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Merge pull request #4494 from lammps/example-input-fixes

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fixed issues with several input scripts, added reference log files
This commit is contained in:
Axel Kohlmeyer
2025-03-13 14:34:44 -04:00
committed by GitHub
parent 084bdb2da6 38903fb7d2
commit 03f71259c1
13 changed files with 723 additions and 53 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
examples/COUPLE/multiple/in.chain
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@ -1,5 +1,5 @@
# FENE beadspring benchmark # FENE beadspring benchmark
variable t index 1.0
units lj units lj
atom_style bond atom_style bond
special_bonds fene special_bonds fene

1
examples/PACKAGES/atc/elastic/Au_u3.eam Symbolic link
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@ -0,0 +1 @@
../../../../potentials/Au_u3.eam

2
examples/PACKAGES/pafi/in.pafi
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@ -9,7 +9,7 @@ read_data pafipath.4.data fix pa NULL PafiPath
## EAM potential ## EAM potential
pair_style eam/fs pair_style eam/fs
pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe pair_coeff * * Fe_mm.eam.fs Fe
mass * 55.85 mass * 55.85
thermo 100 thermo 100

2
examples/PACKAGES/ti/in.ti_spring
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@ -13,7 +13,7 @@
create_atoms 1 box create_atoms 1 box
pair_style eam/alloy pair_style eam/alloy
pair_coeff * * ../../../../potentials/Cu_mishin1.eam.alloy Cu pair_coeff * * Cu_mishin1.eam.alloy Cu
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#

2
examples/SPIN/test_problems/validation_nve/in.spin.iron-nve
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@ -50,5 +50,5 @@ thermo 200
compute outsp all property/atom spx spy spz sp fmx fmy fmz compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 100000 run 10000
# run 1 # run 1

