diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 8a76dca66e..8bfc4ad573 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -108,6 +108,8 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | msst | MSST shock dynamics | +-------------+------------------------------------------------------------------+ +| multi | multi neighboring for systems with large interaction disparities | ++-------------+------------------------------------------------------------------+ | nb3b | use of non-bonded 3-body harmonic pair style | +-------------+------------------------------------------------------------------+ | neb | nudged elastic band (NEB) calculation for barrier finding | diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 864c544fed..4e9e6325c1 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -11,13 +11,17 @@ Syntax comm_modify keyword value ... * zero or more keyword/value pairs may be appended -* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel* +* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel* .. parsed-literal:: - *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances + *mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances *cutoff* value = Rcut (distance units) = communicate atoms from this far away - *cutoff/multi* type value + *cutoff/multi* collection value + collection = atom collection or collection range (supports asterisk notation) + value = Rcut (distance units) = communicate atoms for selected types from this far away + *reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style + *cutoff/multi/old* type value type = atom type or type range (supports asterisk notation) value = Rcut (distance units) = communicate atoms for selected types from this far away *group* value = group-ID = only communicate atoms in the group @@ -28,7 +32,7 @@ Examples .. code-block:: LAMMPS - comm_modify mode multi + comm_modify mode multi reduce/multi comm_modify mode multi group solvent comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 comm_modify vel yes @@ -62,12 +66,18 @@ sub-domain. The distance is by default the maximum of the neighbor cutoff across all atom type pairs. 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 +widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can +be faster. In *multi*, each atom is assigned to a collection which should +correspond to a set of atoms with similar interaction cutoffs. +In this case, each atom collection is assigned its own distance cutoff for communication purposes, and fewer atoms will be -communicated. See the :doc:`neighbor multi ` command for a -neighbor list construction option that may also be beneficial for -simulations of this kind. +communicated. in *multi/old*, a similar technique is used but atoms +are grouped by atom type. See the :doc:`neighbor multi ` and +:doc:`neighbor multi/old ` commands for +neighbor list construction options that may also be beneficial for +simulations of this kind. The *multi* communiction mode is only compatable +with the *multi* neighbor style. The *multi/old* communication mode is compatble +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 @@ -87,12 +97,26 @@ warning is printed, if this bond based estimate is larger than the communication cutoff used. The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to -communication mode *multi* instead. Since in this case the communication -cutoffs are determined per atom type, a type specifier is needed and -cutoff for one or multiple types can be extended. Also ranges of types -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. +communication mode *multi* instead. Since the communication +cutoffs are determined per atom collections, a collection specifier is needed and +cutoff for one or multiple collections can be extended. Also ranges of collections +using the usual asterisk notation can be given. +Collections are indexed from 1 to N where N is the total number of collections. +Note that the arguments for *cutoff/multi* are parsed right before each +simulation to account for potential changes in the number of collections. +Custom cutoffs are preserved between runs but if collections are redefined, +one may want to respecify communication cutoffs. +For granular pair styles,the default cutoff is set to the sum of the +current maximum atomic radii for each collection. +The *cutoff/multi/old* option is similar to *cutoff/multi* except it +operates on atom types as opposed to collections. + +The *reduce/multi* option applies to *multi* and sets the communication +cutoff for a particle equal to the maximum interaction distance between particles +in the same collection. This reduces the number of +ghost atoms that need to be communicated. This method is only compatible with the +*multi* neighbor style and requires a half neighbor list 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..208eca22ec 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 *collection/type* or *collection/interval* *delay* value = N N = delay building until this many steps since last build *every* value = M @@ -47,6 +47,12 @@ Syntax N = max number of neighbors of one atom *binsize* value = size size = bin size for neighbor list construction (distance units) + *collection/type* values = N arg1 ... argN + N = number of custom collections + arg = N separate lists of types (see below) + *collection/interval* values = N arg1 ... argN + N = number of custom collections + arg = N separate cutoffs for intervals (see below) Examples """""""" @@ -58,6 +64,8 @@ Examples neigh_modify exclude group frozen frozen check no neigh_modify exclude group residue1 chain3 neigh_modify exclude molecule/intra rigid + neigh_modify collection/type 2 1*2,5 3*4 + neigh_modify collection/interval 2 1.0 10.0 Description """"""""""" @@ -188,8 +196,9 @@ atom can have. The *binsize* option allows you to specify what size of bins will be used in neighbor list construction to sort and find neighboring atoms. By default, for :doc:`neighbor style bin `, LAMMPS uses bins -that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, the bins are 1/2 the size of the minimum pair -cutoff. Typically these are good values for minimizing the time for +that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi `, +the bins are 1/2 the size of the collection interaction cutoff. +Typically these are good values for minimizing the time for neighbor list construction. This setting overrides the default. If you make it too big, there is little overhead due to looping over bins, but more atoms are checked. If you make it too @@ -197,6 +206,30 @@ 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 *collection/type* option allows you to define collections of atom +types, used by the *multi* neighbor mode. By grouping atom types with +similar physical size or interaction cutoff lengths, one may be able +to improve performance by reducing +overhead. You must first specify the number of collections N to be +defined followed by N lists of types. Each list consists of a series of type +ranges separated by commas. 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 M = the number of atom types, then an asterisk with no numeric +values means all types from 1 to M. A leading asterisk means all types +from 1 to n (inclusive). A trailing asterisk means all types from n to M +(inclusive). A middle asterisk means all types from m to n (inclusive). +Note that all atom types must be included in exactly one of the N collections. + +The *collection/interval* option provides a similar capability. +This command allows a user to define collections by specifying a +series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals +based on their type-dependent cutoffs or their finite size. +You must first specify the number of collections N to be +defined followed by N values representing the upper cutoff of each interval. +This command is particularly useful for granular pairstyles where the interaction distance +of particles depends on their radius and may not depend on their atom type. + Restrictions """""""""""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 98ee0d0b6a..1b10ec8998 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* +* style = *bin* or *nsq* or *multi* or *multi/old* Examples """""""" @@ -55,14 +55,31 @@ 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 collections of different sized particles, where +"size" may mean the physical size of the particle or its cutoff +distance for interacting with other 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, each atom type defines a separate +collection of particles. For systems where two or more atom types +have the same size (either physical size or cutoff distance), the +definition of collections can be customized, which can result in less +overhead and faster performance. See the :doc:`neigh_modify ` +command for how to define custom collections. Whether the collection +definition is customized or not, also see the +:doc:`comm_modify mode multi ` command for communication +options that further improve performance in a manner consistent with +neighbor style multi. + +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. For now we are keeping the old option in case there are use cases +where multi/old outperforms the new multi style. + The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are @@ -90,3 +107,9 @@ Default | 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm | 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm | + +---------- + +.. _bytype-Shire: + +**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020). diff --git a/examples/granregion/in.granregion.funnel b/examples/granregion/in.granregion.funnel index 63e79a7114..ef74ce5109 100644 --- a/examples/granregion/in.granregion.funnel +++ b/examples/granregion/in.granregion.funnel @@ -86,7 +86,7 @@ pair_style gran/hertz/history & ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 pair_coeff * * -neighbor ${skin} bin +neighbor ${skin} multi thermo ${logfreq} comm_style brick diff --git a/examples/granregion/in.granregion.mixer b/examples/granregion/in.granregion.mixer index f9a9d04cbe..383f51f074 100644 --- a/examples/granregion/in.granregion.mixer +++ b/examples/granregion/in.granregion.mixer @@ -49,7 +49,7 @@ pair_style gran/hertz/history & ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 pair_coeff * * -neighbor ${skin} bin +neighbor ${skin} multi thermo ${logfreq} comm_style brick diff --git a/examples/multi/data.powerlaw b/examples/multi/data.powerlaw new file mode 100644 index 0000000000..2ce54cf4a6 --- /dev/null +++ b/examples/multi/data.powerlaw @@ -0,0 +1,20015 @@ +LAMMPS data file via write_data, version 24 Dec 2020, timestep = 400000 + +10000 atoms +1 atom types + +9.95143358025075 331.8139610404791 xlo xhi +9.95143358025075 331.8139610404791 ylo yhi +0 1 zlo zhi +0 0 0 xy xz yz + +Atoms # sphere + +16 1 27.0148 1 21.578661820808055 19.894003593559244 0 0 0 0 +6528 1 1.2402 1 40.11018907053191 29.030167715273407 0 0 1 0 +8976 1 1.0539 1 36.97821790225197 19.05186774766389 0 0 0 0 +168 1 7.3782 1 49.35369389791803 25.320840580930078 0 0 0 0 +194 1 6.9422 1 37.8963499906581 24.060540533134542 0 0 0 0 +208 1 6.6527 1 30.20573931579442 36.96891799058152 0 