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Merge pull request #1383 from akohlmey/final-changes-for-patch 

Several small changes and tweaks for patch release
This commit is contained in:
Axel Kohlmeyer 2019-03-27 17:00:56 -04:00 committed by GitHub
parent e63d2cee87 b685a0a7b8
commit 2ad9355140
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
13 changed files with 1208 additions and 531 deletions
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6
cmake/Modules/generate_lmpgitversion.cmake
View File

@ -5,15 +5,15 @@ set(temp_git_describe "(unknown)")
set(temp_git_info "false")
if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
set(temp_git_info "true")
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
OUTPUT_VARIABLE temp_git_commit
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
OUTPUT_VARIABLE temp_git_branch
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified
execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
OUTPUT_VARIABLE temp_git_describe
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE)

16
doc/Makefile
View File

@ -116,6 +116,13 @@ mobi: epub
@echo "Conversion finished. The MOBI manual file is created."
pdf: $(OBJECTS) $(ANCHORCHECK)
@(\
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
cd ../../; \
)
@(\
. $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\
@ -135,14 +142,7 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
make && \
make && \
mv LAMMPS.pdf ../Manual.pdf && \
cd ../;
@(\
cd src/Developer; \
pdflatex developer; \
pdflatex developer; \
mv developer.pdf ../../Developer.pdf; \
cd ../../; \
)
cd ../;
@rm -rf latex/_sources
@rm -rf latex/PDF
@rm -rf latex/USER

12
examples/micelle/data.micelle
View File

@ -49,7 +49,7 @@
22 0 1 25.100 0.000 0.000
23 0 1 26.295 0.000 0.000
24 110 2 27.490 0.000 0.000
25 128 2 28.685 0.000 0.000
25 128 2 28.685 35.85686 0.000
26 0 1 29.881 0.000 0.000
27 0 1 31.076 0.000 0.000
28 0 1 32.271 0.000 0.000
@ -175,7 +175,7 @@
148 0 1 32.271 4.781 0.000
149 0 1 33.466 4.781 0.000
150 0 1 34.662 4.781 0.000
151 53 2 0.000 5.976 0.000
151 53 2 35.85686 5.976 0.000
152 0 1 1.195 5.976 0.000
153 0 1 2.390 5.976 0.000
154 0 1 3.586 5.976 0.000
@ -655,7 +655,7 @@
628 0 1 32.271 23.905 0.000
629 0 1 33.466 23.905 0.000
630 0 1 34.662 23.905 0.000
631 148 2 0.000 25.100 0.000
631 148 2 35.85686 25.100 0.000
632 0 1 1.195 25.100 0.000
633 0 1 2.390 25.100 0.000
634 0 1 3.586 25.100 0.000
@ -976,7 +976,7 @@
949 25 3 0.677 33.143 0.000
950 25 4 1.353 32.819 0.000
951 26 3 35.071 18.557 0.000
952 26 4 35.480 19.186 0.000
952 26 4 35.48000 19.186 0.000
953 27 3 29.131 15.504 0.000
954 27 4 28.382 15.470 0.000
955 28 3 23.456 33.395 0.000
@ -1096,7 +1096,7 @@
1069 85 3 33.021 33.461 0.000
1070 85 4 33.771 33.455 0.000
1071 86 3 0.552 18.315 0.000
1072 86 4 35.766 18.701 0.000
1072 86 4 -0.09086 18.701 0.000
1073 87 3 28.026 32.796 0.000
1074 87 4 28.562 33.321 0.000
1075 88 3 24.351 29.925 0.000
@ -1112,7 +1112,7 @@
1085 93 3 26.170 16.278 0.000
1086 93 4 26.046 17.017 0.000
1087 94 3 10.380 0.547 0.000
1088 94 4 10.003 35.755 0.000
1088 94 4 10.003 -0.10186 0.000
1089 95 3 0.419 29.308 0.000
1090 95 4 0.837 29.930 0.000
1091 96 3 13.712 28.191 0.000

86
examples/micelle/in.micelle.rigid Normal file
View File

@ -0,0 +1,86 @@
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
special_bonds fene
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
group solute subtract all solvent
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
fix 4 all enforce2d
run 20000
unfix 5
unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
fix 4 all enforce2d
run 20000