188
examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1 Normal file
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@ -0,0 +1,188 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# bcc iron in a 3d periodic box
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style spin
# atom_style spin/kk
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice bcc 2.8665
Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
region box block 0.0 3.0 0.0 3.0 0.0 3.0
create_box 1 box
Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 54 atoms
using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
create_atoms CPU = 0.001 seconds
# setting mass, mag. moments, and interactions for bcc iron
mass 1 55.845
set group all spin/random 31 2.2
Setting atom values ...
WARNING: Set attribute spin/random is deprecated. Please use spin/atom/random instead. (src/set.cpp:293)
54 settings made for spin/random
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 3.5
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.00 21
fix 3 all nve/spin lattice moving
timestep 0.0001
# compute and output options
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_tmag temp v_emag ke pe etotal
thermo 200
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
@article{tranchida2018massively,
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
journal={Journal of Computational Physics},
volume={372},
pages={406--425},
year={2018},
publisher={Elsevier}
doi={10.1016/j.jcp.2018.06.042}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 20 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.773367
ghost atom cutoff = 5.773367
binsize = 2.8866835, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on, cut 5.7733670002446
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Dump 1 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
Per MPI rank memory allocation (min/avg/max) = 5.626 | 5.626 | 5.626 Mbytes
Step Time v_tmag Temp v_emag KinEng PotEng TotEng
0 0 1836.2373 100.00358 -0.26674297 0.6851033 -231.38675 -230.70164
200 0.02 1751.0384 48.019015 -0.27512361 0.32896808 -231.03061 -230.70164
400 0.04 1776.2639 19.035769 -0.28188188 0.13041001 -230.83205 -230.70164
600 0.06 1787.5802 60.069761 -0.2772323 0.41152518 -231.11317 -230.70164
800 0.08 1706.5552 50.79606 -0.27292548 0.34799302 -231.04963 -230.70164
1000 0.1 2120.1611 44.605193 -0.26987056 0.3055807 -231.00722 -230.70164
1200 0.12 1754.9393 64.57232 -0.26943293 0.44237126 -231.14401 -230.70164
1400 0.14 1912.6009 44.177766 -0.26857448 0.3026525 -231.00429 -230.70164
1600 0.16 1875.5315 40.249733 -0.27481087 0.27574238 -230.97738 -230.70164
1800 0.18 1837.1786 62.817536 -0.28092582 0.4303496 -231.13199 -230.70164
2000 0.2 1860.1719 54.167659 -0.28282659 0.37109113 -231.07273 -230.70164
2200 0.22 1691.658 46.643932 -0.29528237 0.31954767 -231.02119 -230.70164
2400 0.24 1525.2579 57.361866 -0.30189945 0.39297397 -231.09462 -230.70164
2600 0.26 1505.1726 56.239347 -0.30898994 0.38528383 -231.08693 -230.70164
2800 0.28 1415.9555 47.818074 -0.31351411 0.32759147 -231.02923 -230.70164
3000 0.3 1248.4308 49.608492 -0.31727375 0.33985725 -231.0415 -230.70164
3200 0.32 1200.7605 51.495405 -0.31565357 0.35278409 -231.05443 -230.70164
3400 0.34 1746.137 56.967184 -0.30906485 0.39027008 -231.09191 -230.70164
3600 0.36 1805.3667 55.030692 -0.30799197 0.37700359 -231.07865 -230.70164
3800 0.38 1609.9498 59.452017 -0.30520539 0.40729315 -231.10894 -230.70164
4000 0.4 1686.1863 57.338707 -0.30240026 0.39281531 -231.09446 -230.70164
4200 0.42 1961.3516 41.421108 -0.30479326 0.28376722 -230.98541 -230.70164
4400 0.44 1971.1808 54.038289 -0.30876936 0.37020484 -231.07185 -230.70164
4600 0.46 1819.428 56.766201 -0.3129157 0.38889319 -231.09054 -230.70164
4800 0.48 1494.1263 47.402453 -0.32868332 0.32474414 -231.02639 -230.70164
5000 0.5 1601.6127 63.404101 -0.33283819 0.43436803 -231.13601 -230.70164
5200 0.52 1567.7429 62.783792 -0.34753005 0.43011843 -231.13176 -230.70164
5400 0.54 1686.234 40.450417 -0.3603489 0.27711722 -230.97876 -230.70164
5600 0.56 1651.1927 64.255456 -0.36569031 0.44020049 -231.14184 -230.70164
5800 0.58 1380.639 75.386226 -0.36870019 0.51645503 -231.2181 -230.70164
6000 0.6 1539.07 40.611642 -0.36303517 0.27822173 -230.97986 -230.70164
6200 0.62 1442.2286 50.254503 -0.36560331 0.34428293 -231.04592 -230.70164
6400 0.64 1263.6928 69.095161 -0.36822748 0.47335628 -231.175 -230.70164
6600 0.66 1468.1529 54.534243 -0.37319988 0.37360252 -231.07524 -230.70164
6800 0.68 1289.4927 60.381892 -0.38478834 0.41366352 -231.11531 -230.70164
7000 0.7 1121.6702 58.691171 -0.39652609 0.40208075 -231.10372 -230.70164
7200 0.72 1018.1068 53.528417 -0.40711639 0.36671182 -231.06835 -230.70164
7400 0.74 1115.0342 78.62129 -0.41729373 0.53861776 -231.24026 -230.70164
7600 0.76 1329.4621 65.650574 -0.41928751 0.44975815 -231.1514 -230.70164
7800 0.78 1154.164 45.603278 -0.41263444 0.31241837 -231.01406 -230.70164
8000 0.8 1090.2959 62.148282 -0.40987933 0.42576469 -231.12741 -230.70164
8200 0.82 1303.4698 63.864431 -0.41301445 0.43752166 -231.13916 -230.70164
8400 0.84 1144.2181 52.222297 -0.41645089 0.35776387 -231.05941 -230.70164
8600 0.86 1005.3359 61.59129 -0.41282114 0.42194885 -231.12359 -230.70164
8800 0.88 1453.8465 70.876149 -0.41920851 0.48555745 -231.1872 -230.70164
9000 0.9 1325.9116 63.675151 -0.42450864 0.43622494 -231.13787 -230.70164
9200 0.92 1213.5738 58.297881 -0.42722791 0.3993864 -231.10103 -230.70164
9400 0.94 1227.437 57.375795 -0.44309693 0.39306939 -231.09471 -230.70164
9600 0.96 1192.79 65.822598 -0.44760999 0.45093664 -231.15258 -230.70164
9800 0.98 1231.5166 69.119896 -0.45335245 0.47352573 -231.17517 -230.70164
10000 1 1284.2809 66.166068 -0.45872955 0.45328969 -231.15493 -230.70164
Loop time of 5.97474 on 1 procs for 10000 steps with 54 atoms
Performance: 14.461 ns/day, 1.660 hours/ns, 1673.714 timesteps/s, 90.381 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 | 2.501 | 2.501 | 2.501 | 0.0 | 41.86
Neigh | 0.016481 | 0.016481 | 0.016481 | 0.0 | 0.28
Comm | 0.37576 | 0.37576 | 0.37576 | 0.0 | 6.29
Output | 0.12311 | 0.12311 | 0.12311 | 0.0 | 2.06
Modify | 2.9317 | 2.9317 | 2.9317 | 0.0 | 49.07
Other | | 0.02661 | | | 0.45
Nlocal: 54 ave 54 max 54 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 777 ave 777 max 777 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1700 ave 1700 max 1700 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3400 ave 3400 max 3400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3400
Ave neighs/atom = 62.962963
Neighbor list builds = 58
Dangerous builds = 0
# run 1
Total wall time: 0:00:06

2
examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice
View File

@ -49,4 +49,4 @@ variable tmag equal c_out_mag[6]
thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo_style custom step time v_tmag temp v_emag ke pe etotal
thermo 200 thermo 200
run 200000 run 20000