0 0 0 +336 1 5.417 1 42.81946909263247 31.018306090834393 0 0 0 0 +346 1 5.3618 1 17.904145680770682 40.365474113094464 0 0 0 0 +364 1 5.1987 1 45.47784864569917 20.574121185710485 0 0 0 0 +412 1 4.8776 1 22.52913680808026 42.40500703613544 0 0 0 0 +439 1 4.6882 1 35.32921707623989 30.55316138336846 0 0 0 0 +511 1 4.3207 1 43.71579096264905 26.313752950912164 0 0 0 0 +527 1 4.2767 1 40.53481826871412 15.977906579131261 0 0 0 0 +529 1 4.2701 1 14.88365052239063 45.532953698817934 0 0 0 0 +543 1 4.2317 1 22.663739581205114 36.42482542930276 0 0 0 0 +5300 1 1.3759 1 11.61412862355682 32.093048107213875 0 1 0 0 +569 1 4.1329 1 11.928958139921995 34.823339484175335 0 0 0 0 +4350 1 1.5228 1 15.212423557099871 48.57106966637227 0 1 0 0 +629 1 3.9339 1 45.09696092099179 35.7722795000036 0 0 0 0 +3990 1 1.5888 1 58.92019192272275 14.95895467917481 0 0 0 0 +675 1 3.8345 1 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-0.0009271690904041339 0.00016359386043164603 0 0 0 2.52838609278567e-05 +5175 -0.0008138196366132594 -0.0001245882968805323 0 0 0 -0.00011990448597305236 +812 -0.0008136999002096582 -0.00032793352272391974 0 0 0 -0.00011465393762998146 +6366 -0.0009225928433018489 0.00012281633743967574 0 0 0 2.3512139399119615e-05 +2359 -0.000851845164590352 0.00013670406898960903 0 0 0 -1.5656583914975637e-05 +5892 -0.0009292154524757727 0.00010987499809583548 0 0 0 -4.494971590096285e-06 +4914 -0.0008170718336393827 -0.0002694197948090762 0 0 0 4.855984716083199e-05 +2232 -0.0013962668408131758 0.0006100496749283238 0 0 0 2.4429236673886335e-06 +6849 -0.0009307674486236736 0.00014548193739797815 0 0 0 -3.382403357989851e-05 +6389 -0.0008276884913987117 -0.0006715424559836795 0 0 0 -0.00017229263836352125 +7592 -0.0008829184044931385 0.00010320778283078764 0 0 0 7.251548574276341e-05 +72 -0.0009328033481941555 0.00016169037482396788 0 0 0 5.611202530371956e-06 +6095 -0.0009074545749811463 0.00012699997222705476 0 0 0 3.797079172498021e-07 +4230 -0.0003945759264238711 0.000354641717450242 0 0 0 -0.000203591873846727 +2606 -0.0008299614938439482 0.00044376074287287397 0 0 0 -2.3080980932453262e-05 +801 -0.0008849997736873634 0.00011181647550225466 0 0 0 -9.806674088218455e-06 +4964 -0.0007701363964966764 0.0004493582278037278 0 0 0 -1.1639819837550187e-05 +6706 -0.000627510244325849 0.00037107718739488817 0 0 0 -0.0002045233207024528 +8919 -0.0008669103943182013 0.0001238206988024208 0 0 0 3.0004565505708964e-05 +5744 -0.00035081420995634844 -0.00019682849701139167 0 0 0 4.641181980210418e-06 +1412 -0.0008667102067001524 -0.00031258100964681994 0 0 0 -0.00021630116013899762 +7166 -0.0012295480431946774 0.0004821607704207658 0 0 0 0.0004508869875806334 +8125 -0.0008814707706954985 9.472619375360002e-05 0 0 0 -1.6727383622794183e-05 +8441 -0.0002449245374533217 -0.0004064470171835513 0 0 0 -5.438234289347048e-05 +6976 -0.00026782590492296373 -0.0003596810748548633 0 0 0 -7.725564834869343e-06 +6337 -0.0010501585618178401 3.1637071442245886e-05 0 0 0 0.0005189063800513128 +7189 -0.0010027915591139453 0.00023723368847990806 0 0 0 -2.1267115444176427e-05 +2680 -0.00030891216853277394 -0.00020457606529057616 0 0 0 -4.82731205087499e-05 +6160 -0.0007557869392639718 -0.00015627695707974944 0 0 0 -2.465884924693401e-05 +535 -0.0008767474296707425 0.00012151744175138143 0 0 0 1.245320689560073e-05 +8425 -0.0007512233785204506 0.0005405466387555643 0 0 0 -0.0001045579395697344 diff --git a/examples/multi/in.colloid b/examples/multi/in.colloid new file mode 100644 index 0000000000..9f9883f61a --- /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 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old + +# 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 100 + +timestep 0.005 + +run 2000 diff --git a/examples/multi/in.granular b/examples/multi/in.granular new file mode 100644 index 0000000000..468d0dcbf1 --- /dev/null +++ b/examples/multi/in.granular @@ -0,0 +1,50 @@ +# 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 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old + +# granular 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 + +thermo_style custom step temp epair etotal press vol +thermo 100 + +timestep 0.005 + +run 2000 diff --git a/examples/multi/in.powerlaw b/examples/multi/in.powerlaw new file mode 100644 index 0000000000..b69e6a56a3 --- /dev/null +++ b/examples/multi/in.powerlaw @@ -0,0 +1,33 @@ +# Shear power-law distributed granular particles + +units lj +atom_style sphere +dimension 2 +read_data data.powerlaw +change_box all triclinic + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-4 + +# dump 1 all custom 20000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 100 + +timestep 0.005 + +run 1000 diff --git a/examples/multi/log.30Nov20.colloid.intel.1 b/examples/multi/log.30Nov20.colloid.intel.1 new file mode 100644 index 0000000000..5dcb8c3bf1 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + 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 #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old + +# 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) = 4.385 | 4.385 | 4.385 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 19.7532 on 1 procs for 50000 steps with 3026 atoms + +Performance: 1093493.133 tau/day, 2531.234 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 | 10.789 | 10.789 | 10.789 | 0.0 | 54.62 +Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59 +Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70 +Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01 +Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11 +Other | | 0.7856 | | | 3.98 + +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: 0:00:19 diff --git a/examples/multi/log.30Nov20.colloid.intel.4 b/examples/multi/log.30Nov20.colloid.intel.4 new file mode 100644 index 0000000000..906400df66 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + 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 #multi/old +neigh_modify delay 0 collection/type 2 1*4 5 +comm_modify mode multi reduce/multi #multi/old + +# 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) = 4.327 | 4.329 | 4.330 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 6.98615 on 4 procs for 50000 steps with 3026 atoms + +Performance: 3091831.080 tau/day, 7157.016 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 | 2.2795 | 2.5856 | 2.9414 | 17.4 | 37.01 +Neigh | 0.62273 | 0.70156 | 0.76736 | 7.4 | 10.04 +Comm | 1.0765 | 1.4945 | 1.8884 | 28.6 | 21.39 +Output | 0.00076496 | 0.0008953 | 0.0012832 | 0.0 | 0.01 +Modify | 1.718 | 1.7755 | 1.827 | 3.7 | 25.41 +Other | | 0.4281 | | | 6.13 + +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..70c7db2afd --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.1 @@ -0,0 +1,183 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + 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 #multi +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi/old #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) = 4.496 | 4.496 | 4.496 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 28.5339 on 1 procs for 50000 steps with 3026 atoms + +Performance: 756994.490 tau/day, 1752.302 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 | 10.918 | 10.918 | 10.918 | 0.0 | 38.26 +Neigh | 10.375 | 10.375 | 10.375 | 0.0 | 36.36 +Comm | 1.2856 | 1.2856 | 1.2856 | 0.0 | 4.51 +Output | 0.0010955 | 0.0010955 | 0.0010955 | 0.0 | 0.00 +Modify | 5.0132 | 5.0132 | 5.0132 | 0.0 | 17.57 +Other | | 0.9412 | | | 3.30 + +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: 0:00:28 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..6d159d9405 --- /dev/null +++ b/examples/multi/log.30Nov20.colloid.old.intel.4 @@ -0,0 +1,183 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + 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 #multi +neigh_modify delay 0 #multi/custom 2 1*4 5 +comm_modify mode multi/old #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) = 4.404 | 4.406 | 4.410 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 10.7578 on 4 procs for 50000 steps with 3026 atoms + +Performance: 2007847.166 tau/day, 4647.794 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 | 2.3814 | 2.6878 | 2.9507 | 15.2 | 24.98 +Neigh | 2.3959 | 2.6615 | 2.9677 | 16.2 | 24.74 +Comm | 2.4113 | 2.9894 | 3.5621 | 29.6 | 27.79 +Output | 0.00077024 | 0.00091029 | 0.0012971 | 0.0 | 0.01 +Modify | 1.7966 | 1.8497 | 1.907 | 3.8 | 17.19 +Other | | 0.5686 | | | 5.29 + +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: 0:00:10 diff --git a/examples/multi/log.30Nov20.granular.intel.1 b/examples/multi/log.30Nov20.granular.intel.1 new file mode 100644 index 0000000000..06d02b8531 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + 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 #multi/old +neigh_modify delay 0 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old + +# 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) = 10.29 | 10.29 | 10.29 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32604952 0 0.32595042 0.17341597 7862.5013 + 2000 0.12631038 0 0.12627198 0.069126477 8216.6956 + 3000 0.069351715 0 0.069330635 0.040799593 8344.1931 + 4000 0.045023755 0 0.04501007 0.029184795 8239.1832 + 5000 0.032735149 0 0.0327252 0.025640841 7943.5691 + 6000 0.026205227 0 0.026197262 0.021206924 7617.6672 + 7000 0.02165475 0 0.021648168 0.018789365 7255.2897 + 8000 0.018299317 0 0.018293755 0.019272158 6887.3386 + 9000 0.016283763 0 0.016278813 0.020434892 6524.0274 + 10000 0.015148918 0 0.015144313 0.021650465 6168.4941 + 11000 0.014180465 0 0.014176155 0.022320009 5823.98 + 12000 0.013505744 0 0.013501639 0.023978674 5492.4853 + 13000 0.013009585 0 0.01300563 0.024391329 5175.7455 + 14000 0.012494373 0 0.012490576 0.027331543 4874.3212 + 15000 0.012057669 0 0.012054004 0.030561239 4589.518 + 16000 0.011510988 0 0.01150749 0.034613772 4321.1694 + 17000 0.011198594 0 0.01119519 0.042263536 4070.0115 + 18000 0.010978603 0 0.010975266 0.053637275 3836.0304 + 19000 0.010768789 0 0.010765516 0.069472547 3619.75 + 20000 0.0102256 0 0.010222492 0.085332898 3420.2738 + 21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821 + 22000 0.006565581 0 0.0065635854 0.14807426 3071.3012 + 23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162 + 24000 0.0040345997 0 0.0040333734 0.237983 2792.2658 + 25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475 + 26000 0.0024157863 0 0.002415052 0.33851944 2578.4972 + 27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264 + 28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871 + 29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208 + 30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452 + 31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456 + 32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224 + 33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345 + 34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045 + 35000 0.00075804791 0 0.0007578175 0.6359631 2072.525 + 36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907 + 37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831 + 38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441 + 39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127 + 