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Merge pull request #1402 from akohlmey/collected-small-changes 

Collected changes for improving CI testing, CMake, and coding convention compliance
This commit is contained in:
Axel Kohlmeyer 2019-04-03 10:51:40 -04:00 committed by GitHub
parent 921d3dadf8 1696432e82
commit f73ccc3025
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
35 changed files with 1157 additions and 1208 deletions
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1
cmake/CMakeLists.txt
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@ -728,6 +728,7 @@ if(PKG_MESSAGE)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
else()
target_compile_definitions(cslib PRIVATE -DMPI_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
endif()

6
cmake/presets/all_off.cmake
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@ -2,9 +2,9 @@
# an existing package selection without losing any other settings
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MOLECULE MPIIO
MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD
VORONOI
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO

6
cmake/presets/all_on.cmake
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@ -4,9 +4,9 @@
# with just a working C++ compiler and an MPI library.
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MOLECULE MPIIO
MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD
VORONOI
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO

2
cmake/presets/nolib.cmake
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@ -4,7 +4,7 @@
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
USER-SMD USER-VTK)
USER-SCAFACOS USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

4
examples/micelle/in.micelle
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@ -58,7 +58,7 @@ pair_coeff 1 4 1.0 1.0 1.12246
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
thermo 50
#dump 1 all atom 2000 dump.micelle
@ -69,4 +69,4 @@ thermo 1000
#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
run 1000

87
examples/micelle/in.micelle-rigid Normal file
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@ -0,0 +1,87 @@
# 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 500
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 50
#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 500
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
fix 4 all enforce2d
run 500

259
examples/micelle/log.28Feb2019.micelle.g++.1
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@ -1,259 +0,0 @@
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

259
examples/micelle/log.28Feb2019.micelle.g++.4
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@ -1,259 +0,0 @@
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

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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 = 0.000175714 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

260
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LAMMPS (29 Mar 2019)
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 = 0.000473022 secs
read_data CPU = 0.0024147 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.00022316 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 500
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 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms
Performance: 2093802.885 tau/day, 4846.766 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21
Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11
Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64
Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86
Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17
Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37
Other | | 0.002726 | | | 2.64
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 197 ave 197 max 197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3094 ave 3094 max 3094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3094
Ave neighs/atom = 2.57833
Ave special neighs/atom = 0.5
Neighbor list builds = 52
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 50
#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 500
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 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms
Performance: 1208012.705 tau/day, 2796.326 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17
Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38
Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92
Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45
Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10
Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34
Other | | 0.00293 | | | 1.64
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 416 ave 416 max 416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8769 ave 8769 max 8769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8769
Ave neighs/atom = 7.3075
Ave special neighs/atom = 0.5
Neighbor list builds = 47
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 0.00015378 secs
150 rigid bodies with 450 atoms
1.30435 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332
1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141
Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms
Performance: 1297278.008 tau/day, 3002.958 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51
Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56
Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83
Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44
Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11
Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66
Other | | 0.003141 | | | 1.89
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 415 ave 415 max 415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8743 ave 8743 max 8743 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8743
Ave neighs/atom = 7.28583
Ave special neighs/atom = 0.5
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:00