4
examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin
View File

@ -32,7 +32,7 @@ neighbor 0.1 bin
neigh_modify every 10 check yes delay 20 neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin 0.0 0.0 0.0 48279 fix 2 all langevin 0.0 0.0 0.001 48279
fix 3 all langevin/spin 200.0 0.01 321 fix 3 all langevin/spin 200.0 0.01 321
fix 4 all nve/spin lattice moving fix 4 all nve/spin lattice moving
timestep 0.001 timestep 0.001
@ -50,4 +50,4 @@ variable tmag equal c_out_mag[6]
thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo_style custom step time v_tmag temp v_emag ke pe etotal
thermo 200 thermo 200
run 200000 run 20000

240
examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1 Normal file
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@ -0,0 +1,240 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# bcc iron in a 3d periodic box
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style spin
# atom_style spin/kk
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice bcc 2.8665
Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
region box block 0.0 3.0 0.0 3.0 0.0 3.0
create_box 1 box
Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 54 atoms
using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
create_atoms CPU = 0.001 seconds
# setting mass, mag. moments, and interactions for bcc iron
mass 1 55.845
set group all spin 2.2 0.0 0.0 1.0
Setting atom values ...
WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268)
54 settings made for spin
velocity all create 400 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
pair_coeff * * spin/exchange exchange 3.4 0.1 0.2171 1.841
pair_coeff * * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin 200.0 200.0 0.1 48279
fix 3 all langevin/spin 0.0 0.0 321
fix 4 all nve/spin lattice moving
timestep 0.001
# compute and output options
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_tmag temp v_emag ke pe etotal
thermo 200
run 20000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
@article{tranchida2018massively,
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
journal={Journal of Computational Physics},
volume={372},
pages={406--425},
year={2018},
publisher={Elsevier}
doi={10.1016/j.jcp.2018.06.042}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 20 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.773367
ghost atom cutoff = 5.773367
binsize = 2.8866835, bins = 3 3 3
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on, cut 5.7733670002446
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) pair spin/neel, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes
Step Time v_tmag Temp v_emag KinEng PotEng TotEng
0 0 1.4336203e-31 400.01433 -22.021022 2.7404132 -253.14103 -250.40061
200 0.2 0.26275543 188.91786 -21.983513 1.2942362 -251.94911 -250.65488
400 0.4 0.56095049 204.95947 -21.977046 1.4041338 -251.914 -250.50987
600 0.6 0.81480981 203.28763 -21.98548 1.3926804 -251.88478 -250.4921
800 0.8 0.97590428 184.8694 -21.974142 1.266501 -251.73716 -250.47066
1000 1 1.1324742 184.65547 -21.986309 1.2650354 -252.03248 -250.76744
1200 1.2 1.5284342 207.55788 -21.974821 1.421935 -251.7769 -250.35497
1400 1.4 1.8310776 220.75396 -21.979994 1.5123385 -251.93989 -250.42755
1600 1.6 2.2057174 236.04272 -21.973951 1.6170785 -251.98625 -250.36917
1800 1.8 2.7760928 195.92697 -21.96808 1.3422541 -251.7495 -250.40725
2000 2 3.2171354 161.33811 -21.975129 1.1052932 -251.86337 -250.75808
2200 2.2 3.8284998 193.21861 -21.968067 1.3236997 -251.86609 -250.54239
2400 2.4 4.4109629 203.79368 -21.971813 1.3961472 -251.92264 -250.52649
2600 2.6 4.5056291 200.81431 -21.960649 1.3757362 -251.80976 -250.43403
2800 2.8 4.6221125 185.57027 -21.972664 1.2713025 -252.0384 -250.76709
3000 3 4.9059897 216.00877 -21.966875 1.4798302 -252.13406 -250.65423
3200 3.2 5.3958965 152.77626 -21.956779 1.0466377 -251.66 -250.61337
3400 3.4 5.9881406 170.70538 -21.964189 1.1694663 -251.9061 -250.73663
3600 3.6 6.134982 210.99981 -21.945137 1.4455149 -251.75025 -250.30474
3800 3.8 6.5940545 239.12527 -21.953159 1.6381964 -251.90813 -250.26993
4000 4 6.9355034 181.99614 -21.938591 1.2468169 -251.59724 -250.35043
4200 4.2 7.3712919 242.52183 -21.932318 1.6614656 -251.71104 -250.04957
4400 4.4 7.5924709 164.34328 -21.942361 1.1258809 -251.64032 -250.51444
4600 4.6 8.1833481 205.94973 -21.941491 1.4109179 -251.57627 -250.16536
4800 4.8 8.40416 169.96914 -21.945774 1.1644225 -251.87887 -250.71444
5000 5 8.4422416 189.79518 -21.94955 1.3002465 -251.80055 -250.50031
5200 5.2 8.3667008 195.86473 -21.934302 1.3418277 -251.64678 -250.30495
5400 5.4 8.7075519 204.82319 -21.947339 1.4032002 -251.85712 -250.45392
5600 5.6 8.6582399 191.25854 -21.933614 1.3102717 -251.51648 -250.2062
5800 5.8 8.896287 180.44446 -21.923523 1.2361867 -251.68003 -250.44384
6000 6 9.1379808 248.49596 -21.938845 1.7023931 -251.84502 -250.14263
6200 6.2 8.9724294 181.67979 -21.939567 1.2446497 -251.81639 -250.57174
6400 6.4 8.7735241 198.31668 -21.952115 1.3586255 -251.97841 -250.61979
6600 6.6 9.0394523 218.6735 -21.934717 1.4980857 -251.85133 -250.35325
6800 6.8 9.5779186 203.83536 -21.937873 1.3964328 -251.98448 -250.58804
7000 7 9.7893273 185.56096 -21.949319 1.2712387 -252.09057 -250.81934
7200 7.2 9.5292481 205.53224 -21.936466 1.4080577 -251.98037 -250.57231
7400 7.4 9.7369072 200.76528 -21.944609 1.3754003 -251.88128 -250.50588