255
examples/micelle/log.27Nov18.micelle.g++.1
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@ -1,255 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.167265 on 1 procs for 1000 steps with 1200 atoms
Performance: 2582728.958 tau/day, 5978.539 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50
Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71
Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84
Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85
Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17
Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20
Other | | 0.006227 | | | 3.72
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727655 0.058608715 -1.4645318 1.9982298
2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463
3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269
4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093
5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711
6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258
7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681
8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989
9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826
10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581
11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643
12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574
13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637
14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177
15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343
16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848
17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551
18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521
19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246
20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005
21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779
22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487
23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085
24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809
25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746
26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058
27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802
28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664
29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755
30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857
31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986
32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653
33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293
34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059
35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758
36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544
37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879
38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042
39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908
40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818
41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862
42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908
43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946
44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027
45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585
46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902
47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933
48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677
49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845
50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147
51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782
52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768
53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038
54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618
55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084
56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598
57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646
58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518
59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311
60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921
Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms
Performance: 1859917.639 tau/day, 4305.365 timesteps/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 | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17
Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42
Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06
Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70
Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01
Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13
Other | | 0.3493 | | | 2.51
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 405 ave 405 max 405 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9565 ave 9565 max 9565 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9565
Ave neighs/atom = 7.97083
Ave special neighs/atom = 0.5
Neighbor list builds = 4876
Dangerous builds = 0
Total wall time: 0:00:14