40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006 + 41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939 + 42000 0.00025394755 0 0.00025387036 0.80529272 1893.064 + 43000 0.00021067821 0 0.00021061418 0.82962095 1872.365 + 44000 0.00017927684 0 0.00017922235 0.85522899 1853.531 + 45000 0.0001464225 0 0.000146378 0.87925998 1837.2423 + 46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227 + 47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605 + 48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227 + 49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811 + 50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507 +Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms + +Performance: 393345.914 tau/day, 910.523 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 | 44.691 | 44.691 | 44.691 | 0.0 | 81.38 +Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39 +Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37 +Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00 +Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43 +Other | | 0.7794 | | | 1.42 + +Nlocal: 3290.00 ave 3290 max 3290 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 525.000 ave 525 max 525 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 26732.0 ave 26732 max 26732 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 26732 +Ave neighs/atom = 8.1252280 +Neighbor list builds = 342 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:54 diff --git a/examples/multi/log.30Nov20.granular.intel.4 b/examples/multi/log.30Nov20.granular.intel.4 new file mode 100644 index 0000000000..3aa05d79c7 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + 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 collection/interval 2 1 20 +comm_modify mode multi vel yes reduce/multi #multi/old + +# 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) = 10.09 | 10.10 | 10.10 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 0 1.4395623 0.66837658 7200 + 1000 0.32605303 0 0.32595393 0.17341558 7862.5037 + 2000 0.12631567 0 0.12627728 0.069188881 8216.7174 + 3000 0.069373812 0 0.069352726 0.040740832 8344.2982 + 4000 0.045084633 0 0.045070929 0.029328609 8239.3656 + 5000 0.032681746 0 0.032671813 0.025416741 7943.7831 + 6000 0.026301239 0 0.026293245 0.021418793 7617.8426 + 7000 0.021666723 0 0.021660138 0.018961011 7255.9338 + 8000 0.018141337 0 0.018135823 0.019306113 6887.4963 + 9000 0.015922309 0 0.015917469 0.020033398 6524.016 + 10000 0.014744547 0 0.014740066 0.020959503 6168.1945 + 11000 0.013872852 0 0.013868636 0.021708943 5823.3153 + 12000 0.013321594 0 0.013317545 0.02332141 5491.4979 + 13000 0.01269964 0 0.012695779 0.024796428 5174.6263 + 14000 0.01227055 0 0.012266821 0.027785072 4873.4516 + 15000 0.012120508 0 0.012116824 0.029656636 4588.8603 + 16000 0.011612027 0 0.011608498 0.034695109 4320.4674 + 17000 0.011216697 0 0.011213288 0.042746966 4069.4275 + 18000 0.010950166 0 0.010946838 0.053528994 3835.5439 + 19000 0.010887635 0 0.010884325 0.069684492 3619.562 + 20000 0.010563449 0 0.010560238 0.08654561 3420.2636 + 21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408 + 22000 0.006929086 0 0.0069269799 0.15018917 3072.0438 + 23000 0.0052239156 0 0.0052223277 0.19067193 2924.441 + 24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426 + 25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912 + 26000 0.002549072 0 0.0025482972 0.33567824 2579.3738 + 27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502 + 28000 0.001772982 0 0.0017724431 0.41079958 2411.9111 + 29000 0.001127719 0 0.0011273762 0.44752241 2341.1888 + 30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611 + 31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328 + 32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674 + 33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696 + 34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504 + 35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077 + 36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251 + 37000 0.0003540723 0 0.00035396468 0.68803919 2005.497 + 38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345 + 39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979 + 40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695 + 41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326 + 42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474 + 43000 0.00021545017 0 0.00021538468 0.82803644 1872.073 + 44000 0.00017293257 0 0.00017288 0.85436769 1852.6548 + 45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087 + 46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977 + 47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913 + 48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082 + 49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875 + 50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247 +Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms + +Performance: 1217551.996 tau/day, 2818.407 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21 +Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31 +Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10 +Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01 +Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32 +Other | | 0.5419 | | | 3.05 + +Nlocal: 822.500 ave 897 max 779 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 190.500 ave 211 max 179 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 6665.75 ave 7329 max 6104 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 26663 +Ave neighs/atom = 8.1042553 +Neighbor list builds = 342 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:17 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..f928621824 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.1 @@ -0,0 +1,175 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + 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 #multi +neigh_modify delay 0 #collection/interval 2 1 20 +comm_modify mode multi/old vel yes #reduce/multi + +# 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) = 10.38 | 10.38 | 10.38 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 74.6636 on 1 procs for 50000 steps with 3290 atoms + +Performance: 289297.713 tau/day, 669.671 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 | 56.696 | 56.696 | 56.696 | 0.0 | 75.93 +Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98 +Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29 +Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00 +Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29 +Other | | 1.125 | | | 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: 0:01:14 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..507de22119 --- /dev/null +++ b/examples/multi/log.30Nov20.granular.old.intel.4 @@ -0,0 +1,175 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + 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 = 0.063 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 #multi +neigh_modify delay 0 #collection/interval 2 1 20 +comm_modify mode multi/old vel yes #reduce/multi + +# 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) = 10.20 | 10.20 | 10.20 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 30.1448 on 4 procs for 50000 steps with 3290 atoms + +Performance: 716540.413 tau/day, 1658.658 timesteps/s +90.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.7565 | 12.704 | 16.036 | 89.8 | 42.14 +Neigh | 0.4494 | 0.56436 | 0.66263 | 11.8 | 1.87 +Comm | 9.5962 | 12.989 | 17.006 | 90.8 | 43.09 +Output | 0.00088467 | 0.0011022 | 0.0015811 | 0.9 | 0.00 +Modify | 2.9732 | 3.0944 | 3.2463 | 7.0 | 10.27 +Other | | 0.7918 | | | 2.63 + +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/examples/multi/log.30Nov20.powerlaw.intel.1 b/examples/multi/log.30Nov20.powerlaw.intel.1 new file mode 100644 index 0000000000..d0ed6e2685 --- /dev/null +++ b/examples/multi/log.30Nov20.powerlaw.intel.1 @@ -0,0 +1,291 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Shear power-law distributed granular particles + +units lj +atom_style sphere +dimension 2 +read_data data.powerlaw +Reading data file ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10000 atoms + reading velocities ... + 10000 velocities + read_data CPU = 0.027 seconds +change_box all triclinic +Changing box ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-4 + +# dump 1 all custom 20000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 200000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 164.7888 + ghost atom cutoff = 164.7888 + binsize = 82.3944, bins = 4 4 1 + 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) = 14.77 | 14.77 | 14.77 Mbytes +Step Temp E_pair TotEng Press Volume Pxy + 0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917 + 1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806 + 2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933 + 3000 0.00022105227 0 0.00022103017 0.58295464 103595.49 -0.011327442 + 4000 0.00020888366 0 0.00020886277 0.5826542 103595.49 -0.014147424 + 5000 0.00019912663 0 0.00019910672 0.58175837 103595.49 -0.015685634 + 6000 0.0001989441 0 0.00019892421 0.58170841 103595.49 -0.017379973 + 7000 0.00019307783 0 0.00019305852 0.58133913 103595.49 -0.019556709 + 8000 0.00018132444 0 0.00018130631 0.58134077 103595.49 -0.021609399 + 9000 0.00017909088 0 0.00017907297 0.58117179 103595.49 -0.023603514 + 10000 0.00018391928 0 0.00018390089 0.58070675 103595.49 -0.026026784 + 11000 0.00018985439 0 0.00018983541 0.58006086 103595.49 -0.028574238 + 12000 0.00018903569 0 0.00018901678 0.5794232 103595.49 -0.031151884 + 13000 0.00019070382 0 0.00019068475 0.57890243 103595.49 -0.033469404 + 14000 0.00019371625 0 0.00019369688 0.5787389 103595.49 -0.035646526 + 15000 0.00019833475 0 0.00019831492 0.57883166 103595.49 -0.037709788 + 16000 0.0002011729 0 0.00020115278 0.57875606 103595.49 -0.039452453 + 17000 0.00020285197 0 0.00020283169 0.5786311 103595.49 -0.040960671 + 18000 0.00020319174 0 0.00020317142 0.57842387 103595.49 -0.042257072 + 19000 0.00020290253 0 0.00020288224 0.57795042 103595.49 -0.043364149 + 20000 0.00020509848 0 0.00020507797 0.5771478 103595.49 -0.044392259 + 21000 0.00021803258 0 0.00021801078 0.57569003 103595.49 -0.044749043 + 22000 0.00020751217 0 0.00020749141 0.57477071 103595.49 -0.045719593 + 23000 0.00022053275 0 0.0002205107 0.57409228 103595.49 -0.047332146 + 24000 0.00022689646 0 0.00022687377 0.57325004 103595.49 -0.04871759 + 25000 0.00025224804 0 0.00025222282 0.57283712 103595.49 -0.050254871 + 26000 0.00025343198 0 0.00025340664 0.57238659 103595.49 -0.051604284 + 27000 0.00026689801 0 0.00026687132 0.57221042 103595.49 -0.052915257 + 28000 0.00027867954 0 0.00027865167 0.57197974 103595.49 -0.053832129 + 29000 0.00028697929 0 0.00028695059 0.57177264 103595.49 -0.054693121 + 30000 0.00028857612 0 0.00028854727 0.57145453 103595.49 -0.055559611 + 31000 0.00029228405 0 0.00029225482 0.5711044 103595.49 -0.056492699 + 32000 0.00029648627 0 0.00029645663 0.57060211 103595.49 -0.05729896 + 33000 0.00030524162 0 0.00030521109 0.57002519 103595.49 -0.058201322 + 34000 0.00031725644 0 0.00031722472 0.56920654 103595.49 -0.059128438 + 35000 0.00032273791 0 0.00032270564 0.56844677 