From d5f34f62967070da33a64f9dd800bf93267be9dd Mon Sep 17 00:00:00 2001 From: Joel Clemmer Date: Fri, 8 Jan 2021 15:27:23 -0700 Subject: [PATCH] Examples and documentation --- doc/src/comm_modify.rst | 16 +- doc/src/neigh_modify.rst | 20 +- doc/src/neighbor.rst | 32 +-- examples/multi/in.colloid | 67 +++++++ examples/multi/in.granular | 58 ++++++ examples/multi/log.30Nov20.colloid.intel.1 | 183 ++++++++++++++++++ examples/multi/log.30Nov20.colloid.intel.4 | 183 ++++++++++++++++++ .../multi/log.30Nov20.colloid.old.intel.1 | 183 ++++++++++++++++++ .../multi/log.30Nov20.colloid.old.intel.4 | 183 ++++++++++++++++++ examples/multi/log.30Nov20.granular.intel.1 | 175 +++++++++++++++++ examples/multi/log.30Nov20.granular.intel.4 | 175 +++++++++++++++++ .../multi/log.30Nov20.granular.old.intel.1 | 175 +++++++++++++++++ .../multi/log.30Nov20.granular.old.intel.4 | 175 +++++++++++++++++ src/comm.cpp | 2 + 14 files changed, 1604 insertions(+), 23 deletions(-) create mode 100644 examples/multi/in.colloid create mode 100644 examples/multi/in.granular create mode 100644 examples/multi/log.30Nov20.colloid.intel.1 create mode 100644 examples/multi/log.30Nov20.colloid.intel.4 create mode 100644 examples/multi/log.30Nov20.colloid.old.intel.1 create mode 100644 examples/multi/log.30Nov20.colloid.old.intel.4 create mode 100644 examples/multi/log.30Nov20.granular.intel.1 create mode 100644 examples/multi/log.30Nov20.granular.intel.4 create mode 100644 examples/multi/log.30Nov20.granular.old.intel.1 create mode 100644 examples/multi/log.30Nov20.granular.old.intel.4 diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 895d3cf4fd..5f084561a1 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -66,9 +66,10 @@ For many systems this is an efficient algorithm, but for systems with widely varying cutoffs for different type pairs, the *multi* mode can be faster. In this case, each atom type is assigned its own distance cutoff for communication purposes, and fewer atoms will be -communicated. See the :doc:`neighbor multi ` command for a +communicated. See the :doc:`neighbor multi ` command for a neighbor list construction option that may also be beneficial for -simulations of this kind. +simulations of this kind. The *multi* mode is compatable with both the +*multi* and *multi/old* neighbor styles. The *cutoff* keyword allows you to extend the ghost cutoff distance for communication mode *single*\ , which is the distance from the borders @@ -95,11 +96,12 @@ using the usual asterisk notation can be given. For granular pair styles, the default cutoff is set to the sum of the current maximum atomic radii for each type. -The *cutoff/bytype* option applies to *multi* and automtically sets communication -cutoffs for each particle type based on the largest interaction distance -between two particles of the same type. This method is only compatible -with Newton on and the *bytype* neighbor style. See the :doc:`neighbor bytype ` -command for more information. +The *multi/reduce* option applies to *multi* and automatically sets communication +cutoffs for different sized particles based on the largest interaction distance +between two particles in the same multi grouping. This reduces the number of +ghost that need to be communicated This method is only compatible with the +*multi* neighbor style and requires only half neighbor lists and Newton on. +See the :doc:`neighbor multi ` command for more information. These are simulation scenarios in which it may be useful or even necessary to set a ghost cutoff > neighbor cutoff: diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 2618953dd7..33f24af96e 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -14,7 +14,7 @@ Syntax .. parsed-literal:: - keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* + keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *multi/custom* *delay* value = N N = delay building until this many steps since last build *every* value = M @@ -47,6 +47,9 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) + *multi/custom* values = N types + N = number of custom groups + types = N separate types or groups of types (see below) Examples """""""" @@ -58,6 +61,7 @@ Examples neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 neigh_modify exclude molecule/intra rigid + neigh_modify multi/custom 2 1*2 3*4 Description """"""""""" @@ -197,6 +201,20 @@ small, the optimal number of atoms is checked, but bin overhead goes up. If you set the binsize to 0.0, LAMMPS will use the default binsize of 1/2 the cutoff. +The *multi/custom* option allows you to define custom groups of atom +types for the *multi* neighbor mode. By grouping atom types with +similar cutoffs, one may be able to improve performance by reducing +overhead. You must first specify the number of custom groups N to be +defined followed by N ranges of types. The range can be specified as a +single numeric value, or a wildcard asterisk can be used to specify a range +of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For +example, if N = the number of atom types, then an asterisk with no numeric +values means all types from 1 to N. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n (inclusive). +Note that any atom types not included in a custom group will be automatically +placed within a new, separate group. + Restrictions """""""""""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index f638160d21..52d59dae75 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -11,7 +11,7 @@ Syntax neighbor skin style * skin = extra distance beyond force cutoff (distance units) -* style = *bin* or *nsq* or *multi* or *bytype* +* style = *bin* or *nsq* or *multi* or *multi/old* Examples """""""" @@ -55,22 +55,24 @@ For the *bin* style, the bin size is set to 1/2 of the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but -other type pairs have a much shorter cutoff. For style *multi* the -bin size is set to 1/2 of the shortest cutoff distance and multiple -sets of bins are defined to search over for different atom types. +other type pairs have a much shorter cutoff. The *multi* style uses +different sized bins for groups of different sized particles. Different +sets of bins are then