255
examples/micelle/log.27Nov18.micelle.g++.4
View File

@ -1,255 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0641922 on 4 procs for 1000 steps with 1200 atoms
Performance: 6729792.131 tau/day, 15578.223 timesteps/s
90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.020663 | 0.021445 | 0.022477 | 0.5 | 33.41
Bond | 0.0014422 | 0.0015128 | 0.001569 | 0.1 | 2.36
Neigh | 0.0067129 | 0.0067645 | 0.0068202 | 0.1 | 10.54
Comm | 0.018454 | 0.019275 | 0.020386 | 0.5 | 30.03
Output | 0.00038171 | 0.00040019 | 0.00044632 | 0.0 | 0.62
Modify | 0.010561 | 0.010904 | 0.011309 | 0.3 | 16.99
Other | | 0.003891 | | | 6.06
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727661 0.05860859 -1.4645325 1.9982402
2000 0.45146247 -1.9766043 0.059408886 -1.4661092 1.7398826
3000 0.43338517 -2.0028125 0.059884381 -1.5099041 1.4716488
4000 0.46674519 -2.0200954 0.066548679 -1.4871905 1.2506693
5000 0.45 -2.0207125 0.055926205 -1.5151613 1.3047457
6000 0.45447759 -2.0585234 0.068004883 -1.5364197 1.1859762
7000 0.43183018 -2.0170545 0.060800296 -1.5247839 1.3074223
8000 0.46657547 -2.053224 0.063224367 -1.523813 1.1785643
9000 0.45 -2.0691221 0.054959029 -1.564538 1.1833657
10000 0.4428252 -2.0473987 0.054306905 -1.5506356 1.181794
11000 0.45407036 -2.0746151 0.065849667 -1.5550734 1.1008545
12000 0.46061944 -2.0580809 0.063129643 -1.5347156 1.0206491
13000 0.45159068 -2.0640832 0.060059758 -1.5528091 1.0813494
14000 0.44141594 -2.0467255 0.062785088 -1.5428923 1.1465772
15000 0.454361 -2.0908595 0.057471037 -1.5794061 0.84297781
16000 0.44061091 -2.0521452 0.064644196 -1.5472573 1.1478647
17000 0.45118383 -2.081348 0.058660999 -1.5718791 1.0101404
18000 0.44664866 -2.0845745 0.060435731 -1.5778623 0.96142277
19000 0.45515339 -2.0914006 0.062174016 -1.5744525 0.87623323
20000 0.45624408 -2.0837697 0.059263054 -1.5686428 0.92810644
21000 0.46791657 -2.1062007 0.067355929 -1.5713181 0.88318793
22000 0.43907391 -2.1005271 0.065885144 -1.5959339 0.77211644
23000 0.43967354 -2.0723459 0.057613471 -1.5754253 1.0371548
24000 0.45716384 -2.0987126 0.055157377 -1.5867723 0.89670061
25000 0.45828285 -2.1041616 0.057736138 -1.5885245 0.79952286
26000 0.45 -2.0743463 0.072455519 -1.5522658 0.88260204
27000 0.46581599 -2.0804974 0.058113258 -1.5569564 0.93053891
28000 0.46904194 -2.0920124 0.059748792 -1.5636125 0.79359618
29000 0.46093196 -2.118556 0.063942334 -1.5940659 0.67707604
30000 0.45733724 -2.1197827 0.066939064 -1.5958875 0.66886075
31000 0.44580762 -2.0977175 0.056969121 -1.5953123 0.81042562
32000 0.44403029 -2.1032264 0.063465127 -1.596101 0.71796412
33000 0.45834072 -2.0934132 0.066035391 -1.569419 0.77873998
34000 0.44981563 -2.0910902 0.07138738 -1.5702621 0.75679805
35000 0.45383392 -2.0926654 0.067553478 -1.5716562 0.9064517
36000 0.44447198 -2.1107114 0.062718917 -1.6038909 0.8538349
37000 0.45838527 -2.1166464 0.062442606 -1.5962005 0.7300635
38000 0.45014075 -2.1096258 0.059293718 -1.6005665 0.73988246
39000 0.44377026 -2.080309 0.063545781 -1.5733628 0.99775641
40000 0.44577324 -2.1134607 0.065271179 -1.6027878 0.64113168
41000 0.45 -2.0937983 0.060881377 -1.5832919 0.78849829
42000 0.46866695 -2.1142283 0.056417605 -1.5895343 0.73788436
43000 0.43211727 -2.0819893 0.061463358 -1.5887688 0.95853724
44000 0.44138397 -2.0921314 0.059643895 -1.5914713 0.89486208
45000 0.45 -2.117209 0.054804331 -1.6127797 0.78564885
46000 0.44285245 -2.1090975 0.057629006 -1.6089851 0.64549424
47000 0.45537009 -2.1164296 0.068582324 -1.5928567 0.73629413
48000 0.45046732 -2.1006362 0.057249591 -1.5932947 0.74317593
49000 0.45425966 -2.1191703 0.064247719 -1.6010414 0.70962368
50000 0.45506149 -2.1184671 0.064911797 -1.5988731 0.69958156
51000 0.46047417 -2.1019719 0.058468259 -1.5834132 0.87219271
52000 0.43808317 -2.092294 0.057280941 -1.597295 0.84156893
53000 0.45012337 -2.1175234 0.064002667 -1.6037725 0.64562439
54000 0.43854679 -2.1236444 0.061316257 -1.6241468 0.72478117
55000 0.46382438 -2.1016563 0.060724666 -1.5774938 0.83311209
56000 0.44951533 -2.0946157 0.055075217 -1.5903998 0.90066109
57000 0.45937401 -2.0983442 0.061558996 -1.577794 0.58606161
58000 0.446669 -2.1146838 0.062385166 -1.6060019 0.73443388
59000 0.43847747 -2.1197461 0.060460257 -1.6211738 0.7230937
60000 0.45294215 -2.1258513 0.061895006 -1.6113915 0.70722168
Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms
Performance: 5681397.232 tau/day, 13151.382 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2114 | 2.2527 | 2.3592 | 4.1 | 49.38
Bond | 0.083713 | 0.09234 | 0.10244 | 2.3 | 2.02
Neigh | 0.72491 | 0.7277 | 0.72957 | 0.2 | 15.95
Comm | 0.79464 | 0.90036 | 0.94957 | 6.5 | 19.74
Output | 0.0014119 | 0.0024976 | 0.0057502 | 3.8 | 0.05
Modify | 0.33757 | 0.35202 | 0.36946 | 2.1 | 7.72
Other | | 0.2346 | | | 5.14
Nlocal: 300 ave 306 max 289 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 227.25 ave 250 max 216 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 2373.25 ave 2489 max 2283 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 9493
Ave neighs/atom = 7.91083
Ave special neighs/atom = 0.5
Neighbor list builds = 4888