7600 7.6 9.9385522 217.68239 -21.920768 1.4912959 -251.6169 -250.1256
7800 7.8 9.8656638 219.17274 -21.92302 1.5015059 -251.50189 -250.00039
8000 8 9.2380618 264.13229 -21.936112 1.8095143 -251.71532 -249.9058
8200 8.2 9.3384949 239.58029 -21.941834 1.6413137 -251.73551 -250.0942
8400 8.4 9.1684312 207.27974 -21.938426 1.4200295 -251.59062 -250.17059
8600 8.6 8.8407032 200.79452 -21.933328 1.3756006 -251.48006 -250.10446
8800 8.8 8.84683 218.44316 -21.949738 1.4965077 -251.92925 -250.43275
9000 9 9.0686442 216.06373 -21.942255 1.4802067 -251.79797 -250.31776
9200 9.2 9.2783597 187.56662 -21.93374 1.2849791 -251.87884 -250.59386
9400 9.4 9.2794158 203.78139 -21.955284 1.396063 -252.09328 -250.69722
9600 9.6 9.3563189 196.15871 -21.948544 1.3438417 -251.85685 -250.51301
9800 9.8 9.6458819 215.38334 -21.94895 1.4755455 -251.92219 -250.44665
10000 10 9.5073837 178.61601 -21.955281 1.2236604 -251.97306 -250.7494
10200 10.2 9.3510908 185.21136 -21.94749 1.2688437 -251.83233 -250.56349
10400 10.4 9.8171891 194.92192 -21.945394 1.3353687 -251.86067 -250.5253
10600 10.6 9.5996138 213.90302 -21.945461 1.4654042 -251.72508 -250.25968
10800 10.8 9.8602813 208.57912 -21.936736 1.4289312 -251.55778 -250.12885
11000 11 10.652287 202.88507 -21.933085 1.3899225 -251.69631 -250.30639
11200 11.2 10.413298 171.86972 -21.919711 1.1774429 -251.16232 -249.98488
11400 11.4 10.589727 179.33897 -21.927537 1.2286132 -251.65266 -250.42405
11600 11.6 11.099271 176.43012 -21.925025 1.2086853 -251.65796 -250.44927
11800 11.8 11.49558 216.78529 -21.935923 1.48515 -251.51958 -250.03443
12000 12 11.190687 206.45545 -21.941866 1.4143824 -251.55494 -250.14055
12200 12.2 11.372777 216.26373 -21.934028 1.4815769 -251.75482 -250.27324
12400 12.4 11.303952 218.67625 -21.928577 1.4981046 -251.73908 -250.24098
12600 12.6 11.065605 188.25083 -21.925979 1.2896665 -251.49808 -250.20841
12800 12.8 11.289265 209.423 -21.933529 1.4347125 -251.85142 -250.41671
13000 13 11.412931 148.86392 -21.93732 1.0198351 -251.88347 -250.86364
13200 13.2 11.677538 187.03356 -21.923919 1.2813272 -251.52124 -250.23991
13400 13.4 12.451801 237.44268 -21.93385 1.6266694 -251.70112 -250.07445
13600 13.6 12.981208 196.47947 -21.926751 1.3460391 -251.80509 -250.45905
13800 13.8 13.301789 191.61721 -21.921891 1.3127288 -251.85541 -250.54268
14000 14 13.726635 212.61693 -21.922086 1.4565934 -252.06804 -250.61145
14200 14.2 13.715662 197.51397 -21.915949 1.3531263 -251.71314 -250.36002
14400 14.4 13.340257 210.15601 -21.927197 1.4397342 -251.73271 -250.29297
14600 14.6 14.118672 175.1782 -21.923635 1.2001087 -251.54286 -250.34275
14800 14.8 14.52801 211.5541 -21.919371 1.4493122 -251.74119 -250.29188
15000 15 14.522566 207.59406 -21.919623 1.4221828 -251.74192 -250.31974
15200 15.2 15.1446 191.32404 -21.902291 1.3107204 -251.52754 -250.21682
15400 15.4 15.815481 160.35385 -21.918453 1.0985502 -251.75506 -250.65651
15600 15.6 16.942896 211.32891 -21.89554 1.4477695 -251.42064 -249.97287
15800 15.8 17.339057 213.03178 -21.903747 1.4594355 -251.5815 -250.12207
16000 16 17.610695 211.72009 -21.899083 1.4504494 -251.51043 -250.05998
16200 16.2 18.352293 236.99887 -21.9043 1.623629 -251.79466 -250.17103
16400 16.4 17.898896 208.62272 -21.904247 1.42923 -251.66653 -250.2373
16600 16.6 18.005606 169.07581 -21.910252 1.1583025 -251.84184 -250.68353
16800 16.8 18.884686 198.75251 -21.900417 1.3616113 -251.8573 -250.49569
17000 17 19.454235 182.70172 -21.904544 1.2516507 -251.66187 -250.41021
17200 17.2 19.497759 157.47203 -21.904461 1.0788075 -251.88582 -250.80701
17400 17.4 19.470705 215.43531 -21.887158 1.4759016 -251.82426 -250.34836
17600 17.6 19.553888 212.82066 -21.89372 1.4579892 -251.79955 -250.34157
17800 17.8 19.646117 236.85339 -21.8983 1.6226323 -251.75304 -250.13041
18000 18 20.205554 253.85283 -21.909061 1.7390919 -251.84228 -250.10319
18200 18.2 20.065135 233.11058 -21.882631 1.5969911 -251.54972 -249.95273
18400 18.4 20.76763 209.7018 -21.895306 1.4366225 -251.79971 -250.36309
18600 18.6 21.369833 214.39422 -21.882332 1.4687693 -251.53344 -250.06467
18800 18.8 21.939164 216.25928 -21.89097 1.4815464 -251.82112 -250.33958
19000 19 22.817363 215.27695 -21.882698 1.4748166 -251.82572 -250.3509
19200 19.2 23.705114 182.22745 -21.879076 1.2484016 -251.43044 -250.18204
19400 19.4 23.441248 222.83743 -21.879144 1.5266119 -251.76376 -250.23715
19600 19.6 23.435558 218.16026 -21.86114 1.4945696 -251.59729 -250.10272
19800 19.8 24.074607 222.78958 -21.87264 1.5262841 -251.7863 -250.26001
20000 20 23.618814 222.44332 -21.870985 1.5239119 -251.37299 -249.84908
Loop time of 22.6158 on 1 procs for 20000 steps with 54 atoms
Performance: 76.407 ns/day, 0.314 hours/ns, 884.338 timesteps/s, 47.754 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.9116 | 8.9116 | 8.9116 | 0.0 | 39.40
Neigh | 0.26535 | 0.26535 | 0.26535 | 0.0 | 1.17
Comm | 0.65637 | 0.65637 | 0.65637 | 0.0 | 2.90
Output | 0.0036141 | 0.0036141 | 0.0036141 | 0.0 | 0.02
Modify | 12.725 | 12.725 | 12.725 | 0.0 | 56.26
Other | | 0.05425 | | | 0.24
Nlocal: 54 ave 54 max 54 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 632 ave 632 max 632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1677 ave 1677 max 1677 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3354 ave 3354 max 3354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3354
Ave neighs/atom = 62.111111
Neighbor list builds = 1000
Dangerous builds = 1000
Total wall time: 0:00:22