used to construct the neighbor lists as as further +described by Shire, Hanley, and Stratford :ref:`(Shire) `. This imposes some extra setup overhead, but the searches themselves -may be much faster for the short-cutoff cases. -See the :doc:`comm_modify mode multi ` command for a -communication option that may also be beneficial for simulations of -this kind. +may be much faster. By default, separate groups of particles are defined +for each atom type. For systems with two or more types with similar +cutoffs, one can reduce the extra overhead by defining custom groupings +using the :doc:`neigh_modify ` command. See the +:doc:`comm_modify mode bytype ` command for compatible +communication options that may be beneficial for simulations of this kind. -The *bytype* style is an extension of the *multi* style that was -presented by Shire, Hanley, and Stratford :ref:`(Shire) `. -For style *bytype*, different bin lists are created for each different -type and separate bin sizes are generated. Whether *bytype* or *multi* -is faster may depend on the specifics of your system. See the -:doc:`comm_modify mode bytype ` command for a compatible -communication option. +An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest +cutoff distance and multiple sets of bins are defined to search over for +different atom types. This algorithm used to be the default *multi* +algorithm in LAMMPS but was found to be significantly slower than the new +approach. Although, there may be instances where the *multi/old* style +could outperform the new style. The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid new file mode 100644 index 0000000000..b332560777 --- /dev/null +++ b/examples/multi/in.colloid @@ -0,0 +1,67 @@ +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +create_atoms 1 box + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +set group all type/fraction 3 0.333 43684 +set group all type/fraction 4 0.250 87811 + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +delete_atoms region sphere2 +create_atoms 5 single 60.0 60.0 0.0 units box +create_atoms 5 single 130.0 130.0 0.0 units box + +set type 1 mass 400 +set type 2 mass 1 + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 & + mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 diff --git a/examples/multi/in.granular b/examples/multi/in.granular new file mode 100644 index 0000000000..00dd4ad2bb --- /dev/null +++ b/examples/multi/in.granular @@ -0,0 +1,58 @@ +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +create_atoms 1 box +change_box all triclinic + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +delete_atoms region sphere2 +create_atoms 2 single 20.0 20.0 0.0 units box +create_atoms 2 single 60.0 60.0 0.0 units box + +set type 2 mass 400 +set type 1 mass 1 +set type 2 diameter 20 +set type 1 diameter 1 + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +#dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type & +# zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 diff --git a/examples/multi/log.30Nov20.colloid.intel.1 b/examples/multi/log.30Nov20.colloid.intel.1 new file mode 100644 index 0000000000..2bc82eaab0 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 5.538 | 5.538 | 5.538 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 + 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 + 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 + 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 + 6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702 + 7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386 + 8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372 + 9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764 + 10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941 + 11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993 + 12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363 + 13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226 + 14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372 + 15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715 + 16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607 + 17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6 + 18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856 + 19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867 + 20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666 + 21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277 + 22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593 + 23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968 + 24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941 + 25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154 + 26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774 + 27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521 + 28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093 + 29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945 + 30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305 + 31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392 + 32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609 + 33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572 + 34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49 + 35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819 + 36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608 + 37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772 + 38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511 + 39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647 + 40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198 + 41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649 + 42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804 + 43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893 + 44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262 + 45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842 + 46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151 + 47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334 + 48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246 + 49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093 + 50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715 +Loop