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000394821 secs
read_data CPU = 0.00212336 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.00018549 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.113919 on 1 procs for 1000 steps with 1200 atoms
Performance: 3792167.464 tau/day, 8778.165 timesteps/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 | 0.076825 | 0.076825 | 0.076825 | 0.0 | 67.44
Bond | 0.0041864 | 0.0041864 | 0.0041864 | 0.0 | 3.67
Neigh | 0.017061 | 0.017061 | 0.017061 | 0.0 | 14.98
Comm | 0.0019042 | 0.0019042 | 0.0019042 | 0.0 | 1.67
Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.15
Modify | 0.011218 | 0.011218 | 0.011218 | 0.0 | 9.85
Other | | 0.002551 | | | 2.24
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727644 0.05860769 -1.4645317 1.9982326
2000 0.46143408 -1.9889684 0.058103225 -1.4698156 1.7806269
3000 0.44459291 -1.9997961 0.068724164 -1.4868496 1.4369618
4000 0.46939549 -2.0330437 0.073499424 -1.4905399 1.3780016
5000 0.44411088 -2.0339936 0.05862049 -1.5316323 1.2544164
6000 0.44034597 -2.0265475 0.066481992 -1.5200864 1.2362891
7000 0.45097378 -2.0331083 0.058467565 -1.5240428 1.2762333
8000 0.45797632 -2.0330255 0.060048036 -1.5153828 1.3862396
9000 0.45297811 -2.0383417 0.067056519 -1.5186845 1.2762554
10000 0.45 -2.0628269 0.065650067 -1.5475518 1.0566213
11000 0.44466757 -2.0593977 0.06190999 -1.5531907 1.1452469
12000 0.46743534 -2.0684295 0.061056278 -1.5403274 1.0824225
13000 0.45601091 -2.0689708 0.054868536 -1.5584713 0.96703283
14000 0.44111882 -2.0553174 0.058249816 -1.5563164 1.0986427
15000 0.43894405 -2.0866829 0.064117804 -1.5839869 0.90031836
16000 0.43856814 -2.0879319 0.056024166 -1.593705 0.96387323
17000 0.45977841 -2.103188 0.058097306 -1.5856955 0.83352919
18000 0.43423341 -2.0813151 0.066623991 -1.5808196 0.98157638
19000 0.44245939 -2.0851261 0.057637655 -1.5853978 0.84228341
20000 0.43144678 -2.0895403 0.06536727 -1.5930858 0.88177768
21000 0.45014968 -2.106686 0.059137572 -1.5977739 0.89408935
22000 0.4575126 -2.1024115 0.063013023 -1.5822672 0.84886734
23000 0.45 -2.10897 0.06724784 -1.5920971 0.66205013
24000 0.43055602 -2.0894725 0.061566464 -1.5977089 0.81764789
25000 0.4366384 -2.0926743 0.059609321 -1.5967905 0.85549875
26000 0.4521714 -2.0963996 0.062031863 -1.5825731 0.80137118
27000 0.45734834 -2.1060987 0.061712636 -1.5874188 0.82899415
28000 0.44803467 -2.0859226 0.061871856 -1.5763894 0.97007526
29000 0.45 -2.1106243 0.063825481 -1.5971738 0.63798376
30000 0.44932806 -2.1006036 0.053053934 -1.598596 0.63907113
31000 0.44713779 -2.1096164 0.066470416 -1.5963808 0.66832708
32000 0.4373357 -2.0941237 0.058871613 -1.5982808 0.78176106
33000 0.44030485 -2.105644 0.058804306 -1.6069017 0.66286458
34000 0.43781175 -2.1233209 0.064611206 -1.6212628 0.56342584
35000 0.45670132 -2.1059408 0.053049584 -1.5965705 0.73992396
36000 0.45555427 -2.1149877 0.057627709 -1.6021854 0.85854939
37000 0.44134236 -2.1106202 0.064444306 -1.6052013 0.74674603
38000 0.44812623 -2.1003681 0.057266258 -1.5953491 0.78239359
39000 0.44167062 -2.11141 0.055354 -1.6147534 0.7066385
40000 0.46103176 -2.1166687 0.062155412 -1.5938657 0.73620955
41000 0.44537102 -2.0993898 0.05631213 -1.5980778 0.87348756
42000 0.44752506 -2.1115212 0.057506521 -1.6068625 0.72999561
43000 0.4483886 -2.1184719 0.066943915 -1.6035131 0.78112063
44000 0.45944897 -2.0916657 0.055242781 -1.5773568 0.98660473
45000 0.46238513 -2.1163075 0.0530031 -1.6013046 0.74416054
46000 0.45979064 -2.1165545 0.060657581 -1.5964895 0.63516974
47000 0.45936546 -2.1140678 0.049931919 -1.6051532 0.76425182
48000 0.45424613 -2.1122681 0.061885599 -1.5965149 0.71981142
49000 0.44449524 -2.1147361 0.06626748 -1.6043438 0.78720467
50000 0.4641185 -2.1114668 0.055104874 -1.5926302 0.70195865
51000 0.44220655 -2.1075773 0.0589109 -1.6068283 0.73806859
52000 0.43097906 -2.1189493 0.061502241 -1.6268271 0.69622593
53000 0.45 -2.137688 0.053631829 -1.6344311 0.48269158
54000 0.43777118 -2.1089246 0.047098534 -1.6244197 0.70423814
55000 0.46061985 -2.1129502 0.062520353 -1.5901938 0.72492307
56000 0.4524841 -2.1195648 0.06580089 -1.6016569 0.52709892
57000 0.44914574 -2.1041993 0.061040876 -1.594387 0.7979988
58000 0.46446286 -2.1181238 0.055741995 -1.598306 0.51009146
59000 0.4632674 -2.1169321 0.050672678 -1.6033781 0.83110911
60000 0.46340478 -2.122846 0.058485209 -1.6013422 0.69966471
Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms
Performance: 3233199.903 tau/day, 7484.259 timesteps/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 | 5.4027 | 5.4027 | 5.4027 | 0.0 | 67.39
Bond | 0.23585 | 0.23585 | 0.23585 | 0.0 | 2.94
Neigh | 1.5188 | 1.5188 | 1.5188 | 0.0 | 18.95
Comm | 0.14452 | 0.14452 | 0.14452 | 0.0 | 1.80
Output | 0.00060487 | 0.00060487 | 0.00060487 | 0.0 | 0.01
Modify | 0.56352 | 0.56352 | 0.56352 | 0.0 | 7.03
Other | | 0.1508 | | | 1.88
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9652 ave 9652 max 9652 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9652
Ave neighs/atom = 8.04333
Ave special neighs/atom = 0.5
Neighbor list builds = 4886
Dangerous builds = 0
Total wall time: 0:00:08