241
examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1 Normal file
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@ -0,0 +1,241 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# bcc iron in a 3d periodic box
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style spin
# atom_style spin/kk
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice bcc 2.8665
Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
region box block 0.0 3.0 0.0 3.0 0.0 3.0
create_box 1 box
Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 54 atoms
using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
create_atoms CPU = 0.001 seconds
# setting mass, mag. moments, and interactions for bcc iron
mass 1 55.845
set group all spin 2.2 0.0 0.0 1.0
Setting atom values ...
WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268)
54 settings made for spin
velocity all create 0 4928459 rot yes dist gaussian
# pair_style hybrid/overlay eam/alloy spin/exchange 3.5
pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe
pair_coeff * * spin/exchange exchange 3.4 0.1 0.2171 1.841
pair_coeff * * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin 0.0 0.0 0.001 48279
fix 3 all langevin/spin 200.0 0.01 321
fix 4 all nve/spin lattice moving
timestep 0.001
# compute and output options
compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_tmag temp v_emag ke pe etotal
thermo 200
run 20000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
@article{tranchida2018massively,
title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin Dynamics and Molecular Dynamics},
author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
journal={Journal of Computational Physics},
volume={372},
pages={406--425},
year={2018},
publisher={Elsevier}
doi={10.1016/j.jcp.2018.06.042}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 20 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.773367
ghost atom cutoff = 5.773367
binsize = 2.8866835, bins = 3 3 3
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair eam/alloy, perpetual, half/full from (2)
attributes: half, newton on, cut 5.7733670002446
pair build: halffull/newton
stencil: none
bin: none
(2) pair spin/exchange, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) pair spin/neel, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes
Step Time v_tmag Temp v_emag KinEng PotEng TotEng
0 0 1.4336203e-31 0 -22.021022 0 -253.14103 -253.14103
200 0.2 185.03537 7.1508965e-05 -21.172867 4.8989274e-07 -252.29287 -252.29287
400 0.4 209.70221 8.8414079e-05 -21.060203 6.0570608e-07 -252.1802 -252.1802
600 0.6 185.48899 0.00010245242 -21.112413 7.0187977e-07 -252.23241 -252.23241
800 0.8 223.05275 8.1457051e-05 -21.018423 5.5804496e-07 -252.13842 -252.13842
1000 1 213.0164 8.9515898e-05 -21.048926 6.1325441e-07 -252.16892 -252.16892
1200 1.2 246.36673 0.0001154676 -20.930718 7.9104402e-07 -252.05072 -252.05072
1400 1.4 196.53774 6.2911172e-05 -21.154732 4.3099109e-07 -252.27473 -252.27473
1600 1.6 182.01716 0.00010355261 -21.16282 7.0941692e-07 -252.28282 -252.28282
1800 1.8 210.96677 8.7541641e-05 -21.088701 5.997292e-07 -252.2087 -252.2087
2000 2 253.99717 0.00010826381 -20.86351 7.416924e-07 -251.98351 -251.98351
2200 2.2 216.1501 9.6113637e-05 -21.030784 6.5845412e-07 -252.15078 -252.15078
2400 2.4 223.43699 8.5950374e-05 -21.009537 5.8882776e-07 -252.12954 -252.12954
2600 2.6 218.14727 0.00010110952 -20.970036 6.9267987e-07 -252.09004 -252.09004
2800 2.8 232.40923 0.00011013217 -20.973661 7.5449212e-07 -252.09366 -252.09366
3000 3 237.03942 0.0001227047 -20.923005 8.4062388e-07 -252.043 -252.043
3200 3.2 193.18057 6.4453691e-05 -21.192632 4.4155855e-07 -252.31263 -252.31263
3400 3.4 215.89559 0.00010926778 -20.99777 7.4857038e-07 -252.11777 -252.11777