103595.49 -0.060009671 + 36000 0.00033013013 0 0.00033009712 0.56795943 103595.49 -0.061074282 + 37000 0.00033942153 0 0.00033938759 0.56749208 103595.49 -0.062058531 + 38000 0.00035141528 0 0.00035138014 0.56682741 103595.49 -0.062953956 + 39000 0.00036126777 0 0.00036123164 0.56655193 103595.49 -0.063757684 + 40000 0.00037765934 0 0.00037762157 0.5661991 103595.49 -0.064535541 + 41000 0.00040834365 0 0.00040830281 0.56554085 103595.49 -0.064688281 + 42000 0.00042857233 0 0.00042852948 0.56474014 103595.49 -0.065262664 + 43000 0.00042692021 0 0.00042687752 0.56362013 103595.49 -0.065276794 + 44000 0.00040298912 0 0.00040294882 0.5631005 103595.49 -0.065626396 + 45000 0.00040947381 0 0.00040943286 0.56291946 103595.49 -0.066167734 + 46000 0.00040202686 0 0.00040198666 0.56273846 103595.49 -0.066543782 + 47000 0.00038914356 0 0.00038910465 0.56265937 103595.49 -0.067359923 + 48000 0.00038429737 0 0.00038425894 0.56274908 103595.49 -0.068231096 + 49000 0.00036912968 0 0.00036909277 0.56261623 103595.49 -0.068791569 + 50000 0.00035203094 0 0.00035199574 0.56257856 103595.49 -0.069298217 + 51000 0.00034403223 0 0.00034399783 0.56236537 103595.49 -0.070273225 + 52000 0.00034132431 0 0.00034129018 0.56220555 103595.49 -0.071740344 + 53000 0.000335692 0 0.00033565843 0.56194913 103595.49 -0.072834415 + 54000 0.00033048196 0 0.00033044891 0.56231491 103595.49 -0.073996938 + 55000 0.00032751145 0 0.00032747869 0.56225025 103595.49 -0.07506664 + 56000 0.00032696951 0 0.00032693682 0.56285506 103595.49 -0.076445354 + 57000 0.00033158698 0 0.00033155382 0.56354729 103595.49 -0.077682996 + 58000 0.00034300009 0 0.00034296579 0.56416964 103595.49 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103595.49 -0.085693663 + 73000 0.00032328895 0 0.00032325662 0.5629287 103595.49 -0.086119464 + 74000 0.00032650113 0 0.00032646848 0.56306166 103595.49 -0.087182721 + 75000 0.00034303222 0 0.00034299792 0.56219559 103595.49 -0.086604025 + 76000 0.00033786129 0 0.0003378275 0.56188071 103595.49 -0.086852177 + 77000 0.00033559735 0 0.00033556379 0.5619155 103595.49 -0.08689764 + 78000 0.00032579863 0 0.00032576605 0.56177059 103595.49 -0.087109469 + 79000 0.00031610815 0 0.00031607654 0.56160391 103595.49 -0.087250861 + 80000 0.00031246546 0 0.00031243422 0.56181676 103595.49 -0.087117648 + 81000 0.00029392131 0 0.00029389192 0.56205441 103595.49 -0.087601617 + 82000 0.00029624453 0 0.00029621491 0.56285229 103595.49 -0.08824145 + 83000 0.00030538821 0 0.00030535767 0.5627754 103595.49 -0.088318188 + 84000 0.00029587833 0 0.00029584874 0.56267246 103595.49 -0.08930338 + 85000 0.00030551128 0 0.00030548073 0.56251282 103595.49 -0.0897211 + 86000 0.00030000969 0 0.00029997969 0.56249642 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103595.49 -0.093871701 + 101000 0.00042149444 0 0.00042145229 0.56424332 103595.49 -0.094001873 + 102000 0.0004580706 0 0.0004580248 0.56378535 103595.49 -0.093786943 + 103000 0.00046113464 0 0.00046108853 0.56428549 103595.49 -0.093463429 + 104000 0.00047583409 0 0.00047578651 0.5645355 103595.49 -0.093225615 + 105000 0.00048367276 0 0.00048362439 0.56469488 103595.49 -0.092935582 + 106000 0.00046931008 0 0.00046926315 0.56464923 103595.49 -0.09282958 + 107000 0.00046460766 0 0.00046456119 0.56502528 103595.49 -0.093077749 + 108000 0.00046398187 0 0.00046393547 0.56532911 103595.49 -0.09321949 + 109000 0.00047530523 0 0.0004752577 0.56561281 103595.49 -0.093217991 + 110000 0.00048531886 0 0.00048527033 0.56549262 103595.49 -0.092956034 + 111000 0.00049659003 0 0.00049654038 0.56507505 103595.49 -0.092554122 + 112000 0.00050113619 0 0.00050108607 0.56528891 103595.49 -0.092227508 + 113000 0.0005138896 0 0.00051383821 0.56550655 103595.49 -0.092096556 + 114000 0.00052560295 0 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0.00083332727 0.55476794 103595.49 -0.094519882 + 170000 0.00077835092 0 0.00077827308 0.55516626 103595.49 -0.094843673 + 171000 0.00074843733 0 0.00074836249 0.55417469 103595.49 -0.094731356 + 172000 0.0007425125 0 0.00074243825 0.55431854 103595.49 -0.095174333 + 173000 0.00074144093 0 0.00074136678 0.55429464 103595.49 -0.094982598 + 174000 0.00072375323 0 0.00072368086 0.55421045 103595.49 -0.09489531 + 175000 0.0007270779 0 0.00072700519 0.55413607 103595.49 -0.094197685 + 176000 0.00071114682 0 0.00071107571 0.55342226 103595.49 -0.093083865 + 177000 0.00069325125 0 0.00069318193 0.55441386 103595.49 -0.093289572 + 178000 0.00067686202 0 0.00067679434 0.55504892 103595.49 -0.093512587 + 179000 0.00068326039 0 0.00068319206 0.55519365 103595.49 -0.093974329 + 180000 0.00075070045 0 0.00075062538 0.55415541 103595.49 -0.09327459 + 181000 0.00077670344 0 0.00077662577 0.55328725 103595.49 -0.092373689 + 182000 0.00077422781 0 0.00077415038 0.553131 103595.49 -0.092353979 + 183000 0.00080250542 0 0.00080242517 0.5519122 103595.49 -0.091897169 + 184000 0.00081235214 0 0.00081227091 0.55172769 103595.49 -0.091906209 + 185000 0.00078879443 0 0.00078871555 0.55145488 103595.49 -0.091198506 + 186000 0.00078497746 0 0.00078489896 0.55202944 103595.49 -0.091674987 + 187000 0.00079483049 0 0.000794751 0.55278073 103595.49 -0.092508295 + 188000 0.00079056756 0 0.0007904885 0.55362903 103595.49 -0.092801369 + 189000 0.00079162262 0 0.00079154346 0.55429061 103595.49 -0.092964781 + 190000 0.00078121133 0 0.00078113321 0.55386716 103595.49 -0.092689851 + 191000 0.00076574893 0 0.00076567235 0.5546533 103595.49 -0.093414672 + 192000 0.00076215201 0 0.0007620758 0.55503049 103595.49 -0.093986391 + 193000 0.00075652635 0 0.0007564507 0.55477696 103595.49 -0.094417347 + 194000 0.00075725781 0 0.00075718208 0.55457687 103595.49 -0.094241721 + 195000 0.0007434693 0 0.00074339496 0.55471575 103595.49 -0.094102015 + 196000 0.00073792493 0 0.00073785114 0.55463671 103595.49 -0.094452279 + 197000 0.00074673445 0 0.00074665978 0.55459327 103595.49 -0.09463863 + 198000 0.00072734835 0 0.00072727561 0.55514628 103595.49 -0.094622434 + 199000 0.00071846919 0 0.00071839734 0.55501969 103595.49 -0.094414887 + 200000 0.00072384651 0 0.00072377412 0.55533335 103595.49 -0.094159469 +Loop time of 443.321 on 1 procs for 200000 steps with 10000 atoms + +Performance: 194892.839 tau/day, 451.141 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 | 362.28 | 362.28 | 362.28 | 0.0 | 81.72 +Neigh | 1.737 | 1.737 | 1.737 | 0.0 | 0.39 +Comm | 5.0082 | 5.0082 | 5.0082 | 0.0 | 1.13 +Output | 0.01774 | 0.01774 | 0.01774 | 0.0 | 0.00 +Modify | 64.992 | 64.992 | 64.992 | 0.0 | 14.66 +Other | | 9.286 | | | 2.09 + +Nlocal: 10000.0 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 487.000 ave 487 max 487 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 34427.0 ave 34427 max 34427 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 34427 +Ave neighs/atom = 3.4427000 +Neighbor list builds = 244 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:07:23 diff --git a/examples/multi/log.30Nov20.powerlaw.intel.4 b/examples/multi/log.30Nov20.powerlaw.intel.4 new file mode 100644 index 0000000000..109b4582db --- /dev/null +++ b/examples/multi/log.30Nov20.powerlaw.intel.4 @@ -0,0 +1,291 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) + using 1 OpenMP thread(s) per MPI task +# Shear power-law distributed granular particles + +units lj +atom_style sphere +dimension 2 +read_data data.powerlaw +Reading data file ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 10000 atoms + reading velocities ... + 10000 velocities + read_data CPU = 0.114 seconds +change_box all triclinic +Changing box ... + triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000) + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200 +comm_modify mode multi vel yes reduce/multi + +# granular potential + +pair_style granular +pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity + +# fixes + +fix 1 all nve/sphere +fix 2 all enforce2d +fix 3 all deform 1 xy erate 1e-4 + +# dump 1 all custom 20000 dump.granular id x y z radius + +thermo_style custom step temp epair etotal press vol pxy +thermo 1000 + +timestep 0.005 + +run 200000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 164.7888 + ghost atom cutoff = 164.7888 + binsize = 82.3944, bins = 4 4 1 + 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) = 12.65 | 12.67 | 12.68 Mbytes +Step Temp E_pair TotEng Press Volume Pxy + 0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917 + 1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806 + 2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933 + 3000 0.00022105227 0 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103595.49 -0.091491356 + 129000 0.00057655488 0 0.00057649723 0.56242057 103595.49 -0.091474584 + 130000 0.00060363901 0 0.00060357864 0.56182729 103595.49 -0.091367782 + 131000 0.00060590757 0 0.00060584698 0.56115572 103595.49 -0.090594163 + 132000 0.00061689139 0 0.0006168297 0.56029248 103595.49 -0.089857939 + 133000 0.00063288773 0 0.00063282444 0.55971427 103595.49 -0.08954619 + 134000 0.00064153654 0 0.00064147238 0.55929877 103595.49 -0.089860563 + 135000 0.00065473169 0 0.00065466622 0.5590797 103595.49 -0.089932375 + 136000 0.0006814182 0 0.00068135006 0.55797116 103595.49 -0.08929097 + 137000 0.00068344911 0 0.00068338077 0.55796657 103595.49 -0.089644888 + 138000 0.00071510067 0 0.00071502916 0.55752379 103595.49 -0.089734088 + 139000 0.00074772787 0 0.0007476531 0.55740054 103595.49 -0.089968295 + 140000 0.00072706311 0 0.0007269904 0.55659113 103595.49 -0.090370844 + 141000 0.0007179286 0 0.00071785681 0.55659012 103595.49 -0.089976688 + 142000 0.00072587657 0 0.00072580399 0.55589037 103595.49 -0.090532153 + 143000 0.00074470967 0 0.0007446352 0.55553128 103595.49 -0.091019969 + 144000 0.00071737422 0 0.00071730248 0.55555994 103595.49 -0.090926005 + 145000 0.00070363824 0 0.00070356787 0.55548936 103595.49 -0.0912353 + 146000 0.00069604487 0 0.00069597527 0.55540516 103595.49 -0.091656715 + 147000 0.00070047196 0 0.00070040191 0.55466746 103595.49 -0.092101291 + 148000 0.00069764904 0 0.00069757927 0.55460283 103595.49 -0.092334573 + 149000 0.00068884707 0 0.00068877819 0.55462796 103595.49 -0.0928736 + 150000 0.00067704593 0 0.00067697823 0.55520015 103595.49 -0.093512131 + 151000 0.00067702275 0 0.00067695505 0.55530068 103595.49 -0.094127311 + 152000 0.000690717 0 0.00069064792 0.55432538 103595.49 -0.094248615 + 153000 0.00067758953 0 0.00067752177 0.55460446 103595.49 -0.094839924 + 154000 0.00067748542 0 0.00067741767 0.55532529 103595.49 -0.095832411 + 155000 0.00068723442 0 0.0006871657 0.55637763 103595.49 -0.096838207 + 156000 0.00071590663 0 0.00071583504 0.5569485 103595.49 -0.097686166 + 157000 0.00078378647 0 0.0007837081 0.55755381 103595.49 -0.097968527 + 158000 0.00080144334 0 0.00080136319 0.55741023 103595.49 -0.098119361 + 159000 0.00079183165 0 0.00079175247 0.55756142 103595.49 -0.097925888 + 160000 0.00081212358 0 0.00081204237 0.55669124 103595.49 -0.098171108 + 161000 0.00082903843 0 0.00082895553 0.55608918 103595.49 -0.097827206 + 162000 0.00084257416 0 0.0008424899 0.5560239 103595.49 -0.096775743 + 163000 0.00086279615 0 0.00086270987 0.55550215 103595.49 -0.095981927 + 164000 0.00092139657 0 0.00092130443 0.55395137 103595.49 -0.095215338 + 165000 0.00095519936 