260
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LAMMPS (29 Mar 2019)
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 = 0.000422001 secs
read_data CPU = 0.00473404 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000183344 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 500
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 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
200 0.45 1.01454 0.10663502 1.5708 4.7598476
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms
Performance: 5066547.720 tau/day, 11728.120 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16
Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95
Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95
Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78
Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62
Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28
Other | | 0.002669 | | | 6.26
Nlocal: 300 ave 304 max 292 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost: 103.5 ave 108 max 98 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 773.5 ave 792 max 735 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 3094
Ave neighs/atom = 2.57833
Ave special neighs/atom = 0.5
Neighbor list builds = 52
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 50
#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 500
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 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms
Performance: 2434100.210 tau/day, 5634.491 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74
Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30
Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32
Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30
Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29
Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73
Other | | 0.002938 | | | 3.31
Nlocal: 300 ave 309 max 291 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 218.75 ave 223 max 216 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 2192.25 ave 2251 max 2113 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8769
Ave neighs/atom = 7.3075
Ave special neighs/atom = 0.5
Neighbor list builds = 47
Dangerous builds = 2
unfix 2
unfix 4
unfix 5
fix 5 solute rigid/small molecule
create bodies CPU = 7.70092e-05 secs
150 rigid bodies with 450 atoms
1.30435 = max distance from body owner to body atom
fix 4 all enforce2d
run 500
Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes
Step Temp E_pair E_mol TotEng Press
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332
1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141
Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms
Performance: 3671840.233 tau/day, 8499.630 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47
Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93
Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98
Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29
Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42
Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11
Other | | 0.00224 | | | 3.81
Nlocal: 300 ave 303 max 295 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 219 ave 224 max 215 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 2185.75 ave 2244 max 2143 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 8743
Ave neighs/atom = 7.28583
Ave special neighs/atom = 0.5
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (29 Mar 2019)
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 = 0.00037837 secs
read_data CPU = 0.00206876 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000177383 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 0.208895 on 1 procs for 1000 steps with 1200 atoms
Performance: 2068027.282 tau/day, 4787.100 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14142 | 0.14142 | 0.14142 | 0.0 | 67.70
Bond | 0.008441 | 0.008441 | 0.008441 | 0.0 | 4.04
Neigh | 0.025716 | 0.025716 | 0.025716 | 0.0 | 12.31
Comm | 0.0036864 | 0.0036864 | 0.0036864 | 0.0 | 1.76
Output | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.17
Modify | 0.023699 | 0.023699 | 0.023699 | 0.0 | 11.35
Other | | 0.00558 | | | 2.67
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 50
#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 1000
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
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
450 0.47220236 -1.9468502 0.065625624 -1.4094157 2.0984288
500 0.4684673 -1.9444333 0.076696283 -1.3996601 2.0528682
550 0.47683128 -1.958676 0.070589719 -1.4116523 2.0856022
600 0.46851243 -1.9338267 0.07060548 -1.3950992 2.26405
650 0.46874142 -1.9462493 0.069134685 -1.4087638 2.1070263
700 0.46437384 -1.9309953 0.071977522 -1.3950309 2.2256923
750 0.47326225 -1.9484255 0.075435845 -1.4001218 2.0880254
800 0.45 -1.9646005 0.064159585 -1.4508159 2.0612696
850 0.46748307 -1.970559 0.060384874 -1.4430806 1.9472879
900 0.46909484 -1.953723 0.062470295 -1.4225488 2.0222909
950 0.45631531 -1.9387753 0.067536568 -1.4153037 2.0638421
1000 0.45 -1.9727646 0.058607721 -1.4645318 1.9982315
Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms
Performance: 1712557.882 tau/day, 3964.254 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17177 | 0.17177 | 0.17177 | 0.0 | 68.09
Bond | 0.0084555 | 0.0084555 | 0.0084555 | 0.0 | 3.35
Neigh | 0.03991 | 0.03991 | 0.03991 | 0.0 | 15.82
Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 1.95
Output | 0.00039077 | 0.00039077 | 0.00039077 | 0.0 | 0.15
Modify | 0.021131 | 0.021131 | 0.021131 | 0.0 | 8.38
Other | | 0.005685 | | | 2.25
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 415 ave 415 max 415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8586 ave 8586 max 8586 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8586
Ave neighs/atom = 7.155
Ave special neighs/atom = 0.5
Neighbor list builds = 86
Dangerous builds = 0
Total wall time: 0:00:00

218
examples/micelle/log.29Mar2019.micelle.g++.4 Normal file
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LAMMPS (29 Mar 2019)
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 = 0.000413656 secs
read_data CPU = 0.00487924 secs
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000178576 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 0.0906248 on 4 procs for 1000 steps with 1200 atoms
Performance: 4766906.584 tau/day, 11034.506 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33
Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70
Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85
Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53
Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68
Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19
Other | | 0.006081 | | | 6.71
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 50
#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 1000
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
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288
500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682
550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023
600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405
650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262
700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692
750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235
800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703
850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884
900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008
950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854
1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447
Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms
Performance: 4917357.613 tau/day, 11382.772 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60
Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54
Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04
Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79
Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74
Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11
Other | | 0.00455 | | | 5.18
Nlocal: 300 ave 305 max 296 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 219.5 ave 228 max 214 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 2146.5 ave 2201 max 2114 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 8586
Ave neighs/atom = 7.155
Ave special neighs/atom = 0.5
Neighbor list builds = 86
Dangerous builds = 0
Total wall time: 0:00:00

0
lib/message/cslib/src/STUBS_MPI/mpi.h → lib/message/cslib/src/STUBS_MPI/mpi_dummy.h
View File

4
lib/message/cslib/src/cslib.cpp
View File

@ -12,7 +12,11 @@
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifdef MPI_YES
#include <mpi.h>
#else
#include <mpi_dummy.h>
#endif
#include <stdio.h>
#include <string.h>
#include <stdlib.h>

4
lib/message/cslib/src/cslib_wrap.cpp
View File

@ -14,7 +14,11 @@
// C style library interface to CSlib class
#ifdef MPI_YES
#include <mpi.h>
#else
#include <mpi_dummy.h>
#endif
#include <string.h>
#include <stdio.h>
#include <stdlib.h>

4
lib/message/cslib/src/msg.cpp
View File

@ -12,7 +12,11 @@
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifdef MPI_YES
#include <mpi.h>
#else
#include <mpi_dummy.h>
#endif
#include <cstdio>
#include <cstring>
#include <cstdlib>

6
lib/message/cslib/src/msg.h
View File

@ -15,7 +15,11 @@
#ifndef MSG_H
#define MSG_H
#ifdef MPI_YES
#include <mpi.h>
#else
#include <mpi_dummy.h>
#endif
namespace CSLIB_NS {
@ -37,7 +41,7 @@ class Msg {
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int lengths[2];
void init(int);
void allocate(int, int &, int *&, int, int &, char *&);
void *smalloc(int);

4
lib/message/cslib/src/msg_file.cpp
View File

@ -12,7 +12,11 @@
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifdef MPI_YES
#include <mpi.h>
#else
#include <mpi_dummy.h>
#endif
#include <stdio.h>
#include <string.h>
#include <stdlib.h>

4
lib/message/cslib/src/msg_mpi_one.cpp
View File

@ -12,7 +12,11 @@
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifdef MPI_YES
#include <mpi.h>
#else
#include <mpi_dummy.h>
#endif
#include <string.h>
#include <stdlib.h>
#include <stdint.h>

4
lib/message/cslib/src/msg_mpi_two.cpp
View File

@ -12,7 +12,11 @@
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifdef MPI_YES
#include <mpi.h>
#else
#include <mpi_dummy.h>
#endif
#include <string.h>
#include <stdlib.h>
#include <stdint.h>

4
lib/message/cslib/src/msg_zmq.cpp
View File

@ -12,7 +12,11 @@
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifdef MPI_YES
#include <mpi.h>
#else
#include <mpi_dummy.h>
#endif
#include <zmq.h>
#include <string.h>
#include <stdlib.h>

10
src/KOKKOS/domain_kokkos.h
View File

@ -36,10 +36,12 @@ class DomainKokkos : public Domain {
void image_flip(int, int, int);
void x2lamda(int);
void lamda2x(int);
// these lines bring in the x2lamda signatures from Domain
// that are not overloaded here
using Domain::x2lamda;
using Domain::lamda2x;
// forward remaining x2lamda() and lambda2x() variants to parent class
void x2lamda(double *a, double *b) { Domain::x2lamda(a,b); }
void lamda2x(double *a, double *b) { Domain::lamda2x(a,b); }
void x2lamda(double *a, double *b, double *c, double *d) {
Domain::x2lamda(a,b,c,d);
}
int closest_image(const int, int) const;