3600 3.6 166.54235 7.286928e-05 -21.241556 4.9921196e-07 -252.36156 -252.36156
3800 3.8 159.38579 5.7560855e-05 -21.290065 3.9433719e-07 -252.41007 -252.41007
4000 4 170.59358 7.7217892e-05 -21.234059 5.2900339e-07 -252.35406 -252.35406
4200 4.2 215.77287 8.7497504e-05 -21.031438 5.9942683e-07 -252.15144 -252.15144
4400 4.4 197.99439 8.3188835e-05 -21.136708 5.6990905e-07 -252.25671 -252.25671
4600 4.6 225.89271 0.00015400081 -20.963516 1.0550269e-06 -252.08352 -252.08352
4800 4.8 202.99311 0.00014034452 -21.013112 9.614705e-07 -252.13311 -252.13311
5000 5 213.82643 0.00011505981 -21.058401 7.8825036e-07 -252.1784 -252.1784
5200 5.2 185.50349 8.6160092e-05 -21.172207 5.902645e-07 -252.29221 -252.29221
5400 5.4 201.98179 0.00010791717 -21.096481 7.3931764e-07 -252.21648 -252.21648
5600 5.6 171.20549 6.8869235e-05 -21.197869 4.718085e-07 -252.31787 -252.31787
5800 5.8 227.95465 0.00012603913 -21.009323 8.6346729e-07 -252.12932 -252.12932
6000 6 200.21111 0.00010449734 -21.110701 7.1588912e-07 -252.2307 -252.2307
6200 6.2 160.58077 7.2836942e-05 -21.267151 4.9899042e-07 -252.38715 -252.38715
6400 6.4 200.05407 9.0509705e-05 -21.073988 6.2006277e-07 -252.19399 -252.19399
6600 6.6 190.65275 0.0001033421 -21.158207 7.0797478e-07 -252.27821 -252.27821
6800 6.8 228.26898 0.00014786596 -20.911618 1.0129983e-06 -252.03162 -252.03162
7000 7 181.38559 7.164051e-05 -21.178965 4.9079392e-07 -252.29897 -252.29897
7200 7.2 206.68689 0.00014900154 -20.996098 1.0207779e-06 -252.1161 -252.1161
7400 7.4 192.31745 7.9639216e-05 -21.152927 5.4559136e-07 -252.27293 -252.27293
7600 7.6 190.74433 8.1341909e-05 -21.140079 5.5725615e-07 -252.26008 -252.26008
7800 7.8 174.0955 6.4367878e-05 -21.239195 4.4097067e-07 -252.3592 -252.35919
8000 8 160.00011 0.00012761576 -21.159302 8.7426845e-07 -252.2793 -252.2793
8200 8.2 210.43151 0.00014479042 -21.034928 9.9192846e-07 -252.15493 -252.15493
8400 8.4 234.76455 0.00017824488 -20.929712 1.2211178e-06 -252.04971 -252.04971
8600 8.6 186.41675 8.9522862e-05 -21.152624 6.1330212e-07 -252.27262 -252.27262
8800 8.8 182.51437 8.1196096e-05 -21.169538 5.5625721e-07 -252.28954 -252.28954
9000 9 205.7602 8.1712224e-05 -21.069704 5.597931e-07 -252.1897 -252.1897
9200 9.2 169.12461 4.5311332e-05 -21.260803 3.1041832e-07 -252.3808 -252.3808
9400 9.4 226.30809 0.00011391282 -20.976322 7.8039252e-07 -252.09632 -252.09632
9600 9.6 167.17205 9.1023114e-05 -21.226931 6.2358003e-07 -252.34693 -252.34693
9800 9.8 204.63476 0.00010727562 -21.045363 7.3492253e-07 -252.16536 -252.16536
10000 10 236.18563 8.998006e-05 -20.973452 6.1643429e-07 -252.09345 -252.09345
10200 10.2 194.32863 7.2352023e-05 -21.144235 4.9566835e-07 -252.26424 -252.26424
10400 10.4 212.89479 0.00011913313 -21.041706 8.1615576e-07 -252.16171 -252.1617
10600 10.6 215.20168 9.7714692e-05 -21.032571 6.6942261e-07 -252.15257 -252.15257
10800 10.8 297.63322 0.00013498385 -20.721355 9.2474566e-07 -251.84135 -251.84135
11000 11 221.40055 0.00010205784 -21.051231 6.9917662e-07 -252.17123 -252.17123
11200 11.2 242.39307 0.00013617253 -20.890742 9.3288909e-07 -252.01074 -252.01074
11400 11.4 165.26613 7.2237463e-05 -21.24741 4.9488352e-07 -252.36741 -252.36741
11600 11.6 216.24435 8.1150764e-05 -21.036156 5.5594665e-07 -252.15616 -252.15616
11800 11.8 183.53912 0.00010117662 -21.186918 6.9313953e-07 -252.30692 -252.30692
12000 12 220.44994 9.647801e-05 -21.023611 6.6095036e-07 -252.14361 -252.14361
12200 12.2 225.17986 9.472867e-05 -21.009823 6.48966e-07 -252.12982 -252.12982
12400 12.4 216.68616 8.9352492e-05 -21.025818 6.1213495e-07 -252.14582 -252.14582
12600 12.6 179.65027 6.5355297e-05 -21.199208 4.4773526e-07 -252.31921 -252.31921
12800 12.8 210.22912 7.5167585e-05 -21.071447 5.1495716e-07 -252.19145 -252.19145