0 0.00095510384 0.55376787 103595.49 -0.0945666 + 166000 0.00092201276 0 0.00092192056 0.55373794 103595.49 -0.093531233 + 167000 0.0008525194 0 0.00085243415 0.55375862 103595.49 -0.09389901 + 168000 0.00081977785 0 0.00081969587 0.5536646 103595.49 -0.093829746 + 169000 0.00079692467 0 0.00079684497 0.55416599 103595.49 -0.094433271 + 170000 0.00077787798 0 0.0007778002 0.55416629 103595.49 -0.095043413 + 171000 0.0007651362 0 0.00076505969 0.55418872 103595.49 -0.095212376 + 172000 0.00074631438 0 0.00074623975 0.55403881 103595.49 -0.095463949 + 173000 0.00074431288 0 0.00074423845 0.55415801 103595.49 -0.095319615 + 174000 0.00073924649 0 0.00073917257 0.55373682 103595.49 -0.094724272 + 175000 0.00070973165 0 0.00070966068 0.55393569 103595.49 -0.094201112 + 176000 0.00069820766 0 0.00069813784 0.55341229 103595.49 -0.093530469 + 177000 0.00070922657 0 0.00070915564 0.55282781 103595.49 -0.093282587 + 178000 0.00073688566 0 0.00073681197 0.55223248 103595.49 -0.092190554 + 179000 0.00072455886 0 0.0007244864 0.55244288 103595.49 -0.09182393 + 180000 0.00071894558 0 0.00071887369 0.55281517 103595.49 -0.092177032 + 181000 0.00071752475 0 0.000717453 0.55297293 103595.49 -0.09230934 + 182000 0.00072247421 0 0.00072240196 0.55287294 103595.49 -0.092465908 + 183000 0.00070596821 0 0.00070589761 0.5526242 103595.49 -0.092013313 + 184000 0.00072460909 0 0.00072453663 0.55230817 103595.49 -0.092211243 + 185000 0.00072499917 0 0.00072492667 0.55273387 103595.49 -0.092920761 + 186000 0.00072852698 0 0.00072845413 0.55358929 103595.49 -0.093428623 + 187000 0.00072515668 0 0.00072508417 0.55336733 103595.49 -0.093440126 + 188000 0.00071355728 0 0.00071348593 0.55408468 103595.49 -0.094819333 + 189000 0.00071703212 0 0.00071696042 0.55424355 103595.49 -0.096198144 + 190000 0.00071808849 0 0.00071801668 0.55504118 103595.49 -0.097199842 + 191000 0.00072458142 0 0.00072450896 0.55493515 103595.49 -0.097564772 + 192000 0.00071472504 0 0.00071465357 0.55572657 103595.49 -0.097663072 + 193000 0.00070803966 0 0.00070796886 0.55546116 103595.49 -0.097306162 + 194000 0.00068236077 0 0.00068229254 0.55581155 103595.49 -0.097141594 + 195000 0.00067304613 0 0.00067297882 0.55559507 103595.49 -0.096646489 + 196000 0.00066680808 0 0.0006667414 0.55512029 103595.49 -0.096241456 + 197000 0.00065829161 0 0.00065822578 0.55545375 103595.49 -0.095808778 + 198000 0.0006617611 0 0.00066169492 0.55551074 103595.49 -0.095423531 + 199000 0.00066805655 0 0.00066798975 0.55581298 103595.49 -0.095287337 + 200000 0.00067263902 0 0.00067257175 0.55601669 103595.49 -0.095551006 +Loop time of 145.127 on 4 procs for 200000 steps with 10000 atoms + +Performance: 595339.507 tau/day, 1378.101 timesteps/s +100.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 57.89 | 91.946 | 113.82 | 229.7 | 63.36 +Neigh | 0.34276 | 0.48607 | 0.56708 | 13.1 | 0.33 +Comm | 6.569 | 28.916 | 63.505 | 417.0 | 19.92 +Output | 0.0087178 | 0.011935 | 0.01563 | 2.3 | 0.01 +Modify | 10.432 | 16.495 | 20.378 | 97.7 | 11.37 +Other | | 7.272 | | | 5.01 + +Nlocal: 2500.00 ave 2990 max 1652 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 228.000 ave 254 max 198 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 8611.25 ave 10364 max 5676 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 34445 +Ave neighs/atom = 3.4445000 +Neighbor list builds = 241 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:25 diff --git a/examples/srd/in.srd.mixture b/examples/srd/in.srd.mixture index ff6e6f5b72..6a0100d800 100644 --- a/examples/srd/in.srd.mixture +++ b/examples/srd/in.srd.mixture @@ -62,7 +62,7 @@ delete_atoms overlap 0.5 small big reset_timestep 0 -neighbor 0.3 bin +neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes diff --git a/python/lammps/core.py b/python/lammps/core.py index 6761f9502c..1e8f739943 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -911,14 +911,14 @@ class lammps(object): else: return None if ctype == LMP_TYPE_SCALAR: - if style == LMP_STYLE_GLOBAL: + if cstyle == LMP_STYLE_GLOBAL: self.lib.lammps_extract_compute.restype = POINTER(c_double) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype) return ptr[0] - elif style == LMP_STYLE_ATOM: + elif cstyle == LMP_STYLE_ATOM: return None - elif style == LMP_STYLE_LOCAL: + elif cstyle == LMP_STYLE_LOCAL: self.lib.lammps_extract_compute.restype = POINTER(c_int) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype) diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 74c8188fc8..fb9d6b81b9 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -43,6 +43,7 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp) single_enable = 1; no_virial_fdotr_compute = 1; centroidstressflag = CENTROID_NOTAVAIL; + finitecutflag = 1; history = 1; size_history = 3; @@ -798,3 +799,23 @@ double PairGranHookeHistory::memory_usage() double bytes = (double)nmax * sizeof(double); return bytes; } + +/* ---------------------------------------------------------------------- + self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairGranHookeHistory::atom2cut(int i) +{ + double cut = atom->radius[i]*2; + return cut; +} + +/* ---------------------------------------------------------------------- + maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairGranHookeHistory::radii2cut(double r1, double r2) +{ + double cut = r1+r2; + return cut; +} diff --git a/src/GRANULAR/pair_gran_hooke_history.h b/src/GRANULAR/pair_gran_hooke_history.h index 70c8c469ca..b8010cf5e0 100644 --- a/src/GRANULAR/pair_gran_hooke_history.h +++ b/src/GRANULAR/pair_gran_hooke_history.h @@ -42,6 +42,8 @@ class PairGranHookeHistory : public Pair { int pack_forward_comm(int, int *, double *, int, int *); void unpack_forward_comm(int, int, double *); double memory_usage(); + double atom2cut(int); + double radii2cut(double,double); protected: double kn,kt,gamman,gammat,xmu; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 63571d8c00..318656fc42 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -67,6 +67,7 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) single_enable = 1; no_virial_fdotr_compute = 1; centroidstressflag = CENTROID_NOTAVAIL; + finitecutflag = 1; single_extra = 12; svector = new double[single_extra]; @@ -1837,3 +1838,50 @@ void PairGranular::transfer_history(double* source, double* target) for (int i = 0; i < size_history; i++) target[i] = history_transfer_factors[i]*source[i]; } + +/* ---------------------------------------------------------------------- + self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairGranular::atom2cut(int i) +{ + double cut; + + cut = atom->radius[i]*2; + if(beyond_contact) { + int itype = atom->type[i]; + if(normal_model[itype][itype] == JKR) { + cut += pulloff_distance(cut, cut, itype, itype); + } + } + + return cut; +} + +/* ---------------------------------------------------------------------- + maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairGranular::radii2cut(double r1, double r2) +{ + double cut = 0.0; + + if(beyond_contact) { + int n = atom->ntypes; + double temp; + + // Check all combinations of i and j to find theoretical maximum pull off distance + for(int i = 0; i < n; i++){ + for(int j = 0; j < n; j++){ + if(normal_model[i][j] == JKR) { + temp = pulloff_distance(r1, r2, i, j); + if(temp > cut) cut = temp; + } + } + } + } + + cut += r1 + r2; + + return cut; +} diff --git a/src/GRANULAR/pair_granular.h b/src/GRANULAR/pair_granular.h index 213d4d8c87..e5e76d175e 100644 --- a/src/GRANULAR/pair_granular.h +++ b/src/GRANULAR/pair_granular.h @@ -40,6 +40,8 @@ class PairGranular : public Pair { int pack_forward_comm(int, int *, double *, int, int *); void unpack_forward_comm(int, int, double *); double memory_usage(); + double atom2cut(int); + double radii2cut(double,double); protected: double dt; diff --git a/src/KOKKOS/nbin_kokkos.h b/src/KOKKOS/nbin_kokkos.h index 5909dce4d3..508e786750 100644 --- a/src/KOKKOS/nbin_kokkos.h +++ b/src/KOKKOS/nbin_kokkos.h @@ -15,11 +15,11 @@ NBinStyle(kk/host, NBinKokkos, - NB_KOKKOS_HOST) + NB_STANDARD | NB_KOKKOS_HOST) NBinStyle(kk/device, NBinKokkos, - NB_KOKKOS_DEVICE) + NB_STANDARD | NB_KOKKOS_DEVICE) #else diff --git a/src/KOKKOS/nbin_ssa_kokkos.h b/src/KOKKOS/nbin_ssa_kokkos.h index e684a0eec0..0288d6e609 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.h +++ b/src/KOKKOS/nbin_ssa_kokkos.h @@ -15,11 +15,11 @@ NBinStyle(ssa/kk/host, NBinSSAKokkos, - NB_SSA | NB_KOKKOS_HOST) + NB_STANDARD | NB_SSA | NB_KOKKOS_HOST) NBinStyle(ssa/kk/device, NBinSSAKokkos, - NB_SSA | NB_KOKKOS_DEVICE) + NB_STANDARD | NB_SSA | NB_KOKKOS_DEVICE) #else diff --git a/src/USER-DPD/nbin_ssa.h b/src/USER-DPD/nbin_ssa.h index 41d94bf672..a814e4c1a2 100644 --- a/src/USER-DPD/nbin_ssa.h +++ b/src/USER-DPD/nbin_ssa.h @@ -15,7 +15,7 @@ NBinStyle(ssa, NBinSSA, - NB_SSA) + NB_STANDARD | NB_SSA) #else diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_2d_ssa.cpp similarity index 95% rename from src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp rename to src/USER-DPD/nstencil_half_bin_2d_ssa.cpp index 803a80f3e3..aca7b9df09 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_2d_ssa.cpp @@ -16,13 +16,13 @@ James Larentzos and Timothy I. Mattox (Engility Corporation) ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton_ssa.h" +#include "nstencil_half_bin_2d_ssa.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) : +NStencilHalfBin2dSSA::NStencilHalfBin2dSSA(LAMMPS *lmp) : NStencilSSA(lmp) {} /* ---------------------------------------------------------------------- @@ -37,7 +37,7 @@ NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) : to locate all the Active Interaction Region (AIR) ghosts for SSA ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewtonSSA::create() +void NStencilHalfBin2dSSA::create() { int i,j,pos = 0; nstencil_ssa[0] = 0; // redundant info, but saves a conditional diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_2d_ssa.h similarity index 66% rename from src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h rename to src/USER-DPD/nstencil_half_bin_2d_ssa.h index db6c687bfb..675bb86532 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.h +++ b/src/USER-DPD/nstencil_half_bin_2d_ssa.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/2d/newton/ssa, - NStencilHalfBin2dNewtonSSA, - NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST) +NStencilStyle(half/bin/2d/ssa, + NStencilHalfBin2dSSA, + NS_HALF | NS_BIN | NS_2D | NS_SSA | NS_ORTHO | NS_GHOST) #else -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H +#ifndef LMP_NSTENCIL_HALF_BIN_2D_SSA_H +#define LMP_NSTENCIL_HALF_BIN_2D_SSA_H #include "nstencil_ssa.h" namespace LAMMPS_NS { -class NStencilHalfBin2dNewtonSSA : public NStencilSSA { +class NStencilHalfBin2dSSA : public NStencilSSA { public: - NStencilHalfBin2dNewtonSSA(class LAMMPS *); - ~NStencilHalfBin2dNewtonSSA() {} + NStencilHalfBin2dSSA(class LAMMPS *); + ~NStencilHalfBin2dSSA() {} void create(); }; diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_3d_ssa.cpp similarity index 97% rename from src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp rename to src/USER-DPD/nstencil_half_bin_3d_ssa.cpp index c20dabe28f..8e33f5414f 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_3d_ssa.cpp @@ -16,13 +16,13 @@ James Larentzos and Timothy I. Mattox (Engility Corporation) ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton_ssa.h" +#include "nstencil_half_bin_3d_ssa.