3
src/KOKKOS/pair_snap_kokkos_impl.h
View File

@ -32,7 +32,7 @@
#define MAXLINE 1024
#define MAXWORD 3
using namespace LAMMPS_NS;
namespace LAMMPS_NS {
// Outstanding issues with quadratic term
// 1. there seems to a problem with compute_optimized energy calc
@ -674,3 +674,4 @@ double PairSNAPKokkos<DeviceType>::memory_usage()
bytes += snaKK.memory_usage();
return bytes;
}
}

4
src/KOKKOS/sna_kokkos_impl.h
View File

@ -20,7 +20,7 @@
#include <cstring>
#include <cstdlib>
using namespace LAMMPS_NS;
namespace LAMMPS_NS {
static const double MY_PI = 3.14159265358979323846; // pi
@ -1300,3 +1300,5 @@ double SNAKokkos<DeviceType>::memory_usage()
bytes += jdim * jdim * jdim * jdim * jdim * sizeof(std::complex<double>);
return bytes;
}
} // namespace LAMMPS_NS

6
src/MESSAGE/fix_client_md.cpp
View File

@ -89,7 +89,7 @@ FixClientMD::~FixClientMD()
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
cs->recv(nfield,fieldID,fieldtype,fieldlen);
// clean-up
@ -173,8 +173,6 @@ void FixClientMD::min_setup(int vflag)
void FixClientMD::post_force(int vflag)
{
int i,j,m;
// energy and virial setup
if (vflag) v_setup(vflag);
@ -286,7 +284,7 @@ void FixClientMD::receive_fev(int vflag)
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
cs->recv(nfield,fieldID,fieldtype,fieldlen);
double *forces = (double *) cs->unpack(FORCES);
double **f = atom->f;

12
src/MESSAGE/message.cpp
View File

@ -22,10 +22,6 @@
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
// customize by adding a new server protocol enum
enum{MD,MC};
/* ---------------------------------------------------------------------- */
void Message::command(int narg, char **arg)
@ -38,12 +34,10 @@ void Message::command(int narg, char **arg)
else error->all(FLERR,"Illegal message command");
lmp->clientserver = clientserver;
// customize by adding a new server protocol
// validate supported protocols
int protocol;
if (strcmp(arg[1],"md") == 0) protocol = MD;
else if (strcmp(arg[1],"mc") == 0) protocol = MC;
else error->all(FLERR,"Unknown message protocol");
if ((strcmp(arg[1],"md") != 0) && (strcmp(arg[1],"mc") != 0))
error->all(FLERR,"Unknown message protocol");
// instantiate CSlib with chosen communication mode

4
src/MESSAGE/server_mc.cpp
View File

@ -37,8 +37,8 @@ ServerMC::ServerMC(LAMMPS *lmp) : Pointers(lmp) {}
void ServerMC::loop()
{
int i,j,m;
double xold[3],xnew[3];
int m;
double xold[3];
tagint atomid;
CSlib *cs = (CSlib *) lmp->cslib;

2
src/MESSAGE/server_md.cpp
View File

@ -78,7 +78,7 @@ ServerMD::~ServerMD()
void ServerMD::loop()
{
int i,j,m;
int j,m;
// cs = instance of CSlib

3
src/USER-MISC/README
View File

@ -67,14 +67,17 @@ improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16
pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style ilp/graphene/hbn, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
pair_style lebedeva/z, Zbigniew Koziol (National Center for Nuclear Research), softquake at gmail dot com, 4 Jan 19
pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style kolmogorov/crespi/full, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17
pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12