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LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000130415 secs
read_data CPU = 0.00132132 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 4.76837e-05 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0377742 on 4 procs for 1000 steps with 1200 atoms
Performance: 11436375.633 tau/day, 26473.092 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016871 | 0.017299 | 0.018185 | 0.4 | 45.80
Bond | 0.0010128 | 0.0010633 | 0.001116 | 0.1 | 2.81
Neigh | 0.004832 | 0.0048565 | 0.0048807 | 0.0 | 12.86
Comm | 0.0066509 | 0.0077528 | 0.0084352 | 0.8 | 20.52
Output | 0.00022054 | 0.00028259 | 0.00046587 | 0.0 | 0.75
Modify | 0.0035386 | 0.0036086 | 0.0036943 | 0.1 | 9.55
Other | | 0.002912 | | | 7.71
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727652 0.058608073 -1.4645321 1.9982444
2000 0.44428815 -1.9902282 0.064240544 -1.4820698 1.7051263
3000 0.46641766 -1.9856844 0.065017468 -1.4546379 1.6939772
4000 0.45734058 -2.0242583 0.070494626 -1.4968042 1.3474276
5000 0.44904747 -2.0086954 0.058801142 -1.501221 1.4632351
6000 0.44961405 -2.0334509 0.05721299 -1.5269985 1.3093586
7000 0.45474928 -2.0453645 0.064725006 -1.5262692 1.1581035
8000 0.44274767 -2.0375379 0.062216035 -1.5329431 1.312914
9000 0.46176571 -2.0473031 0.065581966 -1.5203402 1.2013868
10000 0.45046977 -2.0540466 0.065402724 -1.5385495 0.95819581
11000 0.45016671 -2.0610028 0.056993955 -1.5542172 1.0433435
12000 0.43823039 -2.073155 0.065171939 -1.5701178 1.1400059
13000 0.44482161 -2.0678338 0.063901045 -1.5594819 0.97993813
14000 0.45 -2.0892562 0.061753632 -1.5778776 0.89841778
15000 0.44328626 -2.0859346 0.059956258 -1.5830615 0.90664821
16000 0.45666508 -2.0859262 0.059582346 -1.5700593 0.9702235
17000 0.44832038 -2.0762124 0.059153394 -1.5691122 0.93020504
18000 0.4555831 -2.0844959 0.057986324 -1.5713062 0.87398232
19000 0.45257867 -2.0671736 0.062190389 -1.5527816 0.89208496
20000 0.44010419 -2.1020944 0.062053708 -1.6003033 0.84140973
21000 0.45239369 -2.0820308 0.060981799 -1.5690323 0.98502522
22000 0.44607468 -2.0820602 0.051731316 -1.5846259 0.86120529
23000 0.45088473 -2.0865286 0.05727778 -1.5787418 1.1479844
24000 0.45526919 -2.1086678 0.057378327 -1.5963997 0.86944138
25000 0.46536624 -2.1055425 0.05665328 -1.5839108 0.72895438
26000 0.46716668 -2.1035267 0.057498747 -1.5792505 0.85105386
27000 0.44374699 -2.0932213 0.060937242 -1.5889069 0.93200759
28000 0.45944001 -2.0968869 0.053052954 -1.5847768 0.78909249
29000 0.4543632 -2.10493 0.061511018 -1.5894345 0.85862527
30000 0.44987776 -2.0942536 0.062431086 -1.5823197 0.7349894
31000 0.43829016 -2.0951259 0.060245682 -1.5969553 0.86702973
32000 0.45416601 -2.0991679 0.055978905 -1.5894015 0.75777153
33000 0.4605079 -2.1118364 0.058205688 -1.5935066 0.86041104
34000 0.43638213 -2.0925345 0.067533519 -1.5889825 0.85100425
35000 0.46912252 -2.1082718 0.051646432 -1.5878938 0.73613751
36000 0.45 -2.0966442 0.052507159 -1.5945121 0.88722487
37000 0.44970507 -2.1029685 0.065454263 -1.588184 0.76033821
38000 0.44910233 -2.097751 0.05767009 -1.5913528 0.95830923
39000 0.4322161 -2.1060426 0.062453704 -1.611733 0.74681695
40000 0.46143858 -2.1328575 0.057333011 -1.6144704 0.58326322
41000 0.43180549 -2.1070656 0.064150563 -1.6114694 0.82842684
42000 0.46738909 -2.1067947 0.058017036 -1.5817781 0.73292362
43000 0.43699124 -2.1171964 0.062817262 -1.6177521 0.73354741
44000 0.45262916 -2.1281307 0.055228619 -1.6206502 0.64167946
45000 0.43905419 -2.088789 0.055597999 -1.5945027 0.8002542
46000 0.44485569 -2.1035061 0.067828181 -1.5911929 0.71861494
47000 0.44496824 -2.0968296 0.0632326 -1.5889996 0.75202899
48000 0.46567244 -2.1235948 0.061032118 -1.5972783 0.64094556
49000 0.43202506 -2.0986097 0.053464022 -1.6134806 0.83857984
50000 0.45454698 -2.1263344 0.058119708 -1.6140465 0.67030037
51000 0.43702766 -2.1292347 0.074047424 -1.6185238 0.52896462
52000 0.46367081 -2.1177288 0.06726625 -1.5871781 0.74343227
53000 0.45 -2.1341074 0.062769314 -1.6217131 0.51130365
54000 0.44862492 -2.1272108 0.057723381 -1.6212364 0.54735429
55000 0.44926027 -2.1350444 0.066186625 -1.6199719 0.66821299
56000 0.4544227 -2.1325537 0.065298628 -1.6132111 0.63597556
57000 0.45697003 -2.1323238 0.053312855 -1.6224218 0.55572633
58000 0.45698902 -2.1043208 0.055835989 -1.5918766 0.63502658
59000 0.4425306 -2.1120353 0.056617261 -1.6132563 0.65681272
60000 0.44319296 -2.1171981 0.058330294 -1.6160442 0.63602511
Loop time of 2.63918 on 4 procs for 60000 steps with 1200 atoms
Performance: 9821248.084 tau/day, 22734.371 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1742 | 1.278 | 1.3471 | 5.9 | 48.43
Bond | 0.046621 | 0.06565 | 0.081322 | 5.1 | 2.49
Neigh | 0.46642 | 0.46917 | 0.47105 | 0.3 | 17.78
Comm | 0.47295 | 0.55928 | 0.67758 | 10.5 | 21.19
Output | 0.00073624 | 0.00173 | 0.0047016 | 4.1 | 0.07
Modify | 0.14511 | 0.15226 | 0.15887 | 1.5 | 5.77
Other | | 0.1131 | | | 4.28
Nlocal: 300 ave 309 max 281 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 232.75 ave 234 max 231 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 2450.25 ave 2576 max 2179 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 9801
Ave neighs/atom = 8.1675
Ave special neighs/atom = 0.5
Neighbor list builds = 4887
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000271559 secs
read_data CPU = 0.00115585 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 8.39233e-05 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.107201 on 1 procs for 1000 steps with 1200 atoms
Performance: 4029800.456 tau/day, 9328.242 timesteps/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 | 0.072035 | 0.072035 | 0.072035 | 0.0 | 67.20
Bond | 0.0039918 | 0.0039918 | 0.0039918 | 0.0 | 3.72
Neigh | 0.016078 | 0.016078 | 0.016078 | 0.0 | 15.00
Comm | 0.0018375 | 0.0018375 | 0.0018375 | 0.0 | 1.71
Output | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.15
Modify | 0.010665 | 0.010665 | 0.010665 | 0.0 | 9.95
Other | | 0.002429 | | | 2.27
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 20000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457
2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896
3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634
4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178
5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284
6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653
7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099
8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769
9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447
10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582
11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418
12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497
13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173
14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767
15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999
16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066
17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295
18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102
19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608
20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746
Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms
Performance: 2347175.802 tau/day, 5433.277 timesteps/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 | 1.7349 | 1.7349 | 1.7349 | 0.0 | 47.13
Bond | 0.079483 | 0.079483 | 0.079483 | 0.0 | 2.16
Neigh | 0.49063 | 0.49063 | 0.49063 | 0.0 | 13.33
Comm | 0.049093 | 0.049093 | 0.049093 | 0.0 | 1.33
Output | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.01
Modify | 1.273 | 1.273 | 1.273 | 0.0 | 34.58
Other | | 0.05369 | | | 1.46
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8915 ave 8915 max 8915 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8915
Ave neighs/atom = 7.42917
Ave special neighs/atom = 0.5
Neighbor list builds = 1580
Dangerous builds = 0
unfix 5
unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
create bodies CPU = 0.00012517 secs
150 rigid bodies with 450 atoms
1.04536 = max distance from body owner to body atom
fix 4 all enforce2d
run 20000
Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes
Step Temp E_pair E_mol TotEng Press
20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893
21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317
22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077
23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349
24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923
25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811
26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018
27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673
28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888
29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141
30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915
31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009
32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148
33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113
34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843
35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697
36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963
37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678
38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487
39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123
40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536
Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms
Performance: 2341388.948 tau/day, 5419.882 timesteps/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 | 1.756 | 1.756 | 1.756 | 0.0 | 47.59
Bond | 0.079221 | 0.079221 | 0.079221 | 0.0 | 2.15
Neigh | 0.49085 | 0.49085 | 0.49085 | 0.0 | 13.30
Comm | 0.048317 | 0.048317 | 0.048317 | 0.0 | 1.31
Output | 0.0002315 | 0.0002315 | 0.0002315 | 0.0 | 0.01
Modify | 1.2616 | 1.2616 | 1.2616 | 0.0 | 34.19
Other | | 0.05386 | | | 1.46
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 393 ave 393 max 393 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9091 ave 9091 max 9091 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9091
Ave neighs/atom = 7.57583
Ave special neighs/atom = 0.5
Neighbor list builds = 1582
Dangerous builds = 0
Total wall time: 0:00:07