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) : +NStencilHalfBin3dSSA::NStencilHalfBin3dSSA(LAMMPS *lmp) : NStencilSSA(lmp) {} /* ---------------------------------------------------------------------- @@ -37,7 +37,7 @@ NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) : to locate all the Active Interaction Region (AIR) ghosts for SSA ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewtonSSA::create() +void NStencilHalfBin3dSSA::create() { int i,j,k,pos = 0; nstencil_ssa[0] = 0; // redundant info, but saves a conditional diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h b/src/USER-DPD/nstencil_half_bin_3d_ssa.h similarity index 66% rename from src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h rename to src/USER-DPD/nstencil_half_bin_3d_ssa.h index e351faea80..67dd8dc05b 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.h +++ b/src/USER-DPD/nstencil_half_bin_3d_ssa.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/3d/newton/ssa, - NStencilHalfBin3dNewtonSSA, - NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST) +NStencilStyle(half/bin/3d/ssa, + NStencilHalfBin3dSSA, + NS_HALF | NS_BIN | NS_3D | NS_SSA | NS_ORTHO | NS_GHOST) #else -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H +#ifndef LMP_NSTENCIL_HALF_BIN_3D_SSA_H +#define LMP_NSTENCIL_HALF_BIN_3D_SSA_H #include "nstencil_ssa.h" namespace LAMMPS_NS { -class NStencilHalfBin3dNewtonSSA : public NStencilSSA { +class NStencilHalfBin3dSSA : public NStencilSSA { public: - NStencilHalfBin3dNewtonSSA(class LAMMPS *); - ~NStencilHalfBin3dNewtonSSA() {} + NStencilHalfBin3dSSA(class LAMMPS *); + ~NStencilHalfBin3dSSA() {} void create(); }; diff --git a/src/USER-INTEL/nbin_intel.h b/src/USER-INTEL/nbin_intel.h index 2aa4013dd9..e83b314c6f 100644 --- a/src/USER-INTEL/nbin_intel.h +++ b/src/USER-INTEL/nbin_intel.h @@ -15,7 +15,7 @@ NBinStyle(intel, NBinIntel, - NB_INTEL) + NB_STANDARD | NB_INTEL) #else diff --git a/src/USER-OMP/npair_full_multi_old_omp.cpp b/src/USER-OMP/npair_full_multi_old_omp.cpp new file mode 100644 index 0000000000..46890f6438 --- /dev/null +++ b/src/USER-OMP/npair_full_multi_old_omp.cpp @@ -0,0 +1,142 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_full_multi_old_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairFullMultiOldOmp::NPairFullMultiOldOmp(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction for all neighbors + multi-type stencil is itype dependent and is distance checked + every neighbor pair appears in list of both atoms i and j +------------------------------------------------------------------------- */ + +void NPairFullMultiOldOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + double *cutsq,*distsq; + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in other bins in stencil, including self + // skip if i,j neighbor cutoff is less than bin distance + // skip i = j + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + if (i == j) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >=0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; + list->gnum = 0; +} diff --git a/src/nstencil_half_bin_2d_newtoff.h b/src/USER-OMP/npair_full_multi_old_omp.h similarity index 63% rename from src/nstencil_half_bin_2d_newtoff.h rename to src/USER-OMP/npair_full_multi_old_omp.h index 2c05a1ecc1..608bee6da8 100644 --- a/src/nstencil_half_bin_2d_newtoff.h +++ b/src/USER-OMP/npair_full_multi_old_omp.h @@ -11,26 +11,27 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifdef NSTENCIL_CLASS +#ifdef NPAIR_CLASS -NStencilStyle(half/bin/2d/newtoff, - NStencilHalfBin2dNewtoff, - NS_HALF | NS_BIN | NS_2D | NS_NEWTOFF | NS_ORTHO | NS_TRI) +NPairStyle(full/multi/old/omp, + NPairFullMultiOldOmp, + NP_FULL | NP_MULTI_OLD | NP_OMP | + NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTOFF_H +#ifndef LMP_NPAIR_FULL_MULTI_OLD_OMP_H +#define LMP_NPAIR_FULL_MULTI_OLD_OMP_H -#include "nstencil.h" +#include "npair.h" namespace LAMMPS_NS { -class NStencilHalfBin2dNewtoff : public NStencil { +class NPairFullMultiOldOmp : public NPair { public: - NStencilHalfBin2dNewtoff(class LAMMPS *); - ~NStencilHalfBin2dNewtoff() {} - void create(); + NPairFullMultiOldOmp(class LAMMPS *); + ~NPairFullMultiOldOmp() {} + void build(class NeighList *); }; } diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index ce17b4a5a9..f1eeae6453 100644 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_full_multi_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,7 +31,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi-type stencil is itype dependent and is distance checked + multi stencil is icollection-jcollection dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ @@ -46,14 +47,15 @@ void NPairFullMultiOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -80,6 +82,7 @@ void NPairFullMultiOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -89,43 +92,51 @@ void NPairFullMultiOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in other bins in stencil, including self - // skip if i,j neighbor cutoff is less than bin distance - // skip i = j - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (i == j) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >=0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } + // loop over all atoms in surrounding bins in stencil including self + // skip i = j + // use full stencil for all collection combinations + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + if (i == j) continue; + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } } diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index 2bc90838d6..d1d3ba6808 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_multi_newtoff_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,8 +31,8 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law + multi stencil is icollection-jcollection dependent each owned atom i checks own bin and other bins in stencil - multi-type stencil is itype dependent and is distance checked pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ @@ -48,14 +49,15 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -82,6 +84,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -91,44 +94,52 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in other bins in stencil including self - // only store pair if i < j - // skip if i,j neighbor cutoff is less than bin distance - // stores own/own pairs only once - // stores own/ghost pairs on both procs - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - if (j <= i) continue; - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >=0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + // use full stencil for all collection combinations + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + if (j <= i) continue; + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } } } } diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index dbaad2adec..124b3d7c55 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_multi_newton_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -30,8 +31,8 @@ NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -47,14 +48,15 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -81,6 +83,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -90,80 +93,103 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over rest of atoms in i's bin, ghosts are at end of linked list - // if j is owned atom, store it, since j is beyond i in linked list - // if j is ghost, only store if j coords are "above and to the right" of i - - for (j = bins[i]; j >= 0; j = bins[j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >=0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >=0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } + // if same size: uses half stencil so check central bin + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + + if (icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; + + // if same collection, + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + // if different collections, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = js; j >= 0; j = bins[j]) { + if ((icollection != jcollection) && (j < i)) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } + + // for all collections, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } } ilist[i] = i; diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index dd219a616e..c023d801cd 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -14,6 +14,7 @@ #include "omp_compat.h" #include "npair_half_multi_newton_tri_omp.h" #include "npair_omp.h" +#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -31,8 +32,8 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -48,14 +49,15 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom; + int i,j,k,n,itype,jtype,ibin,jbin,icollection,jcollection,which,ns,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; // loop over each atom, storing neighbors + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -82,6 +84,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -91,55 +94,68 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in bins, including self, in stencil - // skip if i,j neighbor cutoff is less than bin distance - // bins below self are excluded from stencil - // pairs for atoms j "below" i are excluded - // below = lower z or (equal z and lower y) or (equal zy and lower x) - // (equal zyx and j <= i) - // latter excludes self-self interaction but allows superposed atoms - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; + + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { + + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + + // if same size (same collection), use half stencil + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } } - } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >=0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } } ilist[i] = i; diff --git a/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp new file mode 100644 index 0000000000..961bac8fb7 --- /dev/null +++ b/src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp @@ -0,0 +1,145 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_multi_old_newtoff_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMultiOldNewtoffOmp::NPairHalfMultiOldNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfMultiOldNewtoffOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + double *cutsq,*distsq; + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + if (j <= i) continue; + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >=0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_multi_old_newtoff_omp.h b/src/USER-OMP/npair_half_multi_old_newtoff_omp.h new file mode 100644 index 0000000000..c52c7235ff --- /dev/null +++ b/src/USER-OMP/npair_half_multi_old_newtoff_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi/old/newtoff/omp, + NPairHalfMultiOldNewtoffOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMultiOldNewtoffOmp : public NPair { + public: + NPairHalfMultiOldNewtoffOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtoffOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp new file mode 100644 index 0000000000..affae74dbd --- /dev/null +++ b/src/USER-OMP/npair_half_multi_old_newton_omp.cpp @@ -0,0 +1,178 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_multi_old_newton_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMultiOldNewtonOmp::NPairHalfMultiOldNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfMultiOldNewtonOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + double *cutsq,*distsq; + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = bins[i]; j >= 0; j = bins[j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >=0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >=0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/nstencil_half_bin_2d_newton_tri.h b/src/USER-OMP/npair_half_multi_old_newton_omp.h similarity index 62% rename from src/nstencil_half_bin_2d_newton_tri.h rename to src/USER-OMP/npair_half_multi_old_newton_omp.h index 2c5b13b990..a868e6eaac 100644 --- a/src/nstencil_half_bin_2d_newton_tri.h +++ b/src/USER-OMP/npair_half_multi_old_newton_omp.h @@ -11,26 +11,26 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifdef NSTENCIL_CLASS +#ifdef NPAIR_CLASS -NStencilStyle(half/bin/2d/newton/tri, - NStencilHalfBin2dNewtonTri, - NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_TRI) +NPairStyle(half/multi/old/newton/omp, + NPairHalfMultiOldNewtonOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_OMP | NP_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_TRI_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_TRI_H +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_OMP_H -#include "nstencil.h" +#include "npair.h" namespace LAMMPS_NS { -class NStencilHalfBin2dNewtonTri : public NStencil { +class NPairHalfMultiOldNewtonOmp : public NPair { public: - NStencilHalfBin2dNewtonTri(class LAMMPS *); - ~NStencilHalfBin2dNewtonTri() {} - void create(); + NPairHalfMultiOldNewtonOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtonOmp() {} + void build(class NeighList *); }; } diff --git a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp new file mode 100644 index 0000000000..c023b08cb7 --- /dev/null +++ b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp @@ -0,0 +1,154 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_multi_old_newton_tri_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMultiOldNewtonTriOmp::NPairHalfMultiOldNewtonTriOmp(LAMMPS *lmp) : + NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfMultiOldNewtonTriOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int molecular = atom->molecular; + const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + double *cutsq,*distsq; + + // loop over each atom, storing neighbors + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in bins, including self, in stencil + // skip if i,j neighbor cutoff is less than bin distance + // bins below self are excluded from stencil + // pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >=0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h new file mode 100644 index 0000000000..90df0b680f --- /dev/null +++ b/src/USER-OMP/npair_half_multi_old_newton_tri_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi/old/newton/tri/omp, + NPairHalfMultiOldNewtonTriOmp, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMultiOldNewtonTriOmp : public NPair { + public: + NPairHalfMultiOldNewtonTriOmp(class LAMMPS *); + ~NPairHalfMultiOldNewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp index a8d187d958..c6af398548 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "error.h" #include "my_page.h" +#include "neighbor.h" #include "neigh_list.h" #include "npair_omp.h" @@ -25,14 +26,13 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : - NPair(lmp) {} +NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law + multi stencil is icollection-jcollection dependent each owned atom i checks own bin and other bins in stencil - multi-type stencil is itype dependent and is distance checked pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ @@ -49,12 +49,15 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; + // loop over each atom, storing neighbors + + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -75,43 +78,52 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - // loop over all atoms in other bins in stencil including self - // only store pair if i < j - // skip if i,j neighbor cutoff is less than bin distance - // stores own/own pairs only once - // stores own/ghost pairs on both procs - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - if (j <= i) continue; - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + // use full stencil for all collection combinations + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >=0; j = bins[j]) { + if (j <= i) continue; + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } } diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h index bdcc217160..baeb3392d0 100644 --- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.h +++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.h @@ -15,8 +15,7 @@ NPairStyle(half/size/multi/newtoff/omp, NPairHalfSizeMultiNewtoffOmp, - NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP | - NP_ORTHO | NP_TRI) + NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI) #else diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp index 61031c553b..cf69668424 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "error.h" #include "my_page.h" +#include "neighbor.h" #include "neigh_list.h" #include "npair_omp.h" @@ -25,14 +26,13 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : - NPair(lmp) {} +NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -48,12 +48,15 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; + // loop over each atom, storing neighbors + + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -74,70 +77,95 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - // loop over rest of atoms in i's bin, ghosts are at end of linked list - // if j is owned atom, store it, since j is beyond i in linked list - // if j is ghost, only store if j coords are "above and to the right" of i - - for (j = bins[i]; j >= 0; j = bins[j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + // if same size: uses half stencil so check central bin + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + + if(icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; + + // if same collection, + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + // if different collections, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = js; j >= 0; j = bins[j]) { + if(icollection != jcollection and j < i) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } } } + + // for all collections, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } } ilist[i] = i; diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp index 8acfc0e3bc..1084b8b453 100644 --- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "error.h" #include "my_page.h" +#include "neighbor.h" #include "neigh_list.h" #include "npair_omp.h" @@ -31,8 +32,8 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) : /* ---------------------------------------------------------------------- size particles binned neighbor list construction with Newton's 3rd law for triclinic + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ @@ -48,12 +49,15 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) #endif NPAIR_OMP_SETUP(nlocal); - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; + // loop over each atom, storing neighbors + + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -74,53 +78,68 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list) neighptr = ipage.vget(); itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - // loop over all atoms in bins, including self, in stencil - // skip if i,j neighbor cutoff is less than bin distance - // bins below self are excluded from stencil - // pairs for atoms j "below" i are excluded - // below = lower z or (equal z and lower y) or (equal zy and lower x) - // (equal zyx and j <= i) - // latter excludes self-self interaction but allows superposed atoms - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; + + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { + + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); + + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } } - } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } } ilist[i] = i; diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp new file mode 100644 index 0000000000..22128b29df --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp @@ -0,0 +1,126 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_size_multi_old_newtoff_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiOldNewtoffOmp::NPairHalfSizeMultiOldNewtoffOmp(LAMMPS *lmp) : + NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiOldNewtoffOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + if (j <= i) continue; + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h new file mode 100644 index 0000000000..af1be7fa0e --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h @@ -0,0 +1,44 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newtoff/omp, + NPairHalfSizeMultiOldNewtoffOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTOFF | NP_OMP | + NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtoffOmp : public NPair { + public: + NPairHalfSizeMultiOldNewtoffOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtoffOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp new file mode 100644 index 0000000000..6747778dd6 --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp @@ -0,0 +1,151 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_size_multi_old_newton_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiOldNewtonOmp::NPairHalfSizeMultiOldNewtonOmp(LAMMPS *lmp) : + NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiOldNewtonOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = bins[i]; j >= 0; j = bins[j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_omp.h b/src/USER-OMP/npair_half_size_multi_old_newton_omp.h new file mode 100644 index 0000000000..e9cd44c25c --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_newton_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newton/omp, + NPairHalfSizeMultiOldNewtonOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_OMP | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonOmp : public NPair { + public: + NPairHalfSizeMultiOldNewtonOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp new file mode 100644 index 0000000000..73c36681f1 --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp @@ -0,0 +1,134 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "omp_compat.h" +#include "npair_half_size_multi_old_newton_tri_omp.h" +#include "npair_omp.h" +#include "neigh_list.h" +#include "atom.h" +#include "atom_vec.h" +#include "my_page.