4
src/USER-REAXC/reaxc_types.h
View File

@ -392,8 +392,6 @@ typedef struct
double ghost_cutoff;
} boundary_cutoff;
using LAMMPS_NS::Pair;
struct _reax_system
{
reax_interaction reax_param;
@ -411,7 +409,7 @@ struct _reax_system
boundary_cutoff bndry_cuts;
reax_atom *my_atoms;
class Pair *pair_ptr;
class LAMMPS_NS::Pair *pair_ptr;
int my_bonds;
int mincap;
double safezone, saferzone;

24
src/USER-SMD/smd_material_models.h
View File

@ -22,10 +22,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef SMD_MATERIAL_MODELS_H_
#define SMD_MATERIAL_MODELS_H_
#ifndef SMD_MATERIAL_MODELS_H
#define SMD_MATERIAL_MODELS_H
using namespace Eigen;
#include <Eigen/Eigen>
/*
* EOS models
@ -42,22 +42,22 @@ void PerfectGasEOS(const double gamma, const double vol, const double mass, cons
/*
* Material strength models
*/
void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, const double dt,
Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__);
void LinearPlasticStrength(const double G, const double yieldStress, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev,
const double dt, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment);
void LinearStrength(const double mu, const Eigen::Matrix3d sigmaInitial_dev, const Eigen::Matrix3d d_dev, const double dt,
Eigen::Matrix3d &sigmaFinal_dev__, Eigen::Matrix3d &sigma_dev_rate__);
void LinearPlasticStrength(const double G, const double yieldStress, const Eigen::Matrix3d sigmaInitial_dev, const Eigen::Matrix3d d_dev,
const double dt, Eigen::Matrix3d &sigmaFinal_dev__, Eigen::Matrix3d &sigma_dev_rate__, double &plastic_strain_increment);
void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a,
const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep,
const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__,
Matrix3d &sigma_dev_rate__, double &plastic_strain_increment);
const double epdot, const Eigen::Matrix3d sigmaInitial_dev, const Eigen::Matrix3d d_dev, Eigen::Matrix3d &sigmaFinal_dev__,
Eigen::Matrix3d &sigma_dev_rate__, double &plastic_strain_increment);
/*
* Damage models
*/
bool IsotropicMaxStrainDamage(const Matrix3d E, const double maxStrain);
bool IsotropicMaxStressDamage(const Matrix3d E, const double maxStrain);
double JohnsonCookFailureStrain(const double p, const Matrix3d Sdev, const double d1, const double d2, const double d3,
bool IsotropicMaxStrainDamage(const Eigen::Matrix3d E, const double maxStrain);
bool IsotropicMaxStressDamage(const Eigen::Matrix3d E, const double maxStrain);
double JohnsonCookFailureStrain(const double p, const Eigen::Matrix3d Sdev, const double d1, const double d2, const double d3,
const double d4, const double epdot0, const double epdot);