13000 13 157.423 9.2895323e-05 -21.250615 6.3640614e-07 -252.37062 -252.37061
13200 13.2 204.52025 0.00012645764 -21.049044 8.6633447e-07 -252.16904 -252.16904
13400 13.4 198.28053 0.00012118522 -21.066084 8.3021421e-07 -252.18609 -252.18608
13600 13.6 237.99318 8.644348e-05 -20.978488 5.9220593e-07 -252.09849 -252.09849
13800 13.8 222.81023 0.00015789536 -20.951387 1.0817076e-06 -252.07139 -252.07139
14000 14 218.31245 0.00011842157 -21.008674 8.1128101e-07 -252.12867 -252.12867
14200 14.2 197.5018 0.00011399102 -21.081911 7.8092826e-07 -252.20191 -252.20191
14400 14.4 228.11014 0.00015934606 -20.963235 1.091646e-06 -252.08323 -252.08323
14600 14.6 216.45102 9.6033576e-05 -21.034352 6.5790564e-07 -252.15435 -252.15435
14800 14.8 205.97376 0.00014278574 -21.018847 9.7819479e-07 -252.13885 -252.13885
15000 15 230.09259 0.00012803086 -20.986446 8.7711221e-07 -252.10645 -252.10644
15200 15.2 248.21379 0.0001784321 -20.84502 1.2224004e-06 -251.96502 -251.96502
15400 15.4 223.07119 0.00013057001 -20.984451 8.9450744e-07 -252.10445 -252.10445
15600 15.6 194.42126 8.4530618e-05 -21.127055 5.7910131e-07 -252.24705 -252.24705
15800 15.8 207.23453 0.00013807606 -21.035173 9.4592974e-07 -252.15517 -252.15517
16000 16 175.93234 8.2440767e-05 -21.208299 5.6478419e-07 -252.3283 -252.3283
16200 16.2 225.63746 7.4767651e-05 -21.012845 5.1221731e-07 -252.13285 -252.13284
16400 16.4 149.12667 6.624179e-05 -21.331981 4.5380844e-07 -252.45198 -252.45198
16600 16.6 211.41275 0.00012606898 -21.042094 8.6367183e-07 -252.16209 -252.16209
16800 16.8 199.88466 8.2345231e-05 -21.116203 5.641297e-07 -252.2362 -252.2362
17000 17 212.37144 0.00010445794 -21.041826 7.1561919e-07 -252.16183 -252.16183
17200 17.2 160.83603 5.4109632e-05 -21.294207 3.706936e-07 -252.41421 -252.41421
17400 17.4 254.84209 0.00013687967 -20.886397 9.3773358e-07 -252.0064 -252.0064
17600 17.6 237.6091 0.00012462019 -20.958967 8.5374644e-07 -252.07897 -252.07897
17800 17.8 194.26242 7.0286952e-05 -21.145006 4.8152099e-07 -252.26501 -252.26501
18000 18 175.14964 6.1470052e-05 -21.239458 4.2111827e-07 -252.35946 -252.35946
18200 18.2 181.99258 7.2295849e-05 -21.195184 4.9528351e-07 -252.31519 -252.31519
18400 18.4 197.11115 9.9207898e-05 -21.116471 6.7965225e-07 -252.23647 -252.23647
18600 18.6 211.2814 8.4543325e-05 -21.074729 5.7918837e-07 -252.19473 -252.19473
18800 18.8 198.62813 9.4052117e-05 -21.097909 6.4433109e-07 -252.21791 -252.21791
19000 19 226.11003 0.00013827389 -20.951669 9.4728506e-07 -252.07167 -252.07167
19200 19.2 233.61049 0.00013363448 -20.917911 9.1550145e-07 -252.03791 -252.03791
19400 19.4 182.94749 9.0400181e-05 -21.139686 6.1931245e-07 -252.25969 -252.25968
19600 19.6 155.99677 5.9871119e-05 -21.282519 4.1016433e-07 -252.40252 -252.40252
19800 19.8 179.57217 8.5624245e-05 -21.193447 5.8659353e-07 -252.31345 -252.31345
20000 20 243.60222 0.00015451915 -20.911769 1.0585779e-06 -252.03177 -252.03177
Loop time of 21.9748 on 1 procs for 20000 steps with 54 atoms
Performance: 78.636 ns/day, 0.305 hours/ns, 910.134 timesteps/s, 49.147 katom-step/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.1863 | 8.1863 | 8.1863 | 0.0 | 37.25
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.77445 | 0.77445 | 0.77445 | 0.0 | 3.52
Output | 0.0037256 | 0.0037256 | 0.0037256 | 0.0 | 0.02
Modify | 12.954 | 12.954 | 12.954 | 0.0 | 58.95
Other | | 0.05601 | | | 0.25
Nlocal: 54 ave 54 max 54 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 801 ave 801 max 801 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1728 ave 1728 max 1728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3456 ave 3456 max 3456 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3456
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:22