time of 20.4651 on 1 procs for 50000 steps with 3026 atoms + +Performance: 1055453.279 tau/day, 2443.179 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.099 | 11.099 | 11.099 | 0.0 | 54.23 +Neigh | 2.7536 | 2.7536 | 2.7536 | 0.0 | 13.46 +Comm | 0.53353 | 0.53353 | 0.53353 | 0.0 | 2.61 +Output | 0.11209 | 0.11209 | 0.11209 | 0.0 | 0.55 +Modify | 5.1627 | 5.1627 | 5.1627 | 0.0 | 25.23 +Other | | 0.8046 | | | 3.93 + +Nlocal: 3026.00 ave 3026 max 3026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 584.000 ave 584 max 584 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25892.0 ave 25892 max 25892 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25892 +Ave neighs/atom = 8.5565102 +Neighbor list builds = 4330 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:20 diff --git a/examples/multi/log.30Nov20.colloid.intel.4 b/examples/multi/log.30Nov20.colloid.intel.4 new file mode 100644 index 0000000000..48a5846a09 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 multi/custom 2 1*4 5 +comm_modify mode multi multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 + 3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289 + 4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708 + 5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295 + 6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648 + 7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448 + 8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484 + 9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609 + 10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542 + 11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927 + 12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009 + 13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654 + 14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89 + 15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786 + 16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792 + 17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809 + 18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172 + 19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244 + 20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884 + 21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487 + 22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812 + 23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427 + 24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79 + 25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756 + 26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645 + 27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657 + 28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079 + 29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99 + 30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355 + 31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196 + 32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934 + 33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442 + 34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628 + 35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725 + 36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049 + 37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825 + 38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497 + 39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469 + 40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846 + 41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515 + 42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657 + 43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024 + 44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224 + 45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959 + 46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822 + 47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892 + 48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453 + 49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918 + 50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268 +Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms + +Performance: 2966022.789 tau/day, 6865.793 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59 +Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21 +Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96 +Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69 +Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04 +Other | | 0.4737 | | | 6.50 + +Nlocal: 756.500 ave 839 max 673 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 292.500 ave 307 max 282 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 6435.25 ave 7367 max 5493 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 25741 +Ave neighs/atom = 8.5066094 +Neighbor list builds = 4335 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:07 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.1 b/examples/multi/log.30Nov20.colloid.old.intel.1 new file mode 100644 index 0000000000..291e8f89df --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi #multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/old/newton + stencil: half/multi/old/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 + 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 + 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 + 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 + 6000 2.0797015 -0.086800284 1.992214 0.082095164 78182.702 + 7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387 + 8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802 + 9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722 + 10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135 + 11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116 + 12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208 + 13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901 + 14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344 + 15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963 + 16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043 + 17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977 + 18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99 + 19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325 + 20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745 + 21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298 + 22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199 + 23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71 + 24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334 + 25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577 + 26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041 + 27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392 + 28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419 + 29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642 + 30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15 + 31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091 + 32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726 + 33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866 + 34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869 + 35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285 + 36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264 + 37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274 + 38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252 + 39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857 + 40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905 + 41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981 + 42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931 + 43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82 + 44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18 + 45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013 + 46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611 + 47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083 + 48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933 + 49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165 + 50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069 +Loop time of 29.8066 on 1 procs for 50000 steps with 3026 atoms + +Performance: 724671.093 tau/day, 1677.479 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.698 | 11.698 | 11.698 | 0.0 | 39.25 +Neigh | 10.292 | 10.292 | 10.292 | 0.0 | 34.53 +Comm | 1.405 | 1.405 | 1.405 | 0.0 | 4.71 +Output | 0.11474 | 0.11474 | 0.11474 | 0.0 | 0.38 +Modify | 5.3019 | 5.3019 | 5.3019 | 0.0 | 17.79 +Other | | 0.9947 | | | 3.34 + +Nlocal: 3026.00 ave 3026 max 3026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2292.00 ave 2292 max 2292 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25767.0 ave 25767 max 25767 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25767 +Ave neighs/atom = 8.5152016 +Neighbor list builds = 4332 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:29 diff --git a/examples/multi/log.30Nov20.colloid.old.intel.4 b/examples/multi/log.30Nov20.colloid.old.intel.4 new file mode 100644 index 0000000000..0eae8cc8e7 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.1 +Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 +region box block 0 60 0 60 -0.5 0.5 +create_box 5 box +Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds + +#Roughly equally partition atoms between types 1-4 +set group all type/fraction 2 0.500 23984 +Setting atom values ... + 1768 settings made for type/fraction +set group all type/fraction 3 0.333 43684 +Setting atom values ... + 1255 settings made for type/fraction +set group all type/fraction 4 0.250 87811 +Setting atom values ... + 927 settings made for type/fraction + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 60.0 60.0 0.0 30.0 units box +region sphere2 sphere 130.0 130.0 0.0 30.0 units box +delete_atoms region sphere1 +Deleted 289 atoms, new total = 3311 +delete_atoms region sphere2 +Deleted 287 atoms, new total = 3024 +create_atoms 5 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 5 single 130.0 130.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 1 mass 400 +Setting atom values ... + 753 settings made for mass +set type 2 mass 1 +Setting atom values ... + 722 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi #multi/reduce + +# colloid potential + +pair_style colloid 20.0 +pair_coeff * * 144.0 1.0 0.0 0.0 3.0 +pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 +pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 + + + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 2, bins = 95 95 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/old/newton + stencil: half/multi/old/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.438 | 5.441 | 5.444 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395241 0.121 36000 + 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 + 2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 + 3000 1.8956738 -0.090814168 1.8042332 0.075557943 77825.289 + 4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521 + 5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581 + 6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994 + 7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068 + 8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899 + 9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69 + 10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271 + 11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223 + 12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869 + 13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441 + 14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432 + 15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491 + 16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633 + 17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582 + 18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933 + 19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945 + 20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271 + 21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934 + 22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03 + 23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999 + 24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323 + 25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848 + 26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597 + 27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24 + 28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441 + 29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266 + 30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051 + 31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903 + 32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077 + 33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987 + 34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964 + 35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433 + 36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246 + 37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664 + 38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421 + 39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293 + 40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176 + 41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599 + 42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922 + 43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928 + 44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954 + 45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662 + 46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162 + 47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453 + 48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543 + 49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823 + 50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277 +Loop time of 11.239 on 4 procs for 50000 steps with 3026 atoms + +Performance: 1921872.705 tau/day, 4448.779 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3936 | 2.7411 | 3.1078 | 16.7 | 24.39 +Neigh | 2.2948 | 2.6755 | 3.1013 | 18.5 | 23.81 +Comm | 2.522 | 3.3135 | 4.0361 | 31.7 | 29.48 +Output | 0.040863 | 0.041031 | 0.041456 | 0.1 | 0.37 +Modify | 1.844 | 1.9014 | 1.9701 | 3.4 | 16.92 +Other | | 0.5666 | | | 5.04 + +Nlocal: 756.500 ave 838 max 693 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1282.50 ave 1333 max 1216 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 6426.25 ave 7350 max 5786 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 25705 +Ave neighs/atom = 8.4947125 +Neighbor list builds = 4326 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:11 diff --git a/examples/multi/log.30Nov20.granular.intel.1 b/examples/multi/log.30Nov20.granular.intel.1 new file mode 100644 index 0000000000..2e313231ca --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #/old +neigh_modify delay 0 +comm_modify mode multi vel yes + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 + 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 + 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 + 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 + 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 + 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 + 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 + 18000 0.01100067 0 0.010997326 0.04899206 3825.155 + 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 + 20000 0.0091360559 0 0.0091332789 0.088230111 3408.5658 + 21000 0.007733647 0 0.0077312964 0.11769368 3227.7002 + 22000 0.0060202358 0 0.0060184059 0.15272491 3064.3986 + 23000 0.004670574 0 0.0046691543 0.19450724 2918.0014 + 24000 0.0040248313 0 0.004023608 0.24161742 2788.4113 + 25000 0.0032075275 0 0.0032065526 0.2897693 2674.5604 + 26000 0.0021358024 0 0.0021351532 0.33635617 2574.9564 + 27000 0.0016902752 0 0.0016897614 0.37624266 2487.2379 + 28000 0.0014038218 0 0.0014033951 0.41492104 2409.2461 + 29000 0.00090262506 0 0.0009023507 0.45392905 2340.0308 + 30000 0.00049466342 0 0.00049451306 0.49295072 2279.2316 + 31000 0.00056998139 0 0.00056980815 0.53299515 2226.5683 + 32000 0.00057326945 0 0.0005730952 0.56856537 2181.7092 + 33000 0.00044845112 0 0.00044831481 0.59623471 2142.7573 + 34000 0.00059840183 0 0.00059821994 0.61758983 2107.1253 + 35000 0.00075310993 0 0.00075288103 0.63756827 2072.7217 + 36000 0.00053774066 0 0.00053757721 0.66026064 2039.1655 + 37000 0.00030440106 0 0.00030430853 0.69059102 2007.7903 + 38000 0.00034436264 0 0.00034425797 0.72166344 1980.7137 + 39000 0.00039693498 0 0.00039681433 0.74680327 1957.9531 + 40000 0.00035425567 0 0.000354148 0.76604186 1937.3834 + 41000 0.0003094733 0 0.00030937924 0.78323163 1916.7027 + 42000 0.00027259246 0 0.0002725096 0.80315535 1895.0714 + 43000 0.00020659817 0 0.00020653538 0.8274603 1873.5407 + 44000 0.00016023333 0 0.00016018463 0.85418969 1853.8674 + 45000 0.00016111931 0 0.00016107034 0.87913944 1837.1141 + 46000 0.00016130888 0 0.00016125985 0.89921705 1822.7354 + 47000 0.00015755049 0 0.0001575026 0.91653538 1809.0285 + 48000 0.00017794781 0 0.00017789372 0.93582908 1794.7041 + 49000 0.00018878437 0 0.00018872699 0.95775203 1780.032 + 50000 0.0001778042 0 0.00017775016 0.97893714 1765.9439 +Loop time of 77.4487 on 1 procs for 50000 steps with 3290 atoms + +Performance: 278894.354 tau/day, 645.589 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 60.017 | 60.017 | 60.017 | 0.0 | 77.49 +Neigh | 0.47 | 0.47 | 0.47 | 0.0 | 0.61 +Comm | 6.6765 | 6.6765 | 6.6765 | 0.0 | 8.62 +Output | 0.24799 | 0.24799 | 0.24799 | 0.0 | 0.32 +Modify | 8.8677 | 8.8677 | 8.8677 | 0.0 | 11.45 +Other | | 1.17 | | | 1.51 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6295.00 ave 6295 max 6295 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 53729.0 ave 53729 max 53729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 53729 +Ave neighs/atom = 16.331003 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:17 diff --git a/examples/multi/log.30Nov20.granular.intel.4 b/examples/multi/log.30Nov20.granular.intel.4 new file mode 100644 index 0000000000..d53684c596 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi #multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/newton/tri + stencil: half/multi/2d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 11.33 | 11.33 | 11.33 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 + 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 + 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 + 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 + 15000 0.01184269 0 0.01183909 0.028504106 4577.901 + 16000 0.01143291 0 0.011429435 0.033564204 4309.88 + 