97
src/USER-SMD/smd_math.h
View File

@ -9,14 +9,11 @@
*
* ----------------------------------------------------------------------- */
//test
#ifndef SMD_MATH_H_
#define SMD_MATH_H_
#ifndef SMD_MATH_H
#define SMD_MATH_H
#include <Eigen/Eigen>
#include <iostream>
using namespace Eigen;
using namespace std;
namespace SMD_Math {
static inline void LimitDoubleMagnitude(double &x, const double limit) {
@ -31,8 +28,8 @@ static inline void LimitDoubleMagnitude(double &x, const double limit) {
/*
* deviator of a tensor
*/
static inline Matrix3d Deviator(const Matrix3d M) {
Matrix3d eye;
static inline Eigen::Matrix3d Deviator(const Eigen::Matrix3d M) {
Eigen::Matrix3d eye;
eye.setIdentity();
eye *= M.trace() / 3.0;
return M - eye;
@ -53,14 +50,14 @@ static inline Matrix3d Deviator(const Matrix3d M) {
* obtained again from an SVD. The rotation should proper now, i.e., det(R) = +1.
*/
static inline bool PolDec(Matrix3d M, Matrix3d &R, Matrix3d &T, bool scaleF) {
static inline bool PolDec(Eigen::Matrix3d M, Eigen::Matrix3d &R, Eigen::Matrix3d &T, bool scaleF) {
JacobiSVD<Matrix3d> svd(M, ComputeFullU | ComputeFullV); // SVD(A) = U S V*
Vector3d S_eigenvalues = svd.singularValues();
Matrix3d S = svd.singularValues().asDiagonal();
Matrix3d U = svd.matrixU();
Matrix3d V = svd.matrixV();
Matrix3d eye;
Eigen::JacobiSVD<Eigen::Matrix3d> svd(M, Eigen::ComputeFullU | Eigen::ComputeFullV); // SVD(A) = U S V*
Eigen::Vector3d S_eigenvalues = svd.singularValues();
Eigen::Matrix3d S = svd.singularValues().asDiagonal();
Eigen::Matrix3d U = svd.matrixU();
Eigen::Matrix3d V = svd.matrixV();
Eigen::Matrix3d eye;
eye.setIdentity();
// now do polar decomposition into M = R * T, where R is rotation
@ -105,16 +102,12 @@ static inline bool PolDec(Matrix3d M, Matrix3d &R, Matrix3d &T, bool scaleF) {
* Pseudo-inverse via SVD
*/
static inline void pseudo_inverse_SVD(Matrix3d &M) {
static inline void pseudo_inverse_SVD(Eigen::Matrix3d &M) {
//JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV);
JacobiSVD<Matrix3d> svd(M, ComputeFullU); // one Eigevector base is sufficient because matrix is square and symmetric
Eigen::JacobiSVD<Eigen::Matrix3d> svd(M, Eigen::ComputeFullU); // one Eigevector base is sufficient because matrix is square and symmetric
Vector3d singularValuesInv;
Vector3d singularValues = svd.singularValues();
//cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl;
//cout << "Its singular values are:" << endl << singularValues << endl;
Eigen::Vector3d singularValuesInv;
Eigen::Vector3d singularValues = svd.singularValues();
double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16).
for (int row = 0; row < 3; row++) {
@ -126,39 +119,19 @@ static inline void pseudo_inverse_SVD(Matrix3d &M) {
}
M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixU().transpose();
// JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV);
//
// Vector3d singularValuesInv;
// Vector3d singularValues = svd.singularValues();
//
// //cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl;
// //cout << "Its singular values are:" << endl << singularValues << endl;
//
// double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16).
// for (int row = 0; row < 3; row++) {
// if (singularValues(row) > pinvtoler) {
// singularValuesInv(row) = 1.0 / singularValues(row);
// } else {
// singularValuesInv(row) = 0.0;
// }
// }
//
// M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixV().transpose();
}
/*
* test if two matrices are equal
*/
static inline double TestMatricesEqual(Matrix3d A, Matrix3d B, double eps) {
Matrix3d diff;
static inline double TestMatricesEqual(Eigen::Matrix3d A, Eigen::Matrix3d B, double eps) {
Eigen::Matrix3d diff;
diff = A - B;
double norm = diff.norm();
if (norm > eps) {
printf("Matrices A and B are not equal! The L2-norm difference is: %g\n", norm);