290
examples/micelle/log.28Feb2019.micelle.rigid.g++.4 Normal file
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@ -0,0 +1,290 @@
LAMMPS (28 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000175714 secs
read_data CPU = 0.00145626 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 7.22408e-05 secs
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123, bins = 51 51 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0389124 on 4 procs for 1000 steps with 1200 atoms
Performance: 11101855.138 tau/day, 25698.739 timesteps/s
95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016776 | 0.017405 | 0.018435 | 0.5 | 44.73
Bond | 0.0010033 | 0.0011995 | 0.0015519 | 0.6 | 3.08
Neigh | 0.0044944 | 0.0045093 | 0.0045218 | 0.0 | 11.59
Comm | 0.0080328 | 0.0093863 | 0.010242 | 0.9 | 24.12
Output | 0.00021577 | 0.00027579 | 0.00045323 | 0.0 | 0.71
Modify | 0.0034575 | 0.0036355 | 0.0040002 | 0.4 | 9.34
Other | | 0.002501 | | | 6.43
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
group solvent molecule 0
750 atoms in group solvent
group solute subtract all solvent
450 atoms in group solute
unfix 1
unfix 2
unfix 4
fix 1 solvent nve
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
150 rigid bodies with 450 atoms
fix 4 all enforce2d
run 20000
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 26 26 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
1000 0.46008163 -1.9040835 0.08808163 -1.4425689 0.93225869
2000 0.44943348 -1.9355135 0.08808163 -1.4826417 3.8399671
3000 0.4448437 -1.9480307 0.08808163 -1.4988842 2.5506553
4000 0.46013872 -1.9783821 0.08808163 -1.5168212 -1.8963215
5000 0.45520233 -1.9659462 0.08808163 -1.5083921 1.9238897
6000 0.44942049 -1.9663403 0.08808163 -1.513479 3.0633512
7000 0.45975758 -1.988462 0.08808163 -1.5272105 4.8267309
8000 0.45125238 -1.9913522 0.08808163 -1.5370041 -4.6644852
9000 0.45863606 -1.9792375 0.08808163 -1.5188962 4.3655071
10000 0.46264541 -1.9864611 0.08808163 -1.5228656 2.2176464
11000 0.45048361 -1.9907235 0.08808163 -1.5369994 -0.055360699
12000 0.44536719 -2.012875 0.08808163 -1.5633037 -0.2583823
13000 0.44212663 -2.0060111 0.08808163 -1.55907 3.3616171
14000 0.44984353 -2.0335408 0.08808163 -1.5803361 -0.21585645
15000 0.44896672 -2.0385265 0.08808163 -1.5860335 -4.6186206
16000 0.46694997 -2.032795 0.08808163 -1.5657056 0.53443281
17000 0.43208201 -2.0272255 0.08808163 -1.5884373 -6.5239975
18000 0.43281873 -2.0331268 0.08808163 -1.5937406 -0.048319943
19000 0.44704527 -2.0286742 0.08808163 -1.5777408 1.6356417
20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -3.8337952
Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms
Performance: 5025468.853 tau/day, 11633.030 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.39864 | 0.40873 | 0.42192 | 1.6 | 23.77
Bond | 0.02118 | 0.021816 | 0.022785 | 0.4 | 1.27
Neigh | 0.13931 | 0.14031 | 0.14117 | 0.2 | 8.16
Comm | 0.13974 | 0.15328 | 0.16884 | 3.3 | 8.92
Output | 0.00026131 | 0.00044435 | 0.00099206 | 0.0 | 0.03
Modify | 0.93275 | 0.94138 | 0.95072 | 0.7 | 54.76
Other | | 0.05327 | | | 3.10
Nlocal: 300 ave 303 max 298 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 218.5 ave 226 max 215 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 2258.75 ave 2283 max 2216 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 9035
Ave neighs/atom = 7.52917
Ave special neighs/atom = 0.5
Neighbor list builds = 1580
Dangerous builds = 0
unfix 5
unfix 4
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
create bodies CPU = 5.43594e-05 secs
150 rigid bodies with 450 atoms
0.916597 = max distance from body owner to body atom
fix 4 all enforce2d
run 20000
Per MPI rank memory allocation (min/avg/max) = 8.568 | 8.6 | 8.691 Mbytes
Step Temp E_pair E_mol TotEng Press
20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -1.033643
21000 0.4529129 -2.049461 0.08808163 -1.5937651 0.93160285
22000 0.45039188 -2.0530092 0.08808163 -1.5993595 -0.10608965
23000 0.45261583 -2.0336042 0.08808163 -1.5781494 -2.5769871
24000 0.4608331 -2.0404645 0.08808163 -1.57834 3.1931675
25000 0.43479001 -2.0617104 0.08808163 -1.6207242 2.8190122
26000 0.47009651 -2.0754873 0.08808163 -1.605844 -0.9158501
27000 0.45002704 -2.0782104 0.08808163 -1.6248568 0.98629661
28000 0.45126136 -2.0592619 0.08808163 -1.6049065 0.03305448
29000 0.44355328 -2.0572858 0.08808163 -1.6091868 -6.0797989
30000 0.45053899 -2.0530953 0.08808163 -1.5993261 0.38382951
31000 0.46931923 -2.0718827 0.08808163 -1.6028703 2.2346891
32000 0.45348857 -2.0744024 0.08808163 -1.6182393 4.5028966
33000 0.44767742 -2.0597127 0.08808163 -1.6082662 -2.8021641
34000 0.45287544 -2.0857303 0.08808163 -1.6300648 -5.384091
35000 0.44743898 -2.0927246 0.08808163 -1.6414717 1.4800508
36000 0.45627028 -2.0720546 0.08808163 -1.6136336 -2.9961696
37000 0.4641334 -2.0701098 0.08808163 -1.6053065 8.4186854
38000 0.45922901 -2.0962331 0.08808163 -1.6354106 0.38361763
39000 0.4692834 -2.0573815 0.08808163 -1.5883982 -2.2177345
40000 0.46206931 -2.057851 0.08808163 -1.5947231 -1.0405727
Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms
Performance: 6885775.862 tau/day, 15939.296 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.40627 | 0.43037 | 0.45515 | 2.6 | 34.30
Bond | 0.020504 | 0.021573 | 0.022739 | 0.5 | 1.72
Neigh | 0.14337 | 0.14438 | 0.1453 | 0.2 | 11.51
Comm | 0.13776 | 0.16647 | 0.19351 | 5.0 | 13.27
Output | 0.00025082 | 0.00052994 | 0.0013635 | 0.0 | 0.04
Modify | 0.45467 | 0.45822 | 0.46259 | 0.5 | 36.52
Other | | 0.03321 | | | 2.65
Nlocal: 300 ave 304 max 293 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 215.25 ave 217 max 213 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 2340 ave 2378 max 2290 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 9360
Ave neighs/atom = 7.8
Ave special neighs/atom = 0.5
Neighbor list builds = 1579
Dangerous builds = 0
Total wall time: 0:00:03