44
examples/melt/in.melt
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@ -1,33 +1,33 @@
# 3d Lennard-Jones melt # 3d Lennard-Jones melt
units lj units lj
atom_style atomic atom_style atomic
lattice fcc 0.8442 lattice fcc 0.8442
region box block 0 10 0 10 0 10 region box block 0 10 0 10 0 10
create_box 1 box create_box 1 box
create_atoms 1 box create_atoms 1 box
mass 1 1.0 mass 1 1.0
velocity all create 3.0 87287 loop geom velocity all create 3.0 87287 loop geom
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5 pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify every 20 delay 0 check no neigh_modify every 20 delay 0 check no
fix 1 all nve fix 1 all nve
#dump id all atom 50 dump.melt #dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type & #dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 #dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type & #dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 #dump_modify 3 pad 3
thermo 50 thermo 50
run 250 run 250

46
examples/peptide/in.peptide
View File

@ -1,42 +1,42 @@
# Solvated 5-mer peptide # Solvated 5-mer peptide
units real units real
atom_style full atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0 pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic bond_style harmonic
angle_style charmm angle_style charmm
dihedral_style charmm dihedral_style charmm
improper_style harmonic improper_style harmonic
kspace_style pppm 0.0001 kspace_style pppm 0.0001
read_data data.peptide read_data data.peptide
neighbor 2.0 bin neighbor 2.0 bin
neigh_modify delay 5 neigh_modify delay 5
timestep 2.0 timestep 2.0
thermo_style multi thermo_style multi
thermo 50 thermo 50
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
group peptide type <= 12 group peptide type <= 12
#dump 1 peptide atom 10 dump.peptide #dump 1 peptide atom 10 dump.peptide
#dump 2 peptide image 25 image.*.jpg type type & #dump 2 peptide image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 2 pad 3 #dump_modify 2 pad 3
#dump 3 peptide movie 25 movie.mpg type type & #dump 3 peptide movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 3 pad 3 #dump_modify 3 pad 3
#compute bnd all property/local btype batom1 batom2 #compute bnd all property/local btype batom1 batom2
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] #dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300 run 300

2
examples/rerun/in.rdf.first
View File

@ -27,7 +27,7 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve fix 1 all nve
dump 1 all custom 100 lj.dump id type x y z dump 1 all custom 100 lj.dump id type x y z vx vy vz
compute myRDF all rdf 50 cutoff 2.5 compute myRDF all rdf 50 cutoff 2.5
fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector