------------------------------------------------
|
||||
|
||||
Features/Flags:
|
||||
------------------------------------------------------------
|
||||
Symmetry function groups : enabled
|
||||
Symmetry function cache : enabled
|
||||
Timing function available : available
|
||||
Asymmetric polynomial SFs : available
|
||||
SF low neighbor number check : enabled
|
||||
SF derivative memory layout : reduced
|
||||
MPI explicitly disabled : no
|
||||
------------------------------------------------------------
|
||||
|
||||
Please cite the following papers when publishing results obtained with n²p²:
|
||||
-------------------------------------------------------------------------------
|
||||
* General citation for n²p² and the LAMMPS interface:
|
||||
|
||||
Singraber, A.; Behler, J.; Dellago, C.
|
||||
Library-Based LAMMPS Implementation of High-Dimensional
|
||||
Neural Network Potentials.
|
||||
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
|
||||
https://doi.org/10.1021/acs.jctc.8b00770
|
||||
-------------------------------------------------------------------------------
|
||||
* Additionally, if you use the NNP training features of n²p²:
|
||||
|
||||
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
|
||||
Parallel Multistream Training of High-Dimensional Neural
|
||||
Network Potentials.
|
||||
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
|
||||
https://doi.org/10.1021/acs.jctc.8b01092
|
||||
-------------------------------------------------------------------------------
|
||||
* Additionally, if polynomial symmetry functions are used:
|
||||
|
||||
Bircher, M. P.; Singraber, A.; Dellago, C.
|
||||
Improved Description of Atomic Environments Using Low-Cost
|
||||
Polynomial Functions with Compact Support.
|
||||
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
|
||||
https://arxiv.org/abs/2010.14414
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SETTINGS FILE ******************************************************
|
||||
|
||||
Settings file name: hdnnp-data/input.nn
|
||||
Read 120 lines.
|
||||
Found 70 lines with keywords.
|
||||
This settings file defines a short-range only NNP.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NORMALIZATION ******************************************************
|
||||
|
||||
Data set normalization is used.
|
||||
Mean energy per atom : -2.5521343547039809E+01
|
||||
Conversion factor energy : 2.4265748255366972E+02
|
||||
Conversion factor length : 5.8038448995319847E+00
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: ELEMENT MAP ********************************************************
|
||||
|
||||
Number of element strings found: 2
|
||||
Element 0: H ( 1)
|
||||
Element 1: O ( 8)
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: ELEMENTS ***********************************************************
|
||||
|
||||
Number of elements is consistent: 2
|
||||
Atomic energy offsets per element:
|
||||
Element 0: 0.00000000E+00
|
||||
Element 1: 0.00000000E+00
|
||||
Energy offsets are automatically subtracted from reference energies.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: CUTOFF FUNCTIONS ***************************************************
|
||||
|
||||
Parameter alpha for inner cutoff: 0.000000
|
||||
Inner cutoff = Symmetry function cutoff * alpha
|
||||
Equal cutoff function type for all symmetry functions:
|
||||
CutoffFunction::CT_TANHU (2)
|
||||
f(r) = tanh^3(1 - r/rc)
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTIONS *************************************************
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind .... Symmetry function index.
|
||||
ec ..... Central atom element.
|
||||
tp ..... Symmetry function type.
|
||||
sbtp ... Symmetry function subtype (e.g. cutoff type).
|
||||
e1 ..... Neighbor 1 element.
|
||||
e2 ..... Neighbor 2 element.
|
||||
eta .... Gaussian width eta.
|
||||
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
|
||||
angl.... Left cutoff angle for polynomial.
|
||||
angr.... Right cutoff angle for polynomial.
|
||||
la ..... Angle prefactor lambda.
|
||||
zeta ... Angle term exponent zeta.
|
||||
rc ..... Cutoff radius / right cutoff radius for polynomial.
|
||||
a ...... Free parameter alpha (e.g. cutoff alpha).
|
||||
ln ..... Line number in settings file.
|
||||
|
||||
Short range atomic symmetry functions element H :
|
||||
-------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
|
||||
-------------------------------------------------------------------------------------------------
|
||||
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
|
||||
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
|
||||
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
|
||||
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
|
||||
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
|
||||
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
|
||||
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
|
||||
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
|
||||
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
|
||||
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
|
||||
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
|
||||
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
|
||||
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
|
||||
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
|
||||
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
|
||||
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
|
||||
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
|
||||
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
|
||||
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
|
||||
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
|
||||
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
|
||||
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
|
||||
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
|
||||
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
|
||||
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
|
||||
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
|
||||
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
|
||||
-------------------------------------------------------------------------------------------------
|
||||
Short range atomic symmetry functions element O :
|
||||
-------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
|
||||
-------------------------------------------------------------------------------------------------
|
||||
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
|
||||
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
|
||||
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
|
||||
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
|
||||
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
|
||||
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
|
||||
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
|
||||
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
|
||||
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
|
||||
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
|
||||
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
|
||||
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
|
||||
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
|
||||
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
|
||||
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
|
||||
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
|
||||
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
|
||||
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
|
||||
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
|
||||
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
|
||||
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
|
||||
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
|
||||
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
|
||||
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
|
||||
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
|
||||
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
|
||||
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
|
||||
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
|
||||
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
|
||||
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
|
||||
-------------------------------------------------------------------------------------------------
|
||||
Minimum cutoff radius for element H: 12.000000
|
||||
Minimum cutoff radius for element O: 12.000000
|
||||
Maximum cutoff radius (global) : 12.000000
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
|
||||
|
||||
Symmetry function derivatives memory table for element H :
|
||||
-------------------------------------------------------------------------------
|
||||
Relevant symmetry functions for neighbors with element:
|
||||
- H: 15 of 27 ( 55.6 %)
|
||||
- O: 19 of 27 ( 70.4 %)
|
||||
-------------------------------------------------------------------------------
|
||||
Symmetry function derivatives memory table for element O :
|
||||
-------------------------------------------------------------------------------
|
||||
Relevant symmetry functions for neighbors with element:
|
||||
- H: 18 of 30 ( 60.0 %)
|
||||
- O: 16 of 30 ( 53.3 %)
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
|
||||
|
||||
Element H: in total 4 caches, used 17.00 times on average.
|
||||
Element O: in total 4 caches, used 17.00 times on average.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind .... Symmetry function index.
|
||||
ec ..... Central atom element.
|
||||
tp ..... Symmetry function type.
|
||||
sbtp ... Symmetry function subtype (e.g. cutoff type).
|
||||
e1 ..... Neighbor 1 element.
|
||||
e2 ..... Neighbor 2 element.
|
||||
eta .... Gaussian width eta.
|
||||
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
|
||||
angl.... Left cutoff angle for polynomial.
|
||||
angr.... Right cutoff angle for polynomial.
|
||||
la ..... Angle prefactor lambda.
|
||||
zeta ... Angle term exponent zeta.
|
||||
rc ..... Cutoff radius / right cutoff radius for polynomial.
|
||||
a ...... Free parameter alpha (e.g. cutoff alpha).
|
||||
ln ..... Line number in settings file.
|
||||
mi ..... Member index.
|
||||
sfi .... Symmetry function index.
|
||||
e ...... Recalculate exponential term.
|
||||
|
||||
Short range atomic symmetry function groups element H :
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
|
||||
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
|
||||
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
|
||||
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
|
||||
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
|
||||
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
|
||||
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
|
||||
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
|
||||
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
|
||||
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
|
||||
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
|
||||
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
|
||||
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
|
||||
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
|
||||
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
|
||||
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
|
||||
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
|
||||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
|
||||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
|
||||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
|
||||
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
|
||||
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
Short range atomic symmetry function groups element O :
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
|
||||
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
|
||||
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
|
||||
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
|
||||
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
|
||||
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
|
||||
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
|
||||
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
|
||||
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
|
||||
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
|
||||
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
|
||||
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
|
||||
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
|
||||
- - - - - 3.000E-01 4.000E+00 - - 85 6 12
|
||||
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
|
||||
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
|
||||
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
|
||||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
|
||||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
|
||||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
|
||||
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
|
||||
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NEURAL NETWORKS ****************************************************
|
||||
|
||||
Normalize neurons (all elements): 0
|
||||
-------------------------------------------------------------------------------
|
||||
Atomic short range NN for element H :
|
||||
Number of weights : 1325
|
||||
Number of biases : 51
|
||||
Number of connections: 1376
|
||||
Architecture 27 25 25 1
|
||||
-------------------------------------------------------------------------------
|
||||
1 G t t l
|
||||
2 G t t
|
||||
3 G t t
|
||||
4 G t t
|
||||
5 G t t
|
||||
6 G t t
|
||||
7 G t t
|
||||
8 G t t
|
||||
9 G t t
|
||||
10 G t t
|
||||
11 G t t
|
||||
12 G t t
|
||||
13 G t t
|
||||
14 G t t
|
||||
15 G t t
|
||||
16 G t t
|
||||
17 G t t
|
||||
18 G t t
|
||||
19 G t t
|
||||
20 G t t
|
||||
21 G t t
|
||||
22 G t t
|
||||
23 G t t
|
||||
24 G t t
|
||||
25 G t t
|
||||
26 G
|
||||
27 G
|
||||
-------------------------------------------------------------------------------
|
||||
Atomic short range NN for element O :
|
||||
Number of weights : 1400
|
||||
Number of biases : 51
|
||||
Number of connections: 1451
|
||||
Architecture 30 25 25 1
|
||||
-------------------------------------------------------------------------------
|
||||
1 G t t l
|
||||
2 G t t
|
||||
3 G t t
|
||||
4 G t t
|
||||
5 G t t
|
||||
6 G t t
|
||||
7 G t t
|
||||
8 G t t
|
||||
9 G t t
|
||||
10 G t t
|
||||
11 G t t
|
||||
12 G t t
|
||||
13 G t t
|
||||
14 G t t
|
||||
15 G t t
|
||||
16 G t t
|
||||
17 G t t
|
||||
18 G t t
|
||||
19 G t t
|
||||
20 G t t
|
||||
21 G t t
|
||||
22 G t t
|
||||
23 G t t
|
||||
24 G t t
|
||||
25 G t t
|
||||
26 G
|
||||
27 G
|
||||
28 G
|
||||
29 G
|
||||
30 G
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
|
||||
|
||||
Equal scaling type for all symmetry functions:
|
||||
Scaling type::ST_SCALECENTER (3)
|
||||
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
|
||||
Smin = 0.000000
|
||||
Smax = 1.000000
|
||||
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
|
||||
-------------------------------------------------------------------------------
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind ..... Symmetry function index.
|
||||
min ..... Minimum symmetry function value.
|
||||
max ..... Maximum symmetry function value.
|
||||
mean .... Mean symmetry function value.
|
||||
sigma ... Standard deviation of symmetry function values.
|
||||
sf ...... Scaling factor for derivatives.
|
||||
Smin .... Desired minimum scaled symmetry function value.
|
||||
Smax .... Desired maximum scaled symmetry function value.
|
||||
t ....... Scaling type.
|
||||
|
||||
Scaling data for symmetry functions element H :
|
||||
-------------------------------------------------------------------------------
|
||||
ind min max mean sigma sf Smin Smax t
|
||||
-------------------------------------------------------------------------------
|
||||
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
|
||||
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
|
||||
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
|
||||
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
|
||||
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
|
||||
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
|
||||
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
|
||||
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
|
||||
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
|
||||
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
|
||||
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
|
||||
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
|
||||
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
|
||||
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
|
||||
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
|
||||
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
|
||||
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
|
||||
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
|
||||
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
|
||||
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
|
||||
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
|
||||
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
|
||||
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
|
||||
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
|
||||
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
|
||||
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
|
||||
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
|
||||
-------------------------------------------------------------------------------
|
||||
Scaling data for symmetry functions element O :
|
||||
-------------------------------------------------------------------------------
|
||||
ind min max mean sigma sf Smin Smax t
|
||||
-------------------------------------------------------------------------------
|
||||
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
|
||||
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
|
||||
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
|
||||
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
|
||||
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
|
||||
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
|
||||
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
|
||||
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
|
||||
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
|
||||
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
|
||||
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
|
||||
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
|
||||
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
|
||||
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
|
||||
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
|
||||
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
|
||||
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
|
||||
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
|
||||
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
|
||||
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
|
||||
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
|
||||
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
|
||||
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
|
||||
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
|
||||
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
|
||||
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
|
||||
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
|
||||
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
|
||||
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
|
||||
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
|
||||
|
||||
Equal symmetry function statistics for all elements.
|
||||
Collect min/max/mean/sigma : 0
|
||||
Collect extrapolation warnings : 1
|
||||
Write extrapolation warnings immediately to stderr: 0
|
||||
Halt on any extrapolation warning : 0
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
|
||||
|
||||
Short NN weight file name format: hdnnp-data/weights.%03d.data
|
||||
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
|
||||
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: LAMMPS INTERFACE ***************************************************
|
||||
|
||||
Individual extrapolation warnings will not be shown.
|
||||
Extrapolation warning summary will be shown every 5 timesteps.
|
||||
The simulation will be stopped when 100 extrapolation warnings are exceeded.
|
||||
Extrapolation warnings are accumulated over all time steps.
|
||||
-------------------------------------------------------------------------------
|
||||
CAUTION: If the LAMMPS unit system differs from the one used
|
||||
during NN training, appropriate conversion factors
|
||||
must be provided (see keywords cflength and cfenergy).
|
||||
|
||||
Length unit conversion factor: 1.8897261327999999E+00
|
||||
Energy unit conversion factor: 3.6749325399999998E-02
|
||||
|
||||
Checking consistency of cutoff radii (in LAMMPS units):
|
||||
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
|
||||
Maximum symmetry function cutoff: 6.350E+00
|
||||
Cutoff radii are consistent.
|
||||
-------------------------------------------------------------------------------
|
||||
Element mapping string from LAMMPS to n2p2: "1:H,2:O"
|
||||
|
||||
CAUTION: Please ensure that this mapping between LAMMPS
|
||||
atom types and NNP elements is consistent:
|
||||
|
||||
---------------------------
|
||||
LAMMPS type | NNP element
|
||||
---------------------------
|
||||
1 <-> H ( 1)
|
||||
2 <-> O ( 8)
|
||||
---------------------------
|
||||
|
||||
NNP setup for LAMMPS completed.
|
||||
*******************************************************************************
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.36
|
||||
ghost atom cutoff = 8.36
|
||||
binsize = 4.18, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair hdnnp, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.021 | 4.021 | 4.021 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -750069.48 0 -750069.48 -5297.5537
|
||||
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
|
||||
2 30.988787 -750073.91 0 -750069.59 -5023.6945
|
||||
3 58.859866 -750077.88 0 -750069.67 -4427.8346
|
||||
4 82.576399 -750081.26 0 -750069.74 -3275.4378
|
||||
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
|
||||
5 94.968097 -750083.01 0 -750069.76 -1511.6733
|
||||
6 93.724286 -750082.8 0 -750069.73 709.20465
|
||||
7 82.243957 -750081.13 0 -750069.66 3020.5084
|
||||
8 68.611429 -750079.14 0 -750069.57 4922.5176
|
||||
9 62.314385 -750078.21 0 -750069.51 5933.1543
|
||||
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
|
||||
10 69.501045 -750079.21 0 -750069.52 5761.8646
|
||||
Loop time of 3.2801 on 1 procs for 10 steps with 1080 atoms
|
||||
|
||||
Performance: 0.132 ns/day, 182.228 hours/ns, 3.049 timesteps/s, 3.293 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.2794 | 3.2794 | 3.2794 | 0.0 | 99.98
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00030785 | 0.00030785 | 0.00030785 | 0.0 | 0.01
|
||||
Output | 0.00018531 | 0.00018531 | 0.00018531 | 0.0 | 0.01
|
||||
Modify | 0.00013118 | 0.00013118 | 0.00013118 | 0.0 | 0.00
|
||||
Other | | 9.142e-05 | | | 0.00
|
||||
|
||||
Nlocal: 1080 ave 1080 max 1080 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4536 ave 4536 max 4536 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 239270 ave 239270 max 239270 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 239270
|
||||
Ave neighs/atom = 221.5463
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
667
examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.4
Normal file
667
examples/PACKAGES/hdnnp/log.23Aug23.hdnnp.g++.4
Normal file
@ -0,0 +1,667 @@
|
||||
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
###############################################################################
|
||||
# MD simulation for HDNNP water
|
||||
###############################################################################
|
||||
|
||||
###############################################################################
|
||||
# VARIABLES
|
||||
###############################################################################
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Configuration files
|
||||
variable cfgFile string "data.H2O-360mol"
|
||||
# Timesteps
|
||||
variable numSteps equal 10
|
||||
variable dt equal 0.0005
|
||||
# HDNNP
|
||||
variable hdnnpCutoff equal 6.36
|
||||
variable hdnnpDir string "hdnnp-data"
|
||||
|
||||
###############################################################################
|
||||
# GENERAL SETUP
|
||||
###############################################################################
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
read_data ${cfgFile}
|
||||
read_data data.H2O-360mol
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1080 atoms
|
||||
read_data CPU = 0.007 seconds
|
||||
timestep ${dt}
|
||||
timestep 0.0005
|
||||
thermo 1
|
||||
|
||||
###############################################################################
|
||||
# HDNNP
|
||||
###############################################################################
|
||||
pair_style hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_style hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_style hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_coeff * * H O
|
||||
|
||||
###############################################################################
|
||||
# INTEGRATOR
|
||||
###############################################################################
|
||||
fix INT all nve
|
||||
|
||||
###############################################################################
|
||||
# OUTPUT
|
||||
###############################################################################
|
||||
# dump 1 all atom 1 dump.hdnnp
|
||||
|
||||
###############################################################################
|
||||
# SIMULATION
|
||||
###############################################################################
|
||||
run ${numSteps}
|
||||
run 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
|
||||
|
||||
@Article{Singraber19,
|
||||
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
|
||||
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
|
||||
Neural Network Potentials},
|
||||
year = {2019},
|
||||
month = mar,
|
||||
volume = {15},
|
||||
pages = {1827--1840},
|
||||
doi = {10.1021/acs.jctc.8b00770},
|
||||
journal = {J.~Chem.\ Theory Comput.},
|
||||
number = {3}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
|
||||
*******************************************************************************
|
||||
|
||||
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
|
||||
------------------------------------------------------------------
|
||||
|
||||
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
|
||||
(version.h): v2.2.0
|
||||
------------------------------------------------------------
|
||||
Git branch : collected-small-changes
|
||||
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
|
||||
Compile date/time : Aug 23 2023 08:43:11
|
||||
------------------------------------------------------------
|
||||
|
||||
Features/Flags:
|
||||
------------------------------------------------------------
|
||||
Symmetry function groups : enabled
|
||||
Symmetry function cache : enabled
|
||||
Timing function available : available
|
||||
Asymmetric polynomial SFs : available
|
||||
SF low neighbor number check : enabled
|
||||
SF derivative memory layout : reduced
|
||||
MPI explicitly disabled : no
|
||||
------------------------------------------------------------
|
||||
|
||||
Please cite the following papers when publishing results obtained with n²p²:
|
||||
-------------------------------------------------------------------------------
|
||||
* General citation for n²p² and the LAMMPS interface:
|
||||
|
||||
Singraber, A.; Behler, J.; Dellago, C.
|
||||
Library-Based LAMMPS Implementation of High-Dimensional
|
||||
Neural Network Potentials.
|
||||
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
|
||||
https://doi.org/10.1021/acs.jctc.8b00770
|
||||
-------------------------------------------------------------------------------
|
||||
* Additionally, if you use the NNP training features of n²p²:
|
||||
|
||||
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
|
||||
Parallel Multistream Training of High-Dimensional Neural
|
||||
Network Potentials.
|
||||
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
|
||||
https://doi.org/10.1021/acs.jctc.8b01092
|
||||
-------------------------------------------------------------------------------
|
||||
* Additionally, if polynomial symmetry functions are used:
|
||||
|
||||
Bircher, M. P.; Singraber, A.; Dellago, C.
|
||||
Improved Description of Atomic Environments Using Low-Cost
|
||||
Polynomial Functions with Compact Support.
|
||||
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
|
||||
https://arxiv.org/abs/2010.14414
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SETTINGS FILE ******************************************************
|
||||
|
||||
Settings file name: hdnnp-data/input.nn
|
||||
Read 120 lines.
|
||||
Found 70 lines with keywords.
|
||||
This settings file defines a short-range only NNP.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NORMALIZATION ******************************************************
|
||||
|
||||
Data set normalization is used.
|
||||
Mean energy per atom : -2.5521343547039809E+01
|
||||
Conversion factor energy : 2.4265748255366972E+02
|
||||
Conversion factor length : 5.8038448995319847E+00
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: ELEMENT MAP ********************************************************
|
||||
|
||||
Number of element strings found: 2
|
||||
Element 0: H ( 1)
|
||||
Element 1: O ( 8)
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: ELEMENTS ***********************************************************
|
||||
|
||||
Number of elements is consistent: 2
|
||||
Atomic energy offsets per element:
|
||||
Element 0: 0.00000000E+00
|
||||
Element 1: 0.00000000E+00
|
||||
Energy offsets are automatically subtracted from reference energies.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: CUTOFF FUNCTIONS ***************************************************
|
||||
|
||||
Parameter alpha for inner cutoff: 0.000000
|
||||
Inner cutoff = Symmetry function cutoff * alpha
|
||||
Equal cutoff function type for all symmetry functions:
|
||||
CutoffFunction::CT_TANHU (2)
|
||||
f(r) = tanh^3(1 - r/rc)
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTIONS *************************************************
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind .... Symmetry function index.
|
||||
ec ..... Central atom element.
|
||||
tp ..... Symmetry function type.
|
||||
sbtp ... Symmetry function subtype (e.g. cutoff type).
|
||||
e1 ..... Neighbor 1 element.
|
||||
e2 ..... Neighbor 2 element.
|
||||
eta .... Gaussian width eta.
|
||||
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
|
||||
angl.... Left cutoff angle for polynomial.
|
||||
angr.... Right cutoff angle for polynomial.
|
||||
la ..... Angle prefactor lambda.
|
||||
zeta ... Angle term exponent zeta.
|
||||
rc ..... Cutoff radius / right cutoff radius for polynomial.
|
||||
a ...... Free parameter alpha (e.g. cutoff alpha).
|
||||
ln ..... Line number in settings file.
|
||||
|
||||
Short range atomic symmetry functions element H :
|
||||
-------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
|
||||
-------------------------------------------------------------------------------------------------
|
||||
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
|
||||
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
|
||||
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
|
||||
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
|
||||
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
|
||||
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
|
||||
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
|
||||
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
|
||||
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
|
||||
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
|
||||
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
|
||||
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
|
||||
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
|
||||
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
|
||||
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
|
||||
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
|
||||
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
|
||||
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
|
||||
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
|
||||
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
|
||||
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
|
||||
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
|
||||
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
|
||||
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
|
||||
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
|
||||
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
|
||||
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
|
||||
-------------------------------------------------------------------------------------------------
|
||||
Short range atomic symmetry functions element O :
|
||||
-------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
|
||||
-------------------------------------------------------------------------------------------------
|
||||
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
|
||||
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
|
||||
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
|
||||
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
|
||||
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
|
||||
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
|
||||
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
|
||||
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
|
||||
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
|
||||
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
|
||||
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
|
||||
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
|
||||
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
|
||||
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
|
||||
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
|
||||
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
|
||||
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
|
||||
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
|
||||
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
|
||||
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
|
||||
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
|
||||
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
|
||||
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
|
||||
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
|
||||
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
|
||||
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
|
||||
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
|
||||
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
|
||||
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
|
||||
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
|
||||
-------------------------------------------------------------------------------------------------
|
||||
Minimum cutoff radius for element H: 12.000000
|
||||
Minimum cutoff radius for element O: 12.000000
|
||||
Maximum cutoff radius (global) : 12.000000
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
|
||||
|
||||
Symmetry function derivatives memory table for element H :
|
||||
-------------------------------------------------------------------------------
|
||||
Relevant symmetry functions for neighbors with element:
|
||||
- H: 15 of 27 ( 55.6 %)
|
||||
- O: 19 of 27 ( 70.4 %)
|
||||
-------------------------------------------------------------------------------
|
||||
Symmetry function derivatives memory table for element O :
|
||||
-------------------------------------------------------------------------------
|
||||
Relevant symmetry functions for neighbors with element:
|
||||
- H: 18 of 30 ( 60.0 %)
|
||||
- O: 16 of 30 ( 53.3 %)
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
|
||||
|
||||
Element H: in total 4 caches, used 17.00 times on average.
|
||||
Element O: in total 4 caches, used 17.00 times on average.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind .... Symmetry function index.
|
||||
ec ..... Central atom element.
|
||||
tp ..... Symmetry function type.
|
||||
sbtp ... Symmetry function subtype (e.g. cutoff type).
|
||||
e1 ..... Neighbor 1 element.
|
||||
e2 ..... Neighbor 2 element.
|
||||
eta .... Gaussian width eta.
|
||||
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
|
||||
angl.... Left cutoff angle for polynomial.
|
||||
angr.... Right cutoff angle for polynomial.
|
||||
la ..... Angle prefactor lambda.
|
||||
zeta ... Angle term exponent zeta.
|
||||
rc ..... Cutoff radius / right cutoff radius for polynomial.
|
||||
a ...... Free parameter alpha (e.g. cutoff alpha).
|
||||
ln ..... Line number in settings file.
|
||||
mi ..... Member index.
|
||||
sfi .... Symmetry function index.
|
||||
e ...... Recalculate exponential term.
|
||||
|
||||
Short range atomic symmetry function groups element H :
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
|
||||
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
|
||||
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
|
||||
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
|
||||
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
|
||||
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
|
||||
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
|
||||
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
|
||||
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
|
||||
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
|
||||
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
|
||||
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
|
||||
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
|
||||
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
|
||||
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
|
||||
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
|
||||
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
|
||||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
|
||||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
|
||||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
|
||||
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
|
||||
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
Short range atomic symmetry function groups element O :
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
|
||||
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
|
||||
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
|
||||
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
|
||||
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
|
||||
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
|
||||
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
|
||||
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
|
||||
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
|
||||
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
|
||||
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
|
||||
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
|
||||
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
|
||||
- - - - - 3.000E-01 4.000E+00 - - 85 6 12
|
||||
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
|
||||
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
|
||||
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
|
||||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
|
||||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
|
||||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
|
||||
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
|
||||
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NEURAL NETWORKS ****************************************************
|
||||
|
||||
Normalize neurons (all elements): 0
|
||||
-------------------------------------------------------------------------------
|
||||
Atomic short range NN for element H :
|
||||
Number of weights : 1325
|
||||
Number of biases : 51
|
||||
Number of connections: 1376
|
||||
Architecture 27 25 25 1
|
||||
-------------------------------------------------------------------------------
|
||||
1 G t t l
|
||||
2 G t t
|
||||
3 G t t
|
||||
4 G t t
|
||||
5 G t t
|
||||
6 G t t
|
||||
7 G t t
|
||||
8 G t t
|
||||
9 G t t
|
||||
10 G t t
|
||||
11 G t t
|
||||
12 G t t
|
||||
13 G t t
|
||||
14 G t t
|
||||
15 G t t
|
||||
16 G t t
|
||||
17 G t t
|
||||
18 G t t
|
||||
19 G t t
|
||||
20 G t t
|
||||
21 G t t
|
||||
22 G t t
|
||||
23 G t t
|
||||
24 G t t
|
||||
25 G t t
|
||||
26 G
|
||||
27 G
|
||||
-------------------------------------------------------------------------------
|
||||
Atomic short range NN for element O :
|
||||
Number of weights : 1400
|
||||
Number of biases : 51
|
||||
Number of connections: 1451
|
||||
Architecture 30 25 25 1
|
||||
-------------------------------------------------------------------------------
|
||||
1 G t t l
|
||||
2 G t t
|
||||
3 G t t
|
||||
4 G t t
|
||||
5 G t t
|
||||
6 G t t
|
||||
7 G t t
|
||||
8 G t t
|
||||
9 G t t
|
||||
10 G t t
|
||||
11 G t t
|
||||
12 G t t
|
||||
13 G t t
|
||||
14 G t t
|
||||
15 G t t
|
||||
16 G t t
|
||||
17 G t t
|
||||
18 G t t
|
||||
19 G t t
|
||||
20 G t t
|
||||
21 G t t
|
||||
22 G t t
|
||||
23 G t t
|
||||
24 G t t
|
||||
25 G t t
|
||||
26 G
|
||||
27 G
|
||||
28 G
|
||||
29 G
|
||||
30 G
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
|
||||
|
||||
Equal scaling type for all symmetry functions:
|
||||
Scaling type::ST_SCALECENTER (3)
|
||||
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
|
||||
Smin = 0.000000
|
||||
Smax = 1.000000
|
||||
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
|
||||
-------------------------------------------------------------------------------
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind ..... Symmetry function index.
|
||||
min ..... Minimum symmetry function value.
|
||||
max ..... Maximum symmetry function value.
|
||||
mean .... Mean symmetry function value.
|
||||
sigma ... Standard deviation of symmetry function values.
|
||||
sf ...... Scaling factor for derivatives.
|
||||
Smin .... Desired minimum scaled symmetry function value.
|
||||
Smax .... Desired maximum scaled symmetry function value.
|
||||
t ....... Scaling type.
|
||||
|
||||
Scaling data for symmetry functions element H :
|
||||
-------------------------------------------------------------------------------
|
||||
ind min max mean sigma sf Smin Smax t
|
||||
-------------------------------------------------------------------------------
|
||||
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
|
||||
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
|
||||
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
|
||||
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
|
||||
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
|
||||
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
|
||||
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
|
||||
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
|
||||
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
|
||||
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
|
||||
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
|
||||
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
|
||||
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
|
||||
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
|
||||
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
|
||||
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
|
||||
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
|
||||
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
|
||||
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
|
||||
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
|
||||
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
|
||||
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
|
||||
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
|
||||
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
|
||||
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
|
||||
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
|
||||
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
|
||||
-------------------------------------------------------------------------------
|
||||
Scaling data for symmetry functions element O :
|
||||
-------------------------------------------------------------------------------
|
||||
ind min max mean sigma sf Smin Smax t
|
||||
-------------------------------------------------------------------------------
|
||||
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
|
||||
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
|
||||
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
|
||||
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
|
||||
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
|
||||
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
|
||||
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
|
||||
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
|
||||
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
|
||||
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
|
||||
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
|
||||
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
|
||||
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
|
||||
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
|
||||
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
|
||||
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
|
||||
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
|
||||
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
|
||||
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
|
||||
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
|
||||
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
|
||||
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
|
||||
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
|
||||
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
|
||||
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
|
||||
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
|
||||
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
|
||||
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
|
||||
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
|
||||
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
|
||||
|
||||
Equal symmetry function statistics for all elements.
|
||||
Collect min/max/mean/sigma : 0
|
||||
Collect extrapolation warnings : 1
|
||||
Write extrapolation warnings immediately to stderr: 0
|
||||
Halt on any extrapolation warning : 0
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
|
||||
|
||||
Short NN weight file name format: hdnnp-data/weights.%03d.data
|
||||
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
|
||||
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: LAMMPS INTERFACE ***************************************************
|
||||
|
||||
Individual extrapolation warnings will not be shown.
|
||||
Extrapolation warning summary will be shown every 5 timesteps.
|
||||
The simulation will be stopped when 100 extrapolation warnings are exceeded.
|
||||
Extrapolation warnings are accumulated over all time steps.
|
||||
-------------------------------------------------------------------------------
|
||||
CAUTION: If the LAMMPS unit system differs from the one used
|
||||
during NN training, appropriate conversion factors
|
||||
must be provided (see keywords cflength and cfenergy).
|
||||
|
||||
Length unit conversion factor: 1.8897261327999999E+00
|
||||
Energy unit conversion factor: 3.6749325399999998E-02
|
||||
|
||||
Checking consistency of cutoff radii (in LAMMPS units):
|
||||
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
|
||||
Maximum symmetry function cutoff: 6.350E+00
|
||||
Cutoff radii are consistent.
|
||||
-------------------------------------------------------------------------------
|
||||
Element mapping string from LAMMPS to n2p2: "1:H,2:O"
|
||||
|
||||
CAUTION: Please ensure that this mapping between LAMMPS
|
||||
atom types and NNP elements is consistent:
|
||||
|
||||
---------------------------
|
||||
LAMMPS type | NNP element
|
||||
---------------------------
|
||||
1 <-> H ( 1)
|
||||
2 <-> O ( 8)
|
||||
---------------------------
|
||||
|
||||
NNP setup for LAMMPS completed.
|
||||
*******************************************************************************
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.36
|
||||
ghost atom cutoff = 8.36
|
||||
binsize = 4.18, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair hdnnp, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.13 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -750069.48 0 -750069.48 -5297.5537
|
||||
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
|
||||
2 30.988787 -750073.91 0 -750069.59 -5023.6945
|
||||
3 58.859866 -750077.88 0 -750069.67 -4427.8346
|
||||
4 82.576399 -750081.26 0 -750069.74 -3275.4378
|
||||
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
|
||||
5 94.968097 -750083.01 0 -750069.76 -1511.6733
|
||||
6 93.724286 -750082.8 0 -750069.73 709.20465
|
||||
7 82.243957 -750081.13 0 -750069.66 3020.5084
|
||||
8 68.611429 -750079.14 0 -750069.57 4922.5176
|
||||
9 62.314385 -750078.21 0 -750069.51 5933.1543
|
||||
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
|
||||
10 69.501045 -750079.21 0 -750069.52 5761.8646
|
||||
Loop time of 0.930358 on 4 procs for 10 steps with 1080 atoms
|
||||
|
||||
Performance: 0.464 ns/day, 51.687 hours/ns, 10.749 timesteps/s, 11.608 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.85419 | 0.89495 | 0.92919 | 3.5 | 96.19
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00075831 | 0.035035 | 0.075822 | 17.5 | 3.77
|
||||
Output | 0.00018471 | 0.00023973 | 0.00031043 | 0.0 | 0.03
|
||||
Modify | 4.0258e-05 | 4.2308e-05 | 4.4218e-05 | 0.0 | 0.00
|
||||
Other | | 9.199e-05 | | | 0.01
|
||||
|
||||
Nlocal: 270 ave 278 max 262 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 2552 ave 2564 max 2541 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 59817.5 ave 61917 max 57577 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 239270
|
||||
Ave neighs/atom = 221.5463
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
689
examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.1
Normal file
689
examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.1
Normal file
@ -0,0 +1,689 @@
|
||||
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
###############################################################################
|
||||
# MD simulation for HDNNP water
|
||||
###############################################################################
|
||||
|
||||
###############################################################################
|
||||
# VARIABLES
|
||||
###############################################################################
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Configuration files
|
||||
variable cfgFile string "data.H2O-360mol"
|
||||
# Timesteps
|
||||
variable numSteps equal 10
|
||||
variable dt equal 0.0005
|
||||
# HDNNP
|
||||
variable hdnnpCutoff equal 6.36
|
||||
variable hdnnpDir string "hdnnp-data"
|
||||
|
||||
###############################################################################
|
||||
# GENERAL SETUP
|
||||
###############################################################################
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
read_data ${cfgFile} add append offset 1 0 0 0 0
|
||||
read_data data.H2O-360mol add append offset 1 0 0 0 0
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1080 atoms
|
||||
read_data CPU = 0.004 seconds
|
||||
timestep ${dt}
|
||||
timestep 0.0005
|
||||
thermo 1
|
||||
|
||||
###############################################################################
|
||||
# HDNNP
|
||||
###############################################################################
|
||||
pair_style hybrid lj/cut 6.0 hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_coeff * * hdnnp NULL H O
|
||||
pair_coeff 1 * lj/cut 0.1 3.0
|
||||
|
||||
###############################################################################
|
||||
# INTEGRATOR
|
||||
###############################################################################
|
||||
fix INT all nve
|
||||
|
||||
###############################################################################
|
||||
# OUTPUT
|
||||
###############################################################################
|
||||
#dump 1 all atom 1 dump.hdnnp
|
||||
|
||||
###############################################################################
|
||||
# SIMULATION
|
||||
###############################################################################
|
||||
run ${numSteps}
|
||||
run 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
|
||||
|
||||
@Article{Singraber19,
|
||||
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
|
||||
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
|
||||
Neural Network Potentials},
|
||||
year = {2019},
|
||||
month = mar,
|
||||
volume = {15},
|
||||
pages = {1827--1840},
|
||||
doi = {10.1021/acs.jctc.8b00770},
|
||||
journal = {J.~Chem.\ Theory Comput.},
|
||||
number = {3}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
|
||||
*******************************************************************************
|
||||
|
||||
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
|
||||
------------------------------------------------------------------
|
||||
|
||||
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
|
||||
(version.h): v2.2.0
|
||||
------------------------------------------------------------
|
||||
Git branch : collected-small-changes
|
||||
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
|
||||
Compile date/time : Aug 23 2023 08:43:11
|
||||
------------------------------------------------------------
|
||||
|
||||
Features/Flags:
|
||||
------------------------------------------------------------
|
||||
Symmetry function groups : enabled
|
||||
Symmetry function cache : enabled
|
||||
Timing function available : available
|
||||
Asymmetric polynomial SFs : available
|
||||
SF low neighbor number check : enabled
|
||||
SF derivative memory layout : reduced
|
||||
MPI explicitly disabled : no
|
||||
------------------------------------------------------------
|
||||
|
||||
Please cite the following papers when publishing results obtained with n²p²:
|
||||
-------------------------------------------------------------------------------
|
||||
* General citation for n²p² and the LAMMPS interface:
|
||||
|
||||
Singraber, A.; Behler, J.; Dellago, C.
|
||||
Library-Based LAMMPS Implementation of High-Dimensional
|
||||
Neural Network Potentials.
|
||||
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
|
||||
https://doi.org/10.1021/acs.jctc.8b00770
|
||||
-------------------------------------------------------------------------------
|
||||
* Additionally, if you use the NNP training features of n²p²:
|
||||
|
||||
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
|
||||
Parallel Multistream Training of High-Dimensional Neural
|
||||
Network Potentials.
|
||||
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
|
||||
https://doi.org/10.1021/acs.jctc.8b01092
|
||||
-------------------------------------------------------------------------------
|
||||
* Additionally, if polynomial symmetry functions are used:
|
||||
|
||||
Bircher, M. P.; Singraber, A.; Dellago, C.
|
||||
Improved Description of Atomic Environments Using Low-Cost
|
||||
Polynomial Functions with Compact Support.
|
||||
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
|
||||
https://arxiv.org/abs/2010.14414
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SETTINGS FILE ******************************************************
|
||||
|
||||
Settings file name: hdnnp-data/input.nn
|
||||
Read 120 lines.
|
||||
Found 70 lines with keywords.
|
||||
This settings file defines a short-range only NNP.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NORMALIZATION ******************************************************
|
||||
|
||||
Data set normalization is used.
|
||||
Mean energy per atom : -2.5521343547039809E+01
|
||||
Conversion factor energy : 2.4265748255366972E+02
|
||||
Conversion factor length : 5.8038448995319847E+00
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: ELEMENT MAP ********************************************************
|
||||
|
||||
Number of element strings found: 2
|
||||
Element 0: H ( 1)
|
||||
Element 1: O ( 8)
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: ELEMENTS ***********************************************************
|
||||
|
||||
Number of elements is consistent: 2
|
||||
Atomic energy offsets per element:
|
||||
Element 0: 0.00000000E+00
|
||||
Element 1: 0.00000000E+00
|
||||
Energy offsets are automatically subtracted from reference energies.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: CUTOFF FUNCTIONS ***************************************************
|
||||
|
||||
Parameter alpha for inner cutoff: 0.000000
|
||||
Inner cutoff = Symmetry function cutoff * alpha
|
||||
Equal cutoff function type for all symmetry functions:
|
||||
CutoffFunction::CT_TANHU (2)
|
||||
f(r) = tanh^3(1 - r/rc)
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTIONS *************************************************
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind .... Symmetry function index.
|
||||
ec ..... Central atom element.
|
||||
tp ..... Symmetry function type.
|
||||
sbtp ... Symmetry function subtype (e.g. cutoff type).
|
||||
e1 ..... Neighbor 1 element.
|
||||
e2 ..... Neighbor 2 element.
|
||||
eta .... Gaussian width eta.
|
||||
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
|
||||
angl.... Left cutoff angle for polynomial.
|
||||
angr.... Right cutoff angle for polynomial.
|
||||
la ..... Angle prefactor lambda.
|
||||
zeta ... Angle term exponent zeta.
|
||||
rc ..... Cutoff radius / right cutoff radius for polynomial.
|
||||
a ...... Free parameter alpha (e.g. cutoff alpha).
|
||||
ln ..... Line number in settings file.
|
||||
|
||||
Short range atomic symmetry functions element H :
|
||||
-------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
|
||||
-------------------------------------------------------------------------------------------------
|
||||
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
|
||||
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
|
||||
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
|
||||
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
|
||||
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
|
||||
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
|
||||
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
|
||||
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
|
||||
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
|
||||
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
|
||||
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
|
||||
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
|
||||
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
|
||||
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
|
||||
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
|
||||
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
|
||||
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
|
||||
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
|
||||
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
|
||||
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
|
||||
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
|
||||
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
|
||||
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
|
||||
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
|
||||
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
|
||||
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
|
||||
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
|
||||
-------------------------------------------------------------------------------------------------
|
||||
Short range atomic symmetry functions element O :
|
||||
-------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
|
||||
-------------------------------------------------------------------------------------------------
|
||||
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
|
||||
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
|
||||
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
|
||||
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
|
||||
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
|
||||
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
|
||||
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
|
||||
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
|
||||
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
|
||||
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
|
||||
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
|
||||
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
|
||||
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
|
||||
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
|
||||
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
|
||||
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
|
||||
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
|
||||
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
|
||||
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
|
||||
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
|
||||
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
|
||||
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
|
||||
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
|
||||
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
|
||||
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
|
||||
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
|
||||
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
|
||||
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
|
||||
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
|
||||
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
|
||||
-------------------------------------------------------------------------------------------------
|
||||
Minimum cutoff radius for element H: 12.000000
|
||||
Minimum cutoff radius for element O: 12.000000
|
||||
Maximum cutoff radius (global) : 12.000000
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
|
||||
|
||||
Symmetry function derivatives memory table for element H :
|
||||
-------------------------------------------------------------------------------
|
||||
Relevant symmetry functions for neighbors with element:
|
||||
- H: 15 of 27 ( 55.6 %)
|
||||
- O: 19 of 27 ( 70.4 %)
|
||||
-------------------------------------------------------------------------------
|
||||
Symmetry function derivatives memory table for element O :
|
||||
-------------------------------------------------------------------------------
|
||||
Relevant symmetry functions for neighbors with element:
|
||||
- H: 18 of 30 ( 60.0 %)
|
||||
- O: 16 of 30 ( 53.3 %)
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
|
||||
|
||||
Element H: in total 4 caches, used 17.00 times on average.
|
||||
Element O: in total 4 caches, used 17.00 times on average.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind .... Symmetry function index.
|
||||
ec ..... Central atom element.
|
||||
tp ..... Symmetry function type.
|
||||
sbtp ... Symmetry function subtype (e.g. cutoff type).
|
||||
e1 ..... Neighbor 1 element.
|
||||
e2 ..... Neighbor 2 element.
|
||||
eta .... Gaussian width eta.
|
||||
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
|
||||
angl.... Left cutoff angle for polynomial.
|
||||
angr.... Right cutoff angle for polynomial.
|
||||
la ..... Angle prefactor lambda.
|
||||
zeta ... Angle term exponent zeta.
|
||||
rc ..... Cutoff radius / right cutoff radius for polynomial.
|
||||
a ...... Free parameter alpha (e.g. cutoff alpha).
|
||||
ln ..... Line number in settings file.
|
||||
mi ..... Member index.
|
||||
sfi .... Symmetry function index.
|
||||
e ...... Recalculate exponential term.
|
||||
|
||||
Short range atomic symmetry function groups element H :
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
|
||||
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
|
||||
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
|
||||
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
|
||||
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
|
||||
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
|
||||
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
|
||||
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
|
||||
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
|
||||
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
|
||||
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
|
||||
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
|
||||
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
|
||||
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
|
||||
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
|
||||
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
|
||||
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
|
||||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
|
||||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
|
||||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
|
||||
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
|
||||
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
Short range atomic symmetry function groups element O :
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
|
||||
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
|
||||
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
|
||||
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
|
||||
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
|
||||
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
|
||||
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
|
||||
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
|
||||
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
|
||||
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
|
||||
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
|
||||
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
|
||||
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
|
||||
- - - - - 3.000E-01 4.000E+00 - - 85 6 12
|
||||
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
|
||||
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
|
||||
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
|
||||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
|
||||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
|
||||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
|
||||
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
|
||||
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NEURAL NETWORKS ****************************************************
|
||||
|
||||
Normalize neurons (all elements): 0
|
||||
-------------------------------------------------------------------------------
|
||||
Atomic short range NN for element H :
|
||||
Number of weights : 1325
|
||||
Number of biases : 51
|
||||
Number of connections: 1376
|
||||
Architecture 27 25 25 1
|
||||
-------------------------------------------------------------------------------
|
||||
1 G t t l
|
||||
2 G t t
|
||||
3 G t t
|
||||
4 G t t
|
||||
5 G t t
|
||||
6 G t t
|
||||
7 G t t
|
||||
8 G t t
|
||||
9 G t t
|
||||
10 G t t
|
||||
11 G t t
|
||||
12 G t t
|
||||
13 G t t
|
||||
14 G t t
|
||||
15 G t t
|
||||
16 G t t
|
||||
17 G t t
|
||||
18 G t t
|
||||
19 G t t
|
||||
20 G t t
|
||||
21 G t t
|
||||
22 G t t
|
||||
23 G t t
|
||||
24 G t t
|
||||
25 G t t
|
||||
26 G
|
||||
27 G
|
||||
-------------------------------------------------------------------------------
|
||||
Atomic short range NN for element O :
|
||||
Number of weights : 1400
|
||||
Number of biases : 51
|
||||
Number of connections: 1451
|
||||
Architecture 30 25 25 1
|
||||
-------------------------------------------------------------------------------
|
||||
1 G t t l
|
||||
2 G t t
|
||||
3 G t t
|
||||
4 G t t
|
||||
5 G t t
|
||||
6 G t t
|
||||
7 G t t
|
||||
8 G t t
|
||||
9 G t t
|
||||
10 G t t
|
||||
11 G t t
|
||||
12 G t t
|
||||
13 G t t
|
||||
14 G t t
|
||||
15 G t t
|
||||
16 G t t
|
||||
17 G t t
|
||||
18 G t t
|
||||
19 G t t
|
||||
20 G t t
|
||||
21 G t t
|
||||
22 G t t
|
||||
23 G t t
|
||||
24 G t t
|
||||
25 G t t
|
||||
26 G
|
||||
27 G
|
||||
28 G
|
||||
29 G
|
||||
30 G
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
|
||||
|
||||
Equal scaling type for all symmetry functions:
|
||||
Scaling type::ST_SCALECENTER (3)
|
||||
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
|
||||
Smin = 0.000000
|
||||
Smax = 1.000000
|
||||
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
|
||||
-------------------------------------------------------------------------------
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind ..... Symmetry function index.
|
||||
min ..... Minimum symmetry function value.
|
||||
max ..... Maximum symmetry function value.
|
||||
mean .... Mean symmetry function value.
|
||||
sigma ... Standard deviation of symmetry function values.
|
||||
sf ...... Scaling factor for derivatives.
|
||||
Smin .... Desired minimum scaled symmetry function value.
|
||||
Smax .... Desired maximum scaled symmetry function value.
|
||||
t ....... Scaling type.
|
||||
|
||||
Scaling data for symmetry functions element H :
|
||||
-------------------------------------------------------------------------------
|
||||
ind min max mean sigma sf Smin Smax t
|
||||
-------------------------------------------------------------------------------
|
||||
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
|
||||
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
|
||||
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
|
||||
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
|
||||
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
|
||||
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
|
||||
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
|
||||
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
|
||||
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
|
||||
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
|
||||
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
|
||||
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
|
||||
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
|
||||
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
|
||||
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
|
||||
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
|
||||
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
|
||||
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
|
||||
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
|
||||
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
|
||||
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
|
||||
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
|
||||
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
|
||||
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
|
||||
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
|
||||
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
|
||||
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
|
||||
-------------------------------------------------------------------------------
|
||||
Scaling data for symmetry functions element O :
|
||||
-------------------------------------------------------------------------------
|
||||
ind min max mean sigma sf Smin Smax t
|
||||
-------------------------------------------------------------------------------
|
||||
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
|
||||
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
|
||||
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
|
||||
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
|
||||
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
|
||||
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
|
||||
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
|
||||
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
|
||||
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
|
||||
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
|
||||
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
|
||||
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
|
||||
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
|
||||
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
|
||||
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
|
||||
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
|
||||
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
|
||||
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
|
||||
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
|
||||
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
|
||||
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
|
||||
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
|
||||
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
|
||||
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
|
||||
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
|
||||
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
|
||||
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
|
||||
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
|
||||
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
|
||||
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
|
||||
|
||||
Equal symmetry function statistics for all elements.
|
||||
Collect min/max/mean/sigma : 0
|
||||
Collect extrapolation warnings : 1
|
||||
Write extrapolation warnings immediately to stderr: 0
|
||||
Halt on any extrapolation warning : 0
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
|
||||
|
||||
Short NN weight file name format: hdnnp-data/weights.%03d.data
|
||||
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
|
||||
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: LAMMPS INTERFACE ***************************************************
|
||||
|
||||
Individual extrapolation warnings will not be shown.
|
||||
Extrapolation warning summary will be shown every 5 timesteps.
|
||||
The simulation will be stopped when 100 extrapolation warnings are exceeded.
|
||||
Extrapolation warnings are accumulated over all time steps.
|
||||
-------------------------------------------------------------------------------
|
||||
CAUTION: If the LAMMPS unit system differs from the one used
|
||||
during NN training, appropriate conversion factors
|
||||
must be provided (see keywords cflength and cfenergy).
|
||||
|
||||
Length unit conversion factor: 1.8897261327999999E+00
|
||||
Energy unit conversion factor: 3.6749325399999998E-02
|
||||
|
||||
Checking consistency of cutoff radii (in LAMMPS units):
|
||||
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
|
||||
Maximum symmetry function cutoff: 6.350E+00
|
||||
Cutoff radii are consistent.
|
||||
-------------------------------------------------------------------------------
|
||||
Element mapping string from LAMMPS to n2p2: "2:H,3:O"
|
||||
|
||||
CAUTION: Please ensure that this mapping between LAMMPS
|
||||
atom types and NNP elements is consistent:
|
||||
|
||||
---------------------------
|
||||
LAMMPS type | NNP element
|
||||
---------------------------
|
||||
1 <-> --
|
||||
2 <-> H ( 1)
|
||||
3 <-> O ( 8)
|
||||
---------------------------
|
||||
|
||||
NNP setup for LAMMPS completed.
|
||||
*******************************************************************************
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.36
|
||||
ghost atom cutoff = 8.36
|
||||
binsize = 4.18, bins = 6 6 6
|
||||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||
(1) pair lj/cut, perpetual, skip from (3)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair hdnnp, perpetual, skip from (4)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual, half/full trim from (4)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: halffull/newton/trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) neighbor class addition, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.06 | 7.06 | 7.06 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -750069.48 0 -750069.48 -5297.5537
|
||||
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
|
||||
2 30.988787 -750073.91 0 -750069.59 -5023.6945
|
||||
3 58.859866 -750077.88 0 -750069.67 -4427.8346
|
||||
4 82.576399 -750081.26 0 -750069.74 -3275.4378
|
||||
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
|
||||
5 94.968097 -750083.01 0 -750069.76 -1511.6733
|
||||
6 93.724286 -750082.8 0 -750069.73 709.20465
|
||||
7 82.243957 -750081.13 0 -750069.66 3020.5084
|
||||
8 68.611429 -750079.14 0 -750069.57 4922.5176
|
||||
9 62.314385 -750078.21 0 -750069.51 5933.1543
|
||||
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
|
||||
10 69.501045 -750079.21 0 -750069.52 5761.8646
|
||||
Loop time of 3.32416 on 1 procs for 10 steps with 1080 atoms
|
||||
|
||||
Performance: 0.130 ns/day, 184.675 hours/ns, 3.008 timesteps/s, 3.249 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.3234 | 3.3234 | 3.3234 | 0.0 | 99.98
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00032742 | 0.00032742 | 0.00032742 | 0.0 | 0.01
|
||||
Output | 0.00019506 | 0.00019506 | 0.00019506 | 0.0 | 0.01
|
||||
Modify | 0.00011454 | 0.00011454 | 0.00011454 | 0.0 | 0.00
|
||||
Other | | 0.0001165 | | | 0.00
|
||||
|
||||
Nlocal: 1080 ave 1080 max 1080 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4536 ave 4536 max 4536 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
689
examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.4
Normal file
689
examples/PACKAGES/hdnnp/log.23Aug23.hybrid.g++.4
Normal file
@ -0,0 +1,689 @@
|
||||
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-264-g174825fe8c)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
###############################################################################
|
||||
# MD simulation for HDNNP water
|
||||
###############################################################################
|
||||
|
||||
###############################################################################
|
||||
# VARIABLES
|
||||
###############################################################################
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Configuration files
|
||||
variable cfgFile string "data.H2O-360mol"
|
||||
# Timesteps
|
||||
variable numSteps equal 10
|
||||
variable dt equal 0.0005
|
||||
# HDNNP
|
||||
variable hdnnpCutoff equal 6.36
|
||||
variable hdnnpDir string "hdnnp-data"
|
||||
|
||||
###############################################################################
|
||||
# GENERAL SETUP
|
||||
###############################################################################
|
||||
units metal
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
region box block 0.0 2.2695686722465727E+01 0.0 2.3586033624598713E+01 0.0 2.2237130028217017E+01
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
read_data ${cfgFile} add append offset 1 0 0 0 0
|
||||
read_data data.H2O-360mol add append offset 1 0 0 0 0
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (22.695687 23.586034 22.23713)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1080 atoms
|
||||
read_data CPU = 0.007 seconds
|
||||
timestep ${dt}
|
||||
timestep 0.0005
|
||||
thermo 1
|
||||
|
||||
###############################################################################
|
||||
# HDNNP
|
||||
###############################################################################
|
||||
pair_style hybrid lj/cut 6.0 hdnnp ${hdnnpCutoff} dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir ${hdnnpDir} showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_style hybrid lj/cut 6.0 hdnnp 6.36 dir hdnnp-data showew no showewsum 5 resetew no maxew 100 cflength 1.8897261328 cfenergy 0.0367493254
|
||||
pair_coeff * * hdnnp NULL H O
|
||||
pair_coeff 1 * lj/cut 0.1 3.0
|
||||
|
||||
###############################################################################
|
||||
# INTEGRATOR
|
||||
###############################################################################
|
||||
fix INT all nve
|
||||
|
||||
###############################################################################
|
||||
# OUTPUT
|
||||
###############################################################################
|
||||
#dump 1 all atom 1 dump.hdnnp
|
||||
|
||||
###############################################################################
|
||||
# SIMULATION
|
||||
###############################################################################
|
||||
run ${numSteps}
|
||||
run 10
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- ML-HDNNP package: doi:10.1021/acs.jctc.8b00770
|
||||
|
||||
@Article{Singraber19,
|
||||
author = {Singraber, Andreas and Behler, J{"o}rg and Dellago, Christoph},
|
||||
title = {Library-Based {LAMMPS} Implementation of High-Dimensional
|
||||
Neural Network Potentials},
|
||||
year = {2019},
|
||||
month = mar,
|
||||
volume = {15},
|
||||
pages = {1827--1840},
|
||||
doi = {10.1021/acs.jctc.8b00770},
|
||||
journal = {J.~Chem.\ Theory Comput.},
|
||||
number = {3}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
|
||||
*******************************************************************************
|
||||
|
||||
WELCOME TO n²p², A SOFTWARE PACKAGE FOR NEURAL NETWORK POTENTIALS!
|
||||
------------------------------------------------------------------
|
||||
|
||||
n²p² version (from git): patch_2Aug2023-264-g174825fe8c
|
||||
(version.h): v2.2.0
|
||||
------------------------------------------------------------
|
||||
Git branch : collected-small-changes
|
||||
Git revision : 174825fe8c9493cb252d7b9e8dafdcc5d74be96d
|
||||
Compile date/time : Aug 23 2023 08:43:11
|
||||
------------------------------------------------------------
|
||||
|
||||
Features/Flags:
|
||||
------------------------------------------------------------
|
||||
Symmetry function groups : enabled
|
||||
Symmetry function cache : enabled
|
||||
Timing function available : available
|
||||
Asymmetric polynomial SFs : available
|
||||
SF low neighbor number check : enabled
|
||||
SF derivative memory layout : reduced
|
||||
MPI explicitly disabled : no
|
||||
------------------------------------------------------------
|
||||
|
||||
Please cite the following papers when publishing results obtained with n²p²:
|
||||
-------------------------------------------------------------------------------
|
||||
* General citation for n²p² and the LAMMPS interface:
|
||||
|
||||
Singraber, A.; Behler, J.; Dellago, C.
|
||||
Library-Based LAMMPS Implementation of High-Dimensional
|
||||
Neural Network Potentials.
|
||||
J. Chem. Theory Comput. 2019 15 (3), 1827–1840.
|
||||
https://doi.org/10.1021/acs.jctc.8b00770
|
||||
-------------------------------------------------------------------------------
|
||||
* Additionally, if you use the NNP training features of n²p²:
|
||||
|
||||
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C.
|
||||
Parallel Multistream Training of High-Dimensional Neural
|
||||
Network Potentials.
|
||||
J. Chem. Theory Comput. 2019, 15 (5), 3075–3092.
|
||||
https://doi.org/10.1021/acs.jctc.8b01092
|
||||
-------------------------------------------------------------------------------
|
||||
* Additionally, if polynomial symmetry functions are used:
|
||||
|
||||
Bircher, M. P.; Singraber, A.; Dellago, C.
|
||||
Improved Description of Atomic Environments Using Low-Cost
|
||||
Polynomial Functions with Compact Support.
|
||||
arXiv:2010.14414 [cond-mat, physics:physics] 2020.
|
||||
https://arxiv.org/abs/2010.14414
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SETTINGS FILE ******************************************************
|
||||
|
||||
Settings file name: hdnnp-data/input.nn
|
||||
Read 120 lines.
|
||||
Found 70 lines with keywords.
|
||||
This settings file defines a short-range only NNP.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NORMALIZATION ******************************************************
|
||||
|
||||
Data set normalization is used.
|
||||
Mean energy per atom : -2.5521343547039809E+01
|
||||
Conversion factor energy : 2.4265748255366972E+02
|
||||
Conversion factor length : 5.8038448995319847E+00
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: ELEMENT MAP ********************************************************
|
||||
|
||||
Number of element strings found: 2
|
||||
Element 0: H ( 1)
|
||||
Element 1: O ( 8)
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: ELEMENTS ***********************************************************
|
||||
|
||||
Number of elements is consistent: 2
|
||||
Atomic energy offsets per element:
|
||||
Element 0: 0.00000000E+00
|
||||
Element 1: 0.00000000E+00
|
||||
Energy offsets are automatically subtracted from reference energies.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: CUTOFF FUNCTIONS ***************************************************
|
||||
|
||||
Parameter alpha for inner cutoff: 0.000000
|
||||
Inner cutoff = Symmetry function cutoff * alpha
|
||||
Equal cutoff function type for all symmetry functions:
|
||||
CutoffFunction::CT_TANHU (2)
|
||||
f(r) = tanh^3(1 - r/rc)
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTIONS *************************************************
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind .... Symmetry function index.
|
||||
ec ..... Central atom element.
|
||||
tp ..... Symmetry function type.
|
||||
sbtp ... Symmetry function subtype (e.g. cutoff type).
|
||||
e1 ..... Neighbor 1 element.
|
||||
e2 ..... Neighbor 2 element.
|
||||
eta .... Gaussian width eta.
|
||||
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
|
||||
angl.... Left cutoff angle for polynomial.
|
||||
angr.... Right cutoff angle for polynomial.
|
||||
la ..... Angle prefactor lambda.
|
||||
zeta ... Angle term exponent zeta.
|
||||
rc ..... Cutoff radius / right cutoff radius for polynomial.
|
||||
a ...... Free parameter alpha (e.g. cutoff alpha).
|
||||
ln ..... Line number in settings file.
|
||||
|
||||
Short range atomic symmetry functions element H :
|
||||
-------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
|
||||
-------------------------------------------------------------------------------------------------
|
||||
1 H 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 51
|
||||
2 H 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 61
|
||||
3 H 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 52
|
||||
4 H 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 62
|
||||
5 H 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 53
|
||||
6 H 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 63
|
||||
7 H 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 54
|
||||
8 H 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 64
|
||||
9 H 2 ct2 O 1.500E-01 9.000E-01 1.200E+01 0.00 65
|
||||
10 H 2 ct2 H 1.500E-01 1.900E+00 1.200E+01 0.00 55
|
||||
11 H 2 ct2 O 3.000E-01 9.000E-01 1.200E+01 0.00 66
|
||||
12 H 2 ct2 H 3.000E-01 1.900E+00 1.200E+01 0.00 56
|
||||
13 H 2 ct2 O 6.000E-01 9.000E-01 1.200E+01 0.00 67
|
||||
14 H 2 ct2 H 6.000E-01 1.900E+00 1.200E+01 0.00 57
|
||||
15 H 2 ct2 O 1.500E+00 9.000E-01 1.200E+01 0.00 68
|
||||
16 H 2 ct2 H 1.500E+00 1.900E+00 1.200E+01 0.00 58
|
||||
17 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 115
|
||||
18 H 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 114
|
||||
19 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 105
|
||||
20 H 3 ct2 H O 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 103
|
||||
21 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 100
|
||||
22 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 113
|
||||
23 H 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 98
|
||||
24 H 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 112
|
||||
25 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 95
|
||||
26 H 3 ct2 H O 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 93
|
||||
27 H 3 ct2 H O 2.000E-01 0.000E+00 1.200E+01 1 1.0 0.00 90
|
||||
-------------------------------------------------------------------------------------------------
|
||||
Short range atomic symmetry functions element O :
|
||||
-------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln
|
||||
-------------------------------------------------------------------------------------------------
|
||||
1 O 2 ct2 H 1.000E-03 0.000E+00 1.200E+01 0.00 70
|
||||
2 O 2 ct2 O 1.000E-03 0.000E+00 1.200E+01 0.00 80
|
||||
3 O 2 ct2 H 1.000E-02 0.000E+00 1.200E+01 0.00 71
|
||||
4 O 2 ct2 O 1.000E-02 0.000E+00 1.200E+01 0.00 81
|
||||
5 O 2 ct2 H 3.000E-02 0.000E+00 1.200E+01 0.00 72
|
||||
6 O 2 ct2 O 3.000E-02 0.000E+00 1.200E+01 0.00 82
|
||||
7 O 2 ct2 H 6.000E-02 0.000E+00 1.200E+01 0.00 73
|
||||
8 O 2 ct2 O 6.000E-02 0.000E+00 1.200E+01 0.00 83
|
||||
9 O 2 ct2 H 1.500E-01 9.000E-01 1.200E+01 0.00 74
|
||||
10 O 2 ct2 O 1.500E-01 4.000E+00 1.200E+01 0.00 84
|
||||
11 O 2 ct2 H 3.000E-01 9.000E-01 1.200E+01 0.00 75
|
||||
12 O 2 ct2 O 3.000E-01 4.000E+00 1.200E+01 0.00 85
|
||||
13 O 2 ct2 H 6.000E-01 9.000E-01 1.200E+01 0.00 76
|
||||
14 O 2 ct2 O 6.000E-01 4.000E+00 1.200E+01 0.00 86
|
||||
15 O 2 ct2 H 1.500E+00 9.000E-01 1.200E+01 0.00 77
|
||||
16 O 2 ct2 O 1.500E+00 4.000E+00 1.200E+01 0.00 87
|
||||
17 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 110
|
||||
18 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 -1 4.0 0.00 120
|
||||
19 O 3 ct2 H O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 109
|
||||
20 O 3 ct2 O O 1.000E-03 0.000E+00 1.200E+01 1 4.0 0.00 119
|
||||
21 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 -1 4.0 0.00 104
|
||||
22 O 3 ct2 H H 1.000E-02 0.000E+00 1.200E+01 1 4.0 0.00 102
|
||||
23 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 99
|
||||
24 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 108
|
||||
25 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 118
|
||||
26 O 3 ct2 H H 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 97
|
||||
27 O 3 ct2 H O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 107
|
||||
28 O 3 ct2 O O 3.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 117
|
||||
29 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 -1 1.0 0.00 94
|
||||
30 O 3 ct2 H H 7.000E-02 0.000E+00 1.200E+01 1 1.0 0.00 92
|
||||
-------------------------------------------------------------------------------------------------
|
||||
Minimum cutoff radius for element H: 12.000000
|
||||
Minimum cutoff radius for element O: 12.000000
|
||||
Maximum cutoff radius (global) : 12.000000
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION MEMORY *******************************************
|
||||
|
||||
Symmetry function derivatives memory table for element H :
|
||||
-------------------------------------------------------------------------------
|
||||
Relevant symmetry functions for neighbors with element:
|
||||
- H: 15 of 27 ( 55.6 %)
|
||||
- O: 19 of 27 ( 70.4 %)
|
||||
-------------------------------------------------------------------------------
|
||||
Symmetry function derivatives memory table for element O :
|
||||
-------------------------------------------------------------------------------
|
||||
Relevant symmetry functions for neighbors with element:
|
||||
- H: 18 of 30 ( 60.0 %)
|
||||
- O: 16 of 30 ( 53.3 %)
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION CACHE ********************************************
|
||||
|
||||
Element H: in total 4 caches, used 17.00 times on average.
|
||||
Element O: in total 4 caches, used 17.00 times on average.
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION GROUPS *******************************************
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind .... Symmetry function index.
|
||||
ec ..... Central atom element.
|
||||
tp ..... Symmetry function type.
|
||||
sbtp ... Symmetry function subtype (e.g. cutoff type).
|
||||
e1 ..... Neighbor 1 element.
|
||||
e2 ..... Neighbor 2 element.
|
||||
eta .... Gaussian width eta.
|
||||
rs/rl... Shift distance of Gaussian or left cutoff radius for polynomial.
|
||||
angl.... Left cutoff angle for polynomial.
|
||||
angr.... Right cutoff angle for polynomial.
|
||||
la ..... Angle prefactor lambda.
|
||||
zeta ... Angle term exponent zeta.
|
||||
rc ..... Cutoff radius / right cutoff radius for polynomial.
|
||||
a ...... Free parameter alpha (e.g. cutoff alpha).
|
||||
ln ..... Line number in settings file.
|
||||
mi ..... Member index.
|
||||
sfi .... Symmetry function index.
|
||||
e ...... Recalculate exponential term.
|
||||
|
||||
Short range atomic symmetry function groups element H :
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
1 H 2 ct2 H * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 51 1 1
|
||||
- - - - - 1.000E-02 0.000E+00 - - 52 2 3
|
||||
- - - - - 3.000E-02 0.000E+00 - - 53 3 5
|
||||
- - - - - 6.000E-02 0.000E+00 - - 54 4 7
|
||||
- - - - - 1.500E-01 1.900E+00 - - 55 5 10
|
||||
- - - - - 3.000E-01 1.900E+00 - - 56 6 12
|
||||
- - - - - 6.000E-01 1.900E+00 - - 57 7 14
|
||||
- - - - - 1.500E+00 1.900E+00 - - 58 8 16
|
||||
2 H 2 ct2 O * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 61 1 2
|
||||
- - - - - 1.000E-02 0.000E+00 - - 62 2 4
|
||||
- - - - - 3.000E-02 0.000E+00 - - 63 3 6
|
||||
- - - - - 6.000E-02 0.000E+00 - - 64 4 8
|
||||
- - - - - 1.500E-01 9.000E-01 - - 65 5 9
|
||||
- - - - - 3.000E-01 9.000E-01 - - 66 6 11
|
||||
- - - - - 6.000E-01 9.000E-01 - - 67 7 13
|
||||
- - - - - 1.500E+00 9.000E-01 - - 68 8 15
|
||||
3 H 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 105 1 19 1
|
||||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 103 2 20 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 100 3 21 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 98 4 23 0
|
||||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 95 5 25 1
|
||||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 93 6 26 0
|
||||
- - - - - - 2.000E-01 0.000E+00 - 1 1.0 - 90 7 27 1
|
||||
4 H 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 115 1 17 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 114 2 18 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 113 3 22 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 112 4 24 0
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
Short range atomic symmetry function groups element O :
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
ind ec tp sbtp e1 e2 eta rs/rl rc angl angr la zeta a ln mi sfi e
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
1 O 2 ct2 H * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 70 1 1
|
||||
- - - - - 1.000E-02 0.000E+00 - - 71 2 3
|
||||
- - - - - 3.000E-02 0.000E+00 - - 72 3 5
|
||||
- - - - - 6.000E-02 0.000E+00 - - 73 4 7
|
||||
- - - - - 1.500E-01 9.000E-01 - - 74 5 9
|
||||
- - - - - 3.000E-01 9.000E-01 - - 75 6 11
|
||||
- - - - - 6.000E-01 9.000E-01 - - 76 7 13
|
||||
- - - - - 1.500E+00 9.000E-01 - - 77 8 15
|
||||
2 O 2 ct2 O * * 1.200E+01 0.00 * * *
|
||||
- - - - - 1.000E-03 0.000E+00 - - 80 1 2
|
||||
- - - - - 1.000E-02 0.000E+00 - - 81 2 4
|
||||
- - - - - 3.000E-02 0.000E+00 - - 82 3 6
|
||||
- - - - - 6.000E-02 0.000E+00 - - 83 4 8
|
||||
- - - - - 1.500E-01 4.000E+00 - - 84 5 10
|
||||
- - - - - 3.000E-01 4.000E+00 - - 85 6 12
|
||||
- - - - - 6.000E-01 4.000E+00 - - 86 7 14
|
||||
- - - - - 1.500E+00 4.000E+00 - - 87 8 16
|
||||
3 O 3 ct2 H H * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-02 0.000E+00 - -1 4.0 - 104 1 21 1
|
||||
- - - - - - 1.000E-02 0.000E+00 - 1 4.0 - 102 2 22 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 99 3 23 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 97 4 26 0
|
||||
- - - - - - 7.000E-02 0.000E+00 - -1 1.0 - 94 5 29 1
|
||||
- - - - - - 7.000E-02 0.000E+00 - 1 1.0 - 92 6 30 0
|
||||
4 O 3 ct2 H O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 110 1 17 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 109 2 19 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 108 3 24 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 107 4 27 0
|
||||
5 O 3 ct2 O O * * 1.200E+01 * * 0.00 * * * *
|
||||
- - - - - - 1.000E-03 0.000E+00 - -1 4.0 - 120 1 18 1
|
||||
- - - - - - 1.000E-03 0.000E+00 - 1 4.0 - 119 2 20 0
|
||||
- - - - - - 3.000E-02 0.000E+00 - -1 1.0 - 118 3 25 1
|
||||
- - - - - - 3.000E-02 0.000E+00 - 1 1.0 - 117 4 28 0
|
||||
----------------------------------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NEURAL NETWORKS ****************************************************
|
||||
|
||||
Normalize neurons (all elements): 0
|
||||
-------------------------------------------------------------------------------
|
||||
Atomic short range NN for element H :
|
||||
Number of weights : 1325
|
||||
Number of biases : 51
|
||||
Number of connections: 1376
|
||||
Architecture 27 25 25 1
|
||||
-------------------------------------------------------------------------------
|
||||
1 G t t l
|
||||
2 G t t
|
||||
3 G t t
|
||||
4 G t t
|
||||
5 G t t
|
||||
6 G t t
|
||||
7 G t t
|
||||
8 G t t
|
||||
9 G t t
|
||||
10 G t t
|
||||
11 G t t
|
||||
12 G t t
|
||||
13 G t t
|
||||
14 G t t
|
||||
15 G t t
|
||||
16 G t t
|
||||
17 G t t
|
||||
18 G t t
|
||||
19 G t t
|
||||
20 G t t
|
||||
21 G t t
|
||||
22 G t t
|
||||
23 G t t
|
||||
24 G t t
|
||||
25 G t t
|
||||
26 G
|
||||
27 G
|
||||
-------------------------------------------------------------------------------
|
||||
Atomic short range NN for element O :
|
||||
Number of weights : 1400
|
||||
Number of biases : 51
|
||||
Number of connections: 1451
|
||||
Architecture 30 25 25 1
|
||||
-------------------------------------------------------------------------------
|
||||
1 G t t l
|
||||
2 G t t
|
||||
3 G t t
|
||||
4 G t t
|
||||
5 G t t
|
||||
6 G t t
|
||||
7 G t t
|
||||
8 G t t
|
||||
9 G t t
|
||||
10 G t t
|
||||
11 G t t
|
||||
12 G t t
|
||||
13 G t t
|
||||
14 G t t
|
||||
15 G t t
|
||||
16 G t t
|
||||
17 G t t
|
||||
18 G t t
|
||||
19 G t t
|
||||
20 G t t
|
||||
21 G t t
|
||||
22 G t t
|
||||
23 G t t
|
||||
24 G t t
|
||||
25 G t t
|
||||
26 G
|
||||
27 G
|
||||
28 G
|
||||
29 G
|
||||
30 G
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION SCALING ******************************************
|
||||
|
||||
Equal scaling type for all symmetry functions:
|
||||
Scaling type::ST_SCALECENTER (3)
|
||||
Gs = Smin + (Smax - Smin) * (G - Gmean) / (Gmax - Gmin)
|
||||
Smin = 0.000000
|
||||
Smax = 1.000000
|
||||
Symmetry function scaling statistics from file: hdnnp-data/scaling.data
|
||||
-------------------------------------------------------------------------------
|
||||
|
||||
Abbreviations:
|
||||
--------------
|
||||
ind ..... Symmetry function index.
|
||||
min ..... Minimum symmetry function value.
|
||||
max ..... Maximum symmetry function value.
|
||||
mean .... Mean symmetry function value.
|
||||
sigma ... Standard deviation of symmetry function values.
|
||||
sf ...... Scaling factor for derivatives.
|
||||
Smin .... Desired minimum scaled symmetry function value.
|
||||
Smax .... Desired maximum scaled symmetry function value.
|
||||
t ....... Scaling type.
|
||||
|
||||
Scaling data for symmetry functions element H :
|
||||
-------------------------------------------------------------------------------
|
||||
ind min max mean sigma sf Smin Smax t
|
||||
-------------------------------------------------------------------------------
|
||||
1 1.09E+00 9.62E+00 2.27E+00 6.79E-01 1.17E-01 0.00 1.00 3
|
||||
2 7.33E-01 5.00E+00 1.33E+00 3.39E-01 2.34E-01 0.00 1.00 3
|
||||
3 7.60E-01 7.14E+00 1.65E+00 5.08E-01 1.57E-01 0.00 1.00 3
|
||||
4 5.48E-01 3.77E+00 1.02E+00 2.54E-01 3.11E-01 0.00 1.00 3
|
||||
5 4.01E-01 4.15E+00 9.09E-01 2.98E-01 2.67E-01 0.00 1.00 3
|
||||
6 3.62E-01 2.27E+00 6.49E-01 1.48E-01 5.25E-01 0.00 1.00 3
|
||||
7 1.89E-01 2.23E+00 4.57E-01 1.60E-01 4.90E-01 0.00 1.00 3
|
||||
8 2.67E-01 1.32E+00 4.24E-01 8.05E-02 9.49E-01 0.00 1.00 3
|
||||
9 2.45E-01 9.48E-01 3.62E-01 5.30E-02 1.42E+00 0.00 1.00 3
|
||||
10 2.22E-01 2.76E+00 5.39E-01 2.01E-01 3.94E-01 0.00 1.00 3
|
||||
11 1.47E-01 5.56E-01 2.68E-01 2.62E-02 2.45E+00 0.00 1.00 3
|
||||
12 9.91E-02 1.73E+00 2.96E-01 1.16E-01 6.14E-01 0.00 1.00 3
|
||||
13 6.51E-02 3.45E-01 1.85E-01 1.97E-02 3.57E+00 0.00 1.00 3
|
||||
14 3.17E-02 9.13E-01 1.50E-01 5.35E-02 1.13E+00 0.00 1.00 3
|
||||
15 2.92E-03 2.65E-01 7.65E-02 1.88E-02 3.82E+00 0.00 1.00 3
|
||||
16 3.21E-04 2.87E-01 4.58E-02 2.33E-02 3.49E+00 0.00 1.00 3
|
||||
17 2.47E-04 1.38E-01 1.77E-02 9.75E-03 7.23E+00 0.00 1.00 3
|
||||
18 5.10E-03 5.83E-01 2.39E-02 3.78E-02 1.73E+00 0.00 1.00 3
|
||||
19 3.23E-04 2.16E-01 1.71E-02 1.40E-02 4.63E+00 0.00 1.00 3
|
||||
20 4.96E-02 1.69E+00 1.45E-01 1.10E-01 6.11E-01 0.00 1.00 3
|
||||
21 3.41E-03 3.16E-01 1.84E-02 2.01E-02 3.20E+00 0.00 1.00 3
|
||||
22 1.31E-04 1.03E-01 6.37E-03 6.61E-03 9.76E+00 0.00 1.00 3
|
||||
23 3.38E-02 9.16E-01 8.13E-02 5.79E-02 1.13E+00 0.00 1.00 3
|
||||
24 4.17E-04 1.58E-01 4.66E-03 9.86E-03 6.35E+00 0.00 1.00 3
|
||||
25 7.35E-04 5.92E-02 3.70E-03 3.31E-03 1.71E+01 0.00 1.00 3
|
||||
26 8.98E-03 1.94E-01 2.41E-02 1.10E-02 5.40E+00 0.00 1.00 3
|
||||
27 2.12E-04 8.78E-03 2.06E-03 5.88E-04 1.17E+02 0.00 1.00 3
|
||||
-------------------------------------------------------------------------------
|
||||
Scaling data for symmetry functions element O :
|
||||
-------------------------------------------------------------------------------
|
||||
ind min max mean sigma sf Smin Smax t
|
||||
-------------------------------------------------------------------------------
|
||||
1 1.51E+00 1.00E+01 2.65E+00 6.78E-01 1.18E-01 0.00 1.00 3
|
||||
2 4.44E-01 4.62E+00 9.66E-01 3.37E-01 2.39E-01 0.00 1.00 3
|
||||
3 1.19E+00 7.53E+00 2.03E+00 5.06E-01 1.58E-01 0.00 1.00 3
|
||||
4 2.76E-01 3.39E+00 6.59E-01 2.50E-01 3.21E-01 0.00 1.00 3
|
||||
5 8.06E-01 4.54E+00 1.30E+00 2.94E-01 2.68E-01 0.00 1.00 3
|
||||
6 1.05E-01 1.89E+00 3.07E-01 1.42E-01 5.60E-01 0.00 1.00 3
|
||||
7 5.69E-01 2.62E+00 8.48E-01 1.57E-01 4.89E-01 0.00 1.00 3
|
||||
8 2.33E-02 9.36E-01 1.11E-01 6.98E-02 1.10E+00 0.00 1.00 3
|
||||
9 5.14E-01 1.85E+00 7.25E-01 9.80E-02 7.46E-01 0.00 1.00 3
|
||||
10 1.11E-01 2.91E+00 4.75E-01 2.34E-01 3.57E-01 0.00 1.00 3
|
||||
11 3.53E-01 1.07E+00 5.35E-01 4.52E-02 1.39E+00 0.00 1.00 3
|
||||
12 3.04E-02 2.53E+00 3.17E-01 2.10E-01 4.00E-01 0.00 1.00 3
|
||||
13 1.60E-01 6.63E-01 3.70E-01 3.08E-02 1.99E+00 0.00 1.00 3
|
||||
14 2.78E-03 2.30E+00 1.77E-01 1.86E-01 4.35E-01 0.00 1.00 3
|
||||
15 9.56E-03 3.91E-01 1.53E-01 2.79E-02 2.62E+00 0.00 1.00 3
|
||||
16 3.75E-06 2.04E+00 5.41E-02 1.43E-01 4.91E-01 0.00 1.00 3
|
||||
17 2.47E-03 3.43E-01 1.67E-02 2.19E-02 2.93E+00 0.00 1.00 3
|
||||
18 1.74E-05 5.63E-02 9.55E-04 3.36E-03 1.78E+01 0.00 1.00 3
|
||||
19 5.48E-02 3.02E+00 2.04E-01 2.01E-01 3.37E-01 0.00 1.00 3
|
||||
20 1.38E-03 4.99E-01 1.28E-02 3.18E-02 2.01E+00 0.00 1.00 3
|
||||
21 6.69E-03 2.67E-01 3.09E-02 1.71E-02 3.84E+00 0.00 1.00 3
|
||||
22 1.70E-02 1.42E+00 7.63E-02 9.29E-02 7.14E-01 0.00 1.00 3
|
||||
23 1.98E-02 4.08E-01 4.88E-02 2.55E-02 2.58E+00 0.00 1.00 3
|
||||
24 5.28E-04 2.33E-01 7.21E-03 1.45E-02 4.30E+00 0.00 1.00 3
|
||||
25 1.11E-05 3.53E-02 4.25E-04 2.05E-03 2.83E+01 0.00 1.00 3
|
||||
26 1.60E-02 8.22E-01 5.08E-02 5.28E-02 1.24E+00 0.00 1.00 3
|
||||
27 3.99E-03 7.86E-01 3.69E-02 5.05E-02 1.28E+00 0.00 1.00 3
|
||||
28 4.05E-05 9.84E-02 1.21E-03 5.79E-03 1.02E+01 0.00 1.00 3
|
||||
29 6.04E-03 9.93E-02 1.62E-02 5.52E-03 1.07E+01 0.00 1.00 3
|
||||
30 2.96E-03 1.55E-01 1.16E-02 8.94E-03 6.59E+00 0.00 1.00 3
|
||||
-------------------------------------------------------------------------------
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: SYMMETRY FUNCTION STATISTICS ***************************************
|
||||
|
||||
Equal symmetry function statistics for all elements.
|
||||
Collect min/max/mean/sigma : 0
|
||||
Collect extrapolation warnings : 1
|
||||
Write extrapolation warnings immediately to stderr: 0
|
||||
Halt on any extrapolation warning : 0
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: NEURAL NETWORK WEIGHTS *********************************************
|
||||
|
||||
Short NN weight file name format: hdnnp-data/weights.%03d.data
|
||||
Setting short NN weights for element H from file: hdnnp-data/weights.001.data
|
||||
Setting short NN weights for element O from file: hdnnp-data/weights.008.data
|
||||
*******************************************************************************
|
||||
|
||||
*** SETUP: LAMMPS INTERFACE ***************************************************
|
||||
|
||||
Individual extrapolation warnings will not be shown.
|
||||
Extrapolation warning summary will be shown every 5 timesteps.
|
||||
The simulation will be stopped when 100 extrapolation warnings are exceeded.
|
||||
Extrapolation warnings are accumulated over all time steps.
|
||||
-------------------------------------------------------------------------------
|
||||
CAUTION: If the LAMMPS unit system differs from the one used
|
||||
during NN training, appropriate conversion factors
|
||||
must be provided (see keywords cflength and cfenergy).
|
||||
|
||||
Length unit conversion factor: 1.8897261327999999E+00
|
||||
Energy unit conversion factor: 3.6749325399999998E-02
|
||||
|
||||
Checking consistency of cutoff radii (in LAMMPS units):
|
||||
LAMMPS Cutoff (via pair_coeff) : 6.360E+00
|
||||
Maximum symmetry function cutoff: 6.350E+00
|
||||
Cutoff radii are consistent.
|
||||
-------------------------------------------------------------------------------
|
||||
Element mapping string from LAMMPS to n2p2: "2:H,3:O"
|
||||
|
||||
CAUTION: Please ensure that this mapping between LAMMPS
|
||||
atom types and NNP elements is consistent:
|
||||
|
||||
---------------------------
|
||||
LAMMPS type | NNP element
|
||||
---------------------------
|
||||
1 <-> --
|
||||
2 <-> H ( 1)
|
||||
3 <-> O ( 8)
|
||||
---------------------------
|
||||
|
||||
NNP setup for LAMMPS completed.
|
||||
*******************************************************************************
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.36
|
||||
ghost atom cutoff = 8.36
|
||||
binsize = 4.18, bins = 6 6 6
|
||||
4 neighbor lists, perpetual/occasional/extra = 4 0 0
|
||||
(1) pair lj/cut, perpetual, skip from (3)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair hdnnp, perpetual, skip from (4)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual, half/full trim from (4)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: halffull/newton/trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) neighbor class addition, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
### NNP EW SUMMARY ### TS: 0 EW 0 EWPERSTEP 0.000e+00
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -750069.48 0 -750069.48 -5297.5537
|
||||
1 8.5815594 -750070.71 0 -750069.51 -5249.2914
|
||||
2 30.988787 -750073.91 0 -750069.59 -5023.6945
|
||||
3 58.859866 -750077.88 0 -750069.67 -4427.8346
|
||||
4 82.576399 -750081.26 0 -750069.74 -3275.4378
|
||||
### NNP EW SUMMARY ### TS: 5 EW 0 EWPERSTEP 0.000e+00
|
||||
5 94.968097 -750083.01 0 -750069.76 -1511.6733
|
||||
6 93.724286 -750082.8 0 -750069.73 709.20465
|
||||
7 82.243957 -750081.13 0 -750069.66 3020.5084
|
||||
8 68.611429 -750079.14 0 -750069.57 4922.5176
|
||||
9 62.314385 -750078.21 0 -750069.51 5933.1543
|
||||
### NNP EW SUMMARY ### TS: 10 EW 0 EWPERSTEP 0.000e+00
|
||||
10 69.501045 -750079.21 0 -750069.52 5761.8646
|
||||
Loop time of 0.936871 on 4 procs for 10 steps with 1080 atoms
|
||||
|
||||
Performance: 0.461 ns/day, 52.048 hours/ns, 10.674 timesteps/s, 11.528 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.86567 | 0.89891 | 0.93611 | 3.1 | 95.95
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00035446 | 0.037585 | 0.070835 | 15.3 | 4.01
|
||||
Output | 0.00018528 | 0.00023648 | 0.00030553 | 0.0 | 0.03
|
||||
Modify | 4.2224e-05 | 4.4078e-05 | 4.6256e-05 | 0.0 | 0.00
|
||||
Other | | 9.307e-05 | | | 0.01
|
||||
|
||||
Nlocal: 270 ave 278 max 262 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 2552 ave 2564 max 2541 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,10 +1,9 @@
|
||||
##########################################
|
||||
# CMake build system for plugin examples.
|
||||
# -*- CMake -*- build system for plugin examples.
|
||||
# The is meant to be used as a template for plugins that are
|
||||
# distributed independent from the LAMMPS package.
|
||||
##########################################
|
||||
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
project(paceplugin VERSION 1.0 LANGUAGES CXX)
|
||||
|
||||
|
||||
@ -91,7 +91,6 @@ mesh: create_atoms mesh command
|
||||
micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
||||
min: energy minimization of 2d LJ melt
|
||||
mliap: examples for using several bundled MLIAP potentials
|
||||
mscg: parameterize a multi-scale coarse-graining (MSCG) model
|
||||
msst: MSST shock dynamics
|
||||
nb3b: use of nonbonded 3-body harmonic pair style
|
||||
neb: nudged elastic band (NEB) calculation for barrier finding
|
||||
|
||||
@ -1,10 +1,9 @@
|
||||
##########################################
|
||||
# CMake build system for plugin examples.
|
||||
# -*- CMake -*- file for building plugins.
|
||||
# The is meant to be used as a template for plugins that are
|
||||
# distributed independent from the LAMMPS package.
|
||||
##########################################
|
||||
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
project(kimplugin VERSION 1.0 LANGUAGES CXX)
|
||||
|
||||
@ -31,12 +30,7 @@ target_link_libraries(kimplugin PRIVATE KIM-API::kim-api)
|
||||
# need libcurl
|
||||
find_package(CURL)
|
||||
if(CURL_FOUND)
|
||||
if(CMAKE_VERSION VERSION_LESS 3.12)
|
||||
target_include_directories(kimplugin PRIVATE ${CURL_INCLUDE_DIRS})
|
||||
target_link_libraries(kimplugin PRIVATE ${CURL_LIBRARIES})
|
||||
else()
|
||||
target_link_libraries(kimplugin PRIVATE CURL::libcurl)
|
||||
endif()
|
||||
target_link_libraries(kimplugin PRIVATE CURL::libcurl)
|
||||
target_compile_definitions(kimplugin PRIVATE -DLMP_KIM_CURL)
|
||||
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
|
||||
mark_as_advanced(LMP_DEBUG_CURL)
|
||||
|
||||
@ -1,10 +0,0 @@
|
||||
Running this example requires that LAMMPS be built with the MSCG
|
||||
package and its fix mscg command. The fix uses the Multi-Scale
|
||||
Coarse-Graining (MS-CG) library, freely available at
|
||||
https://github.com/uchicago-voth/MSCG-release, to compute optimized
|
||||
coarse-grained force field parameters. The MS-CG library was
|
||||
developed by Jacob Wagner in Greg Voth's group at the University of
|
||||
Chicago.
|
||||
|
||||
See the lib/mscg/README file for instructions on how to download and
|
||||
install the MS-CG library for use with LAMMPS.
|
||||
@ -1,12 +0,0 @@
|
||||
block_size 1
|
||||
start_frame 1
|
||||
n_frames 19
|
||||
nonbonded_cutoff 10.0
|
||||
basis_type 0
|
||||
primary_output_style 0
|
||||
output_solution_flag 1
|
||||
output_spline_coeffs_flag 1
|
||||
pair_nonbonded_bspline_basis_order 6
|
||||
pair_nonbonded_basis_set_resolution 0.7
|
||||
pair_nonbonded_output_binwidth 0.1
|
||||
matrix_type 0
|
||||
File diff suppressed because it is too large
Load Diff
20180
examples/mscg/dump.meoh
20180
examples/mscg/dump.meoh
File diff suppressed because it is too large
Load Diff
@ -1,22 +0,0 @@
|
||||
units real
|
||||
atom_style full
|
||||
pair_style zero 10.0
|
||||
|
||||
read_data data.meoh
|
||||
pair_coeff * *
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step
|
||||
|
||||
# Test 1a: range finder functionality
|
||||
fix 1 all mscg 1 range on
|
||||
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
|
||||
print "TEST_1a mscg range finder"
|
||||
unfix 1
|
||||
|
||||
# Test 1b: force matching functionality
|
||||
fix 1 all mscg 1
|
||||
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
|
||||
print "TEST_1b mscg force matching"
|
||||
|
||||
print TEST_DONE
|
||||
@ -1,105 +0,0 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
pair_style zero 10.0
|
||||
|
||||
read_data data.meoh
|
||||
Reading data file ...
|
||||
orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 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 = 0.007 seconds
|
||||
pair_coeff * *
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step
|
||||
|
||||
# Test 1a: range finder functionality
|
||||
fix 1 all mscg 1 range on
|
||||
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 0 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 = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
|
||||
Step
|
||||
0
|
||||
250
|
||||
500
|
||||
750
|
||||
1000
|
||||
1250
|
||||
1500
|
||||
1750
|
||||
2000
|
||||
2250
|
||||
2500
|
||||
2750
|
||||
3000
|
||||
3250
|
||||
3500
|
||||
3750
|
||||
4000
|
||||
4250
|
||||
4500
|
||||
Loop time of 0.245891 on 1 procs for 19 steps with 1000 atoms
|
||||
|
||||
print "TEST_1a mscg range finder"
|
||||
TEST_1a mscg range finder
|
||||
unfix 1
|
||||
|
||||
# Test 1b: force matching functionality
|
||||
fix 1 all mscg 1
|
||||
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
|
||||
Step
|
||||
0
|
||||
250
|
||||
500
|
||||
750
|
||||
1000
|
||||
1250
|
||||
1500
|
||||
1750
|
||||
2000
|
||||
2250
|
||||
2500
|
||||
2750
|
||||
3000
|
||||
3250
|
||||
3500
|
||||
3750
|
||||
4000
|
||||
4250
|
||||
4500
|
||||
Loop time of 0.433986 on 1 procs for 19 steps with 1000 atoms
|
||||
|
||||
print "TEST_1b mscg force matching"
|
||||
TEST_1b mscg force matching
|
||||
|
||||
print TEST_DONE
|
||||
TEST_DONE
|
||||
Total wall time: 0:00:00
|
||||
@ -1,71 +0,0 @@
|
||||
3.000000 9.109433117503674e+00
|
||||
3.100000 6.562933520937051e+00
|
||||
3.200000 3.803570347770783e+00
|
||||
3.300000 1.524835163098694e+00
|
||||
3.400000 3.680752991750511e-02
|
||||
3.500000 -6.369395346711866e-01
|
||||
3.600000 -6.624341032589213e-01
|
||||
3.700000 -2.983998819283989e-01
|
||||
3.800000 1.996942072449469e-01
|
||||
3.900000 6.507540486137935e-01
|
||||
4.000000 9.561503221901252e-01
|
||||
4.100000 1.082978861799261e+00
|
||||
4.200000 1.046366050930359e+00
|
||||
4.300000 8.917742185869113e-01
|
||||
4.400000 6.773070351372578e-01
|
||||
4.500000 4.561974686292022e-01
|
||||
4.600000 2.640422255436971e-01
|
||||
4.700000 1.180848207166380e-01
|
||||
4.800000 2.124502216672507e-02
|
||||
4.900000 -3.366915456585443e-02
|
||||
5.000000 -5.974945208074427e-02
|
||||
5.100000 -7.177537677873873e-02
|
||||
5.200000 -8.204929079011507e-02
|
||||
5.300000 -9.745573177789707e-02
|
||||
5.400000 -1.196283642109915e-01
|
||||
5.500000 -1.463411396781238e-01
|
||||
5.600000 -1.729465415853768e-01
|
||||
5.700000 -1.938138298537278e-01
|
||||
5.800000 -2.037672856165882e-01
|
||||
5.900000 -1.995060297815394e-01
|
||||
6.000000 -1.805447650094144e-01
|
||||
6.100000 -1.489384048916932e-01
|
||||
6.200000 -1.085276302304308e-01
|
||||
6.300000 -6.416601955090541e-02
|
||||
6.400000 -2.094717961426480e-02
|
||||
6.500000 1.656812406982645e-02
|
||||
6.600000 4.511482523443927e-02
|
||||
6.700000 6.322611594801032e-02
|
||||
6.800000 7.107524696431811e-02
|
||||
6.900000 7.005702917383723e-02
|
||||
7.000000 6.235932355899154e-02
|
||||
7.100000 5.053453114940768e-02
|
||||
7.200000 3.707108297716843e-02
|
||||
7.300000 2.397003518601587e-02
|
||||
7.400000 1.245439896007831e-02
|
||||
7.500000 3.015413982707119e-03
|
||||
7.600000 -4.408442264121739e-03
|
||||
7.700000 -1.024733994435217e-02
|
||||
7.800000 -1.511598231239246e-02
|
||||
7.900000 -1.962949115765983e-02
|
||||
8.000000 -2.422153184874873e-02
|
||||
8.100000 -2.902066868449916e-02
|
||||
8.200000 -3.387453677654857e-02
|
||||
8.300000 -3.843224513464188e-02
|
||||
8.400000 -4.222901944115068e-02
|
||||
8.500000 -4.477084482559266e-02
|
||||
8.600000 -4.561910863915099e-02
|
||||
8.700000 -4.447439067652353e-02
|
||||
8.800000 -4.123808661911404e-02
|
||||
8.900000 -3.601776131390161e-02
|
||||
9.000000 -2.911033476210515e-02
|
||||
9.100000 -2.098441550402311e-02
|
||||
9.200000 -1.226263400387303e-02
|
||||
9.300000 -3.703976034631109e-03
|
||||
9.400000 3.815231963949414e-03
|
||||
9.500000 9.355387087425532e-03
|
||||
9.600000 1.205664749783030e-02
|
||||
9.700000 1.131702059340882e-02
|
||||
9.800000 6.971799313021964e-03
|
||||
9.900000 -5.270015594498346e-04
|
||||
10.000000 -9.931209090702869e-03
|
||||
@ -1,104 +0,0 @@
|
||||
# Header information on force file
|
||||
|
||||
1_1
|
||||
N 99 R 0.200000 10.000000
|
||||
|
||||
1 0.200000 127.263594 80.411422
|
||||
2 0.300000 119.349776 77.864922
|
||||
3 0.400000 111.690609 75.318423
|
||||
4 0.500000 104.286092 72.771923
|
||||
5 0.600000 97.136225 70.225423
|
||||
6 0.700000 90.241007 67.678924
|
||||
7 0.800000 83.600440 65.132424
|
||||
8 0.900000 77.214522 62.585925
|
||||
9 1.000000 71.083255 60.039425
|
||||
10 1.100000 65.206637 57.492925
|
||||
11 1.200000 59.584670 54.946426
|
||||
12 1.300000 54.217352 52.399926
|
||||
13 1.400000 49.104684 49.853427
|
||||
14 1.500000 44.246667 47.306927
|
||||
15 1.600000 39.643299 44.760427
|
||||
16 1.700000 35.294581 42.213928
|
||||
17 1.800000 31.200513 39.667428
|
||||
18 1.900000 27.361096 37.120929
|
||||
19 2.000000 23.776328 34.574429
|
||||
20 2.100000 20.446210 32.027929
|
||||
21 2.200000 17.370742 29.481430
|
||||
22 2.300000 14.549924 26.934930
|
||||
23 2.400000 11.983756 24.388431
|
||||
24 2.500000 9.672238 21.841931
|
||||
25 2.600000 7.615370 19.295432
|
||||
26 2.700000 5.813151 16.748932
|
||||
27 2.800000 4.265583 14.202432
|
||||
28 2.900000 2.972665 11.655933
|
||||
29 3.000000 1.934397 9.109433
|
||||
30 3.100000 1.150778 6.562934
|
||||
31 3.200000 0.632453 3.803570
|
||||
32 3.300000 0.366033 1.524835
|
||||
33 3.400000 0.287951 0.036808
|
||||
34 3.500000 0.317957 -0.636940
|
||||
35 3.600000 0.382926 -0.662434
|
||||
36 3.700000 0.430968 -0.298400
|
||||
37 3.800000 0.435903 0.199694
|
||||
38 3.900000 0.393381 0.650754
|
||||
39 4.000000 0.313035 0.956150
|
||||
40 4.100000 0.211079 1.082979
|
||||
41 4.200000 0.104612 1.046366
|
||||
42 4.300000 0.007705 0.891774
|
||||
43 4.400000 -0.070749 0.677307
|
||||
44 4.500000 -0.127425 0.456197
|
||||
45 4.600000 -0.163437 0.264042
|
||||
46 4.700000 -0.182543 0.118085
|
||||
47 4.800000 -0.189509 0.021245
|
||||
48 4.900000 -0.188888 -0.033669
|
||||
49 5.000000 -0.184217 -0.059749
|
||||
50 5.100000 -0.177641 -0.071775
|
||||
51 5.200000 -0.169950 -0.082049
|
||||
52 5.300000 -0.160975 -0.097456
|
||||
53 5.400000 -0.150120 -0.119628
|
||||
54 5.500000 -0.136822 -0.146341
|
||||
55 5.600000 -0.120858 -0.172947
|
||||
56 5.700000 -0.102520 -0.193814
|
||||
57 5.800000 -0.082640 -0.203767
|
||||
58 5.900000 -0.062477 -0.199506
|
||||
59 6.000000 -0.043474 -0.180545
|
||||
60 6.100000 -0.027000 -0.148938
|
||||
61 6.200000 -0.014127 -0.108528
|
||||
62 6.300000 -0.005492 -0.064166
|
||||
63 6.400000 -0.001236 -0.020947
|
||||
64 6.500000 -0.001018 0.016568
|
||||
65 6.600000 -0.004102 0.045115
|
||||
66 6.700000 -0.009519 0.063226
|
||||
67 6.800000 -0.016234 0.071075
|
||||
68 6.900000 -0.023290 0.070057
|
||||
69 7.000000 -0.029911 0.062359
|
||||
70 7.100000 -0.035556 0.050535
|
||||
71 7.200000 -0.039936 0.037071
|
||||
72 7.300000 -0.042988 0.023970
|
||||
73 7.400000 -0.044809 0.012454
|
||||
74 7.500000 -0.045583 0.003015
|
||||
75 7.600000 -0.045513 -0.004408
|
||||
76 7.700000 -0.044781 -0.010247
|
||||
77 7.800000 -0.043512 -0.015116
|
||||
78 7.900000 -0.041775 -0.019629
|
||||
79 8.000000 -0.039583 -0.024222
|
||||
80 8.100000 -0.036920 -0.029021
|
||||
81 8.200000 -0.033776 -0.033875
|
||||
82 8.300000 -0.030160 -0.038432
|
||||
83 8.400000 -0.026127 -0.042229
|
||||
84 8.500000 -0.021777 -0.044771
|
||||
85 8.600000 -0.017258 -0.045619
|
||||
86 8.700000 -0.012753 -0.044474
|
||||
87 8.800000 -0.008467 -0.041238
|
||||
88 8.900000 -0.004605 -0.036018
|
||||
89 9.000000 -0.001348 -0.029110
|
||||
90 9.100000 0.001156 -0.020984
|
||||
91 9.200000 0.002819 -0.012263
|
||||
92 9.300000 0.003617 -0.003704
|
||||
93 9.400000 0.003612 0.003815
|
||||
94 9.500000 0.002953 0.009355
|
||||
95 9.600000 0.001882 0.012057
|
||||
96 9.700000 0.000714 0.011317
|
||||
97 9.800000 -0.000201 0.006972
|
||||
98 9.900000 -0.000523 -0.000527
|
||||
99 10.000000 0.000000 -0.009931
|
||||
@ -1,2 +0,0 @@
|
||||
n: 1 1 6 11 3.000000000000000e+00 1.000000000000000e+01
|
||||
9.109454054135307e+00 6.178334150703818e+00 -6.242976259059743e+00 4.778144787445235e+00 -1.082885612852992e+00 4.521835893850554e-01 -6.477047196208028e-01 2.947887062333265e-01 -4.195609079009661e-02 1.111775827831465e-02 -8.823466147380592e-02 -1.696076806027540e-02 3.192205281984208e-02 3.656991607866288e-03 -9.931306149957592e-03
|
||||
@ -1 +0,0 @@
|
||||
1 1 2.852369 10.000000 fm
|
||||
@ -1,17 +0,0 @@
|
||||
fm_matrix_rows:3000; fm_matrix_columns:15;
|
||||
Singular vector:
|
||||
2.307693e+00
|
||||
1.998418e+00
|
||||
1.400114e+00
|
||||
1.183608e+00
|
||||
9.718949e-01
|
||||
7.471241e-01
|
||||
5.277965e-01
|
||||
5.084369e-01
|
||||
3.510398e-01
|
||||
2.997000e-01
|
||||
2.142454e-01
|
||||
1.201800e-01
|
||||
7.143923e-02
|
||||
3.077326e-02
|
||||
1.835581e-02
|
||||
@ -1,2 +0,0 @@
|
||||
<EFBFBD>ٝ\
|
||||
8"@<40>!D:<3A><>@<40>v<EFBFBD><76><EFBFBD><EFBFBD><18>H<EFBFBD><48><EFBFBD><EFBFBD> @H3H<33>S<7F><53>Ԗ p<><70><EFBFBD>??<3F><>俀% s<><73><EFBFBD>?:y<><79>D{<7B><><EFBFBD>z<EFBFBD>A<EFBFBD>Ć?#Tg<54><67><EFBFBD><EFBFBD><EFBFBD>l#<23><>)^<5E><><EFBFBD><EFBFBD><EFBFBD>YX<>?K<>pkD<6B>m?<3F>
|
||||
@ -1,10 +1,9 @@
|
||||
##########################################
|
||||
# CMake build system for plugin examples.
|
||||
# -*- CMake -*- file for plugin examples.
|
||||
# The is meant to be used as a template for plugins that are
|
||||
# distributed independent from the LAMMPS package.
|
||||
##########################################
|
||||
|
||||
cmake_minimum_required(VERSION 3.10)
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
# enforce out-of-source build
|
||||
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
|
||||
@ -36,9 +35,8 @@ else()
|
||||
add_compile_options(/Zc:__cplusplus)
|
||||
add_compile_options(/wd4244)
|
||||
add_compile_options(/wd4267)
|
||||
if(LAMMPS_EXCEPTIONS)
|
||||
add_compile_options(/EHsc)
|
||||
endif()
|
||||
add_compile_options(/wd4250)
|
||||
add_compile_options(/EHsc)
|
||||
endif()
|
||||
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
|
||||
endif()
|
||||
|
||||
Reference in New Issue
Block a user