2
src/KIM/kim_query.cpp
View File

@ -64,8 +64,10 @@
#include "input.h"
#include "variable.h"
#if defined(LMP_KIM_CURL)
#include <sys/types.h>
#include <curl/curl.h>
#endif
using namespace LAMMPS_NS;

6
src/domain.cpp
View File

@ -763,9 +763,9 @@ void Domain::image_check()
continue;
}
delx = unwrap[i][0] - unwrap[k][0];
dely = unwrap[i][1] - unwrap[k][1];
delz = unwrap[i][2] - unwrap[k][2];
delx = fabs(unwrap[i][0] - unwrap[k][0]);
dely = fabs(unwrap[i][1] - unwrap[k][1]);
delz = fabs(unwrap[i][2] - unwrap[k][2]);
if (xperiodic && delx > xprd_half) flag = 1;
if (yperiodic && dely > yprd_half) flag = 1;

3
src/modify.cpp
View File

@ -28,6 +28,7 @@
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -1058,7 +1059,7 @@ int Modify::check_rigid_group_overlap(int groupbit)
int n = 0;
for (int ifix = 0; ifix < nfix; ifix++) {
if (strncmp("rigid",fix[ifix]->style,5) == 0) {
if (utils::strmatch(fix[ifix]->style,"^rigid")) {
const int * const body = (const int *)fix[ifix]->extract("body",dim);
if ((body == NULL) || (dim != 1)) break;