cout << "Here is matrix A:" << endl << A << endl;
cout << "Here is matrix B:" << endl << B << endl;
std::cout << "Matrices A and B are not equal! The L2-norm difference is: " << norm << "\n"
<< "Here is matrix A:\n" << A << "\n"
<< "Here is matrix B:\n" << B << std::endl;
}
return norm;
}
@ -167,12 +140,12 @@ static inline double TestMatricesEqual(Matrix3d A, Matrix3d B, double eps) {
Limit eigenvalues of a matrix to upper and lower bounds.
------------------------------------------------------------------------- */
static inline Matrix3d LimitEigenvalues(Matrix3d S, double limitEigenvalue) {
static inline Eigen::Matrix3d LimitEigenvalues(Eigen::Matrix3d S, double limitEigenvalue) {
/*
* compute Eigenvalues of matrix S
*/
SelfAdjointEigenSolver < Matrix3d > es;
Eigen::SelfAdjointEigenSolver < Eigen::Matrix3d > es;
es.compute(S);
double max_eigenvalue = es.eigenvalues().maxCoeff();
@ -183,17 +156,17 @@ static inline Matrix3d LimitEigenvalues(Matrix3d S, double limitEigenvalue) {
if ((amax_eigenvalue > limitEigenvalue) || (amin_eigenvalue > limitEigenvalue)) {
if (amax_eigenvalue > amin_eigenvalue) { // need to scale with max_eigenvalue
double scale = amax_eigenvalue / limitEigenvalue;
Matrix3d V = es.eigenvectors();
Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix
Eigen::Matrix3d V = es.eigenvectors();
Eigen::Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix
S_diag /= scale;
Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix
Eigen::Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix
return S_scaled;
} else { // need to scale using min_eigenvalue
double scale = amin_eigenvalue / limitEigenvalue;
Matrix3d V = es.eigenvectors();
Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix
Eigen::Matrix3d V = es.eigenvectors();
Eigen::Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix
S_diag /= scale;
Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix
Eigen::Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix
return S_scaled;
}
} else { // limiting does not apply
@ -201,17 +174,17 @@ static inline Matrix3d LimitEigenvalues(Matrix3d S, double limitEigenvalue) {
}
}
static inline bool LimitMinMaxEigenvalues(Matrix3d &S, double min, double max) {
static inline bool LimitMinMaxEigenvalues(Eigen::Matrix3d &S, double min, double max) {
/*
* compute Eigenvalues of matrix S
*/
SelfAdjointEigenSolver < Matrix3d > es;
Eigen::SelfAdjointEigenSolver < Eigen::Matrix3d > es;
es.compute(S);
if ((es.eigenvalues().maxCoeff() > max) || (es.eigenvalues().minCoeff() < min)) {
Matrix3d S_diag = es.eigenvalues().asDiagonal();
Matrix3d V = es.eigenvectors();
Eigen::Matrix3d S_diag = es.eigenvalues().asDiagonal();
Eigen::Matrix3d V = es.eigenvectors();
for (int i = 0; i < 3; i++) {
if (S_diag(i, i) < min) {
//printf("limiting eigenvalue %f --> %f\n", S_diag(i, i), min);
@ -229,10 +202,10 @@ static inline bool LimitMinMaxEigenvalues(Matrix3d &S, double min, double max) {
}
}
static inline void reconstruct_rank_deficient_shape_matrix(Matrix3d &K) {
static inline void reconstruct_rank_deficient_shape_matrix(Eigen::Matrix3d &K) {
JacobiSVD<Matrix3d> svd(K, ComputeFullU | ComputeFullV);
Vector3d singularValues = svd.singularValues();
Eigen::JacobiSVD<Eigen::Matrix3d> svd(K, Eigen::ComputeFullU | Eigen::ComputeFullV);
Eigen::Vector3d singularValues = svd.singularValues();
for (int i = 0; i < 3; i++) {
if (singularValues(i) < 1.0e-8) {

2
src/special.cpp
View File

@ -1225,7 +1225,7 @@ void Special::dihedral_trim()
------------------------------------------------------------------------- */
int Special::rendezvous_ids(int n, char *inbuf,
int &flag, int *&proclist, char *&outbuf,
int &flag, int *& /*proclist*/, char *& /*outbuf*/,
void *ptr)
{
Special *sptr = (Special *) ptr;