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 + 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 + 19000 0.010225905 0 0.010222797 0.063669586 3607.6622 + 20000 0.0091390249 0 0.0091362471 0.088165396 3408.567 + 21000 0.0077382016 0 0.0077358496 0.11770473 3227.6936 + 22000 0.0060173113 0 0.0060154823 0.15261992 3064.3873 + 23000 0.0046667554 0 0.004665337 0.19453813 2917.9782 + 24000 0.0040425764 0 0.0040413476 0.24145834 2788.3897 + 25000 0.0031933187 0 0.0031923481 0.28989732 2674.5164 + 26000 0.0021139018 0 0.0021132592 0.33598721 2574.9313 + 27000 0.0017005052 0 0.0016999884 0.37665029 2487.1628 + 28000 0.001443434 0 0.0014429952 0.41572112 2409.3271 + 29000 0.00089885805 0 0.00089858484 0.45343123 2340.2314 + 30000 0.00048558336 0 0.00048543577 0.49175966 2279.2156 + 31000 0.00058132898 0 0.00058115228 0.53236819 2226.2347 + 32000 0.00057751441 0 0.00057733887 0.56915062 2181.2736 + 33000 0.00044720497 0 0.00044706904 0.59696122 2142.5709 + 34000 0.00060927898 0 0.00060909379 0.61734988 2107.128 + 35000 0.00077422577 0 0.00077399045 0.63696024 2072.6004 + 36000 0.00055753008 0 0.00055736062 0.65981839 2038.8237 + 37000 0.0003140158 0 0.00031392035 0.69018918 2007.323 + 38000 0.00034970199 0 0.0003495957 0.72155094 1980.1702 + 39000 0.00041435514 0 0.00041422919 0.7468053 1957.3837 + 40000 0.00037229543 0 0.00037218227 0.76581519 1936.8032 + 41000 0.00031027679 0 0.00031018248 0.78321128 1916.1103 + 42000 0.00026621832 0 0.00026613741 0.80267694 1894.4646 + 43000 0.00020544063 0 0.00020537818 0.82714181 1872.768 + 44000 0.00015635243 0 0.00015630491 0.85496512 1853.0303 + 45000 0.00014985611 0 0.00014981056 0.87924561 1836.4779 + 46000 0.00015645346 0 0.00015640591 0.89896131 1822.2004 + 47000 0.00016007816 0 0.00016002951 0.91662026 1808.4601 + 48000 0.00017439363 0 0.00017434063 0.93565314 1794.1244 + 49000 0.00018647711 0 0.00018642043 0.95733125 1779.401 + 50000 0.00018463414 0 0.00018457802 0.96449755 1765.1506 +Loop time of 22.3987 on 4 procs for 50000 steps with 3290 atoms + +Performance: 964340.770 tau/day, 2232.270 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.5158 | 12.318 | 15.836 | 92.1 | 54.99 +Neigh | 0.092527 | 0.11392 | 0.13595 | 5.6 | 0.51 +Comm | 2.7127 | 6.2337 | 10.096 | 131.0 | 27.83 +Output | 0.088027 | 0.088284 | 0.088812 | 0.1 | 0.39 +Modify | 2.8544 | 3.0435 | 3.2034 | 9.2 | 13.59 +Other | | 0.6017 | | | 2.69 + +Nlocal: 822.500 ave 859 max 785 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 395.750 ave 424 max 368 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 13439.5 ave 14346 max 12017 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 53758 +Ave neighs/atom = 16.339818 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:22 diff --git a/examples/multi/log.30Nov20.granular.old.intel.1 b/examples/multi/log.30Nov20.granular.old.intel.1 new file mode 100644 index 0000000000..ad827423c5 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/old/newton/tri + stencil: half/multi/old/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.75 | 11.75 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 + 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 + 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 + 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 + 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 + 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 + 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 + 18000 0.01100067 0 0.010997326 0.04899206 3825.155 + 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 + 20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658 + 21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002 + 22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986 + 23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014 + 24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113 + 25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604 + 26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564 + 27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379 + 28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461 + 29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308 + 30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316 + 31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683 + 32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093 + 33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574 + 34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254 + 35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217 + 36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654 + 37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901 + 38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136 + 39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531 + 40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834 + 41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027 + 42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714 + 43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408 + 44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677 + 45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144 + 46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355 + 47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285 + 48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043 + 49000 0.00018879338 0 0.000188736 0.95775166 1780.0323 + 50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442 +Loop time of 80.8597 on 1 procs for 50000 steps with 3290 atoms + +Performance: 267129.375 tau/day, 618.355 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 61.524 | 61.524 | 61.524 | 0.0 | 76.09 +Neigh | 2.2021 | 2.2021 | 2.2021 | 0.0 | 2.72 +Comm | 6.748 | 6.748 | 6.748 | 0.0 | 8.35 +Output | 0.25904 | 0.25904 | 0.25904 | 0.0 | 0.32 +Modify | 8.9408 | 8.9408 | 8.9408 | 0.0 | 11.06 +Other | | 1.186 | | | 1.47 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6295.00 ave 6295 max 6295 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 53729.0 ave 53729 max 53729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 53729 +Ave neighs/atom = 16.331003 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:20 diff --git a/examples/multi/log.30Nov20.granular.old.intel.4 b/examples/multi/log.30Nov20.granular.old.intel.4 new file mode 100644 index 0000000000..e41741b536 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (30 Nov 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.5 +Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 +region box block 0 60 0 60 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3600 atoms + create_atoms CPU = 0.001 seconds +change_box all triclinic +Changing box ... + triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) + +# remove two spheres of small particles and add large particles in the voids +region sphere1 sphere 20.0 20.0 0.0 10.0 units box +region sphere2 sphere 60.0 60.0 0.0 10.0 units box +delete_atoms region sphere1 +Deleted 154 atoms, new total = 3446 +delete_atoms region sphere2 +Deleted 158 atoms, new total = 3288 +create_atoms 2 single 20.0 20.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds +create_atoms 2 single 60.0 60.0 0.0 units box +Created 1 atoms + create_atoms CPU = 0.000 seconds + +set type 2 mass 400 +Setting atom values ... + 2 settings made for mass +set type 1 mass 1 +Setting atom values ... + 3288 settings made for mass +set type 2 diameter 20 +Setting atom values ... + 2 settings made for diameter +set type 1 diameter 1 +Setting atom values ... + 3288 settings made for diameter + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi/old +neigh_modify delay 0 +comm_modify mode multi vel yes #multi/reduce + +# colloid potential + +pair_style granular +pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-3 + +dump 1 all custom 1000 dump.granular id x y z radius + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 21 + ghost atom cutoff = 21 + binsize = 1, bins = 85 85 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair granular, perpetual + attributes: half, newton on, size, history + pair build: half/size/multi/old/newton/tri + stencil: half/multi/old/2d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.49 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 + 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 + 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 + 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 + 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 + 6000 0.025856 0 0.025848141 0.021241317 7603.5534 + 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 + 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 + 9000 0.01637016 0 0.016365184 0.020261904 6515.3445 + 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 + 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 + 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 + 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 + 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 + 15000 0.01184269 0 0.01183909 0.028504106 4577.901 + 16000 0.01143291 0 0.011429435 0.033564204 4309.88 + 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 + 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 + 19000 0.010225905 0 0.010222797 0.063669588 3607.6622 + 20000 0.0091390255 0 0.0091362477 0.088165402 3408.567 + 21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936 + 22000 0.00601731 0 0.0060154811 0.15261994 3064.3873 + 23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782 + 24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897 + 25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164 + 26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312 + 27000 0.001700508 0 0.0016999912 0.37665013 2487.1626 + 28000 0.0014434246 0 0.0014429859 0.41572163 2409.327 + 29000 0.00089885063 0 0.00089857742 0.453431 2340.2313 + 30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155 + 31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349 + 32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738 + 33000 0.00044719326 0 0.00044705733 0.59696179 2142.571 + 34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282 + 35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008 + 36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242 + 37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235 + 38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706 + 39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838 + 40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034 + 41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108 + 42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649 + 43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672 + 44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284 + 45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755 + 46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989 + 47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606 + 48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258 + 49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032 + 50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534 +Loop time of 30.9351 on 4 procs for 50000 steps with 3290 atoms + +Performance: 698235.574 tau/day, 1616.286 timesteps/s +89.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.3702 | 12.796 | 16.045 | 84.3 | 41.36 +Neigh | 0.43499 | 0.55158 | 0.64861 | 12.8 | 1.78 +Comm | 10.183 | 13.476 | 16.961 | 83.7 | 43.56 +Output | 0.088474 | 0.088715 | 0.089272 | 0.1 | 0.29 +Modify | 3.0446 | 3.1809 | 3.3227 | 7.4 | 10.28 +Other | | 0.8418 | | | 2.72 + +Nlocal: 822.500 ave 859 max 785 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 3049.75 ave 3089 max 2999 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 13440.5 ave 14459 max 11964 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 53762 +Ave neighs/atom = 16.341033 +Neighbor list builds = 348 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:30 diff --git a/src/comm.cpp b/src/comm.cpp index 84e3b9ad65..542ddfdf10 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -248,6 +248,8 @@ void Comm::init() error->all(FLERR,"Cannot use multi/reduce communication with Newton off"); if (neighbor->any_full()) error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list"); + if (neighbor->style != Neighbor::MULTI) + error->all(FLERR,"Cannot use multi/reduce communication without multi-style neighbor lists"); } }