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiOldNewtonTriOmp::NPairHalfSizeMultiOldNewtonTriOmp(LAMMPS *lmp) : + NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list) +{ + const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; + const int history = list->history; + const int mask_history = 3 << SBBITS; + + NPAIR_OMP_INIT; +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list) +#endif + NPAIR_OMP_SETUP(nlocal); + + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + // each thread has its own page allocator + MyPage &ipage = list->ipage[tid]; + ipage.reset(); + + for (i = ifrom; i < ito; i++) { + + n = 0; + neighptr = ipage.vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over all atoms in bins, including self, in stencil + // skip if i,j neighbor cutoff is less than bin distance + // bins below self are excluded from stencil + // pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[i] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage.vgot(n); + if (ipage.status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + NPAIR_OMP_CLOSE; + list->inum = nlocal; +} diff --git a/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h new file mode 100644 index 0000000000..fccaf210f7 --- /dev/null +++ b/src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newton/tri/omp, + NPairHalfSizeMultiOldNewtonTriOmp, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_TRI | NP_OMP) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_OMP_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_OMP_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonTriOmp : public NPair { + public: + NPairHalfSizeMultiOldNewtonTriOmp(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonTriOmp() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.h b/src/USER-OMP/npair_halffull_newtoff_omp.h index 451ed801a2..2d304f0c04 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.h +++ b/src/USER-OMP/npair_halffull_newtoff_omp.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newtoff/omp, NPairHalffullNewtoffOmp, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI |NP_OMP) NPairStyle(halffull/newtoff/skip/omp, NPairHalffullNewtoffOmp, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP) #else diff --git a/src/USER-OMP/npair_halffull_newton_omp.h b/src/USER-OMP/npair_halffull_newton_omp.h index 67a006b313..c4abf95d6d 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.h +++ b/src/USER-OMP/npair_halffull_newton_omp.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newton/omp, NPairHalffullNewtonOmp, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI| NP_OMP) NPairStyle(halffull/newton/skip/omp, NPairHalffullNewtonOmp, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP) #else diff --git a/src/USER-OMP/npair_skip_omp.h b/src/USER-OMP/npair_skip_omp.h index e3fa9624af..d15ba59717 100644 --- a/src/USER-OMP/npair_skip_omp.h +++ b/src/USER-OMP/npair_skip_omp.h @@ -19,36 +19,36 @@ NPairStyle(skip/omp, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/half/respa/omp, NPairSkipRespa, NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/half/size/omp, NPairSkipSize, - NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | + NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/size/off2on/omp, NPairSkipSizeOff2on, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/size/off2on/oneside/omp, NPairSkipSizeOff2onOneside, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP) NPairStyle(skip/ghost/omp, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST) #endif diff --git a/src/comm.cpp b/src/comm.cpp index ec56bbe28d..650c39bac3 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -35,7 +35,6 @@ #include "update.h" #include - #ifdef _OPENMP #include #endif @@ -58,6 +57,9 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) bordergroup = 0; cutghostuser = 0.0; cutusermulti = nullptr; + cutusermultiold = nullptr; + ncollections = 0; + ncollections_cutoff = 0; ghost_velocity = 0; user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0; @@ -76,6 +78,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) grid2proc = nullptr; xsplit = ysplit = zsplit = nullptr; rcbnew = 0; + multi_reduce = 0; // use of OpenMP threads // query OpenMP for number of threads/process set by user at run-time @@ -117,6 +120,7 @@ Comm::~Comm() memory->destroy(ysplit); memory->destroy(zsplit); memory->destroy(cutusermulti); + memory->destroy(cutusermultiold); delete [] customfile; delete [] outfile; } @@ -144,9 +148,16 @@ void Comm::copy_arrays(Comm *oldcomm) memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double)); } + ncollections = oldcomm->ncollections; + ncollections_cutoff = oldcomm->ncollections_cutoff; if (oldcomm->cutusermulti) { - memory->create(cutusermulti,atom->ntypes+1,"comm:cutusermulti"); - memcpy(cutusermulti,oldcomm->cutusermulti,atom->ntypes+1); + memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti"); + memcpy(cutusermulti,oldcomm->cutusermulti,ncollections_cutoff); + } + + if (oldcomm->cutusermultiold) { + memory->create(cutusermultiold,atom->ntypes+1,"comm:cutusermultiold"); + memcpy(cutusermultiold,oldcomm->cutusermultiold,atom->ntypes+1); } if (customfile) @@ -235,6 +246,18 @@ void Comm::init() maxexchange_fix_dynamic = 0; for (int i = 0; i < nfix; i++) if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; + + if ((mode == Comm::MULTI) && (neighbor->style != Neighbor::MULTI)) + error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists"); + + if (multi_reduce) { + if (force->newton == 0) + 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 (mode != Comm::MULTI) + error->all(FLERR,"Cannot use multi/reduce communication without mode multi"); + } } /* ---------------------------------------------------------------------- @@ -270,13 +293,26 @@ void Comm::modify_params(int narg, char **arg) if (strcmp(arg[iarg+1],"single") == 0) { // need to reset cutghostuser when switching comm mode if (mode == Comm::MULTI) cutghostuser = 0.0; + if (mode == Comm::MULTIOLD) cutghostuser = 0.0; memory->destroy(cutusermulti); - cutusermulti = nullptr; + memory->destroy(cutusermultiold); mode = Comm::SINGLE; } else if (strcmp(arg[iarg+1],"multi") == 0) { + if (neighbor->style != Neighbor::MULTI) + error->all(FLERR,"Cannot use comm mode 'multi' without 'multi' style neighbor lists"); // need to reset cutghostuser when switching comm mode if (mode == Comm::SINGLE) cutghostuser = 0.0; + if (mode == Comm::MULTIOLD) cutghostuser = 0.0; + memory->destroy(cutusermultiold); mode = Comm::MULTI; + } else if (strcmp(arg[iarg+1],"multi/old") == 0) { + if (neighbor->style == Neighbor::MULTI) + error->all(FLERR,"Cannot use comm mode 'multi/old' with 'multi' style neighbor lists"); + // need to reset cutghostuser when switching comm mode + if (mode == Comm::SINGLE) cutghostuser = 0.0; + if (mode == Comm::MULTI) cutghostuser = 0.0; + memory->destroy(cutusermulti); + mode = Comm::MULTIOLD; } else error->all(FLERR,"Illegal comm_modify command"); iarg += 2; } else if (strcmp(arg[iarg],"group") == 0) { @@ -291,8 +327,9 @@ void Comm::modify_params(int narg, char **arg) } else if (strcmp(arg[iarg],"cutoff") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); if (mode == Comm::MULTI) - error->all(FLERR, - "Use cutoff/multi keyword to set cutoff in multi mode"); + error->all(FLERR, "Use cutoff/multi keyword to set cutoff in multi mode"); + if (mode == Comm::MULTIOLD) + error->all(FLERR, "Use cutoff/multi/old keyword to set cutoff in multi mode"); cutghostuser = utils::numeric(FLERR,arg[iarg+1],false,lmp); if (cutghostuser < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); @@ -302,16 +339,45 @@ void Comm::modify_params(int narg, char **arg) double cut; if (mode == Comm::SINGLE) error->all(FLERR,"Use cutoff keyword to set cutoff in single mode"); + if (mode == Comm::MULTIOLD) + error->all(FLERR,"Use cutoff/multi/old keyword to set cutoff in multi/old mode"); if (domain->box_exist == 0) - error->all(FLERR, - "Cannot set cutoff/multi before simulation box is defined"); + error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); + + // Check if # of collections has changed, if so erase any previously defined cutoffs + // Neighbor will reset ncollections if collections are redefined + if (! cutusermulti || ncollections_cutoff != neighbor->ncollections) { + ncollections_cutoff = neighbor->ncollections; + memory->destroy(cutusermulti); + memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti"); + for (i=0; i < ncollections_cutoff; ++i) + cutusermulti[i] = -1.0; + } + utils::bounds(FLERR,arg[iarg+1],1,ncollections_cutoff,nlo,nhi,error); + cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); + cutghostuser = MAX(cutghostuser,cut); + if (cut < 0.0) + error->all(FLERR,"Invalid cutoff in comm_modify command"); + // collections use 1-based indexing externally and 0-based indexing internally + for (i=nlo; i<=nhi; ++i) + cutusermulti[i-1] = cut; + iarg += 3; + } else if (strcmp(arg[iarg],"cutoff/multi/old") == 0) { + int i,nlo,nhi; + double cut; + if (mode == Comm::SINGLE) + error->all(FLERR,"Use cutoff keyword to set cutoff in single mode"); + if (mode == Comm::MULTI) + error->all(FLERR,"Use cutoff/multi keyword to set cutoff in multi mode"); + if (domain->box_exist == 0) + error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined"); const int ntypes = atom->ntypes; if (iarg+3 > narg) error->all(FLERR,"Illegal comm_modify command"); - if (cutusermulti == nullptr) { - memory->create(cutusermulti,ntypes+1,"comm:cutusermulti"); + if (cutusermultiold == nullptr) { + memory->create(cutusermultiold,ntypes+1,"comm:cutusermultiold"); for (i=0; i < ntypes+1; ++i) - cutusermulti[i] = -1.0; + cutusermultiold[i] = -1.0; } utils::bounds(FLERR,arg[iarg+1],1,ntypes,nlo,nhi,error); cut = utils::numeric(FLERR,arg[iarg+2],false,lmp); @@ -319,8 +385,13 @@ void Comm::modify_params(int narg, char **arg) if (cut < 0.0) error->all(FLERR,"Invalid cutoff in comm_modify command"); for (i=nlo; i<=nhi; ++i) - cutusermulti[i] = cut; + cutusermultiold[i] = cut; iarg += 3; + } else if (strcmp(arg[iarg],"reduce/multi") == 0) { + if (mode == Comm::SINGLE) + error->all(FLERR,"Use reduce/multi in mode multi only"); + multi_reduce = 1; + iarg += 1; } else if (strcmp(arg[iarg],"vel") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command"); if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 1; @@ -667,6 +738,13 @@ double Comm::get_comm_cutoff() error->warning(FLERR,"Communication cutoff adjusted to {}",maxcommcutoff); } + // Check maximum interval size for neighbor multi + if (neighbor->interval_collection_flag) { + for (int i = 0; i < neighbor->ncollections; i++){ + maxcommcutoff = MAX(maxcommcutoff, neighbor->collection2cut[i]); + } + } + return maxcommcutoff; } diff --git a/src/comm.h b/src/comm.h index 0bcd23cd8a..df016c0b72 100644 --- a/src/comm.h +++ b/src/comm.h @@ -25,14 +25,17 @@ class Comm : protected Pointers { // LAYOUT_NONUNIFORM = logical bricks, but diff sizes via LB // LAYOUT_TILED = general tiling, due to RCB LB enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; - int mode; // 0 = single cutoff, 1 = multi-type cutoff - enum{SINGLE,MULTI}; + int mode; // 0 = single cutoff, 1 = multi-collection cutoff, 2 = multiold-type cutoff + enum{SINGLE,MULTI,MULTIOLD}; int me,nprocs; // proc info int ghost_velocity; // 1 if ghost atoms have velocity, 0 if not double cutghost[3]; // cutoffs used for acquiring ghost atoms - double cutghostuser; // user-specified ghost cutoff (mode == 0) - double *cutusermulti; // per type user ghost cutoff (mode == 1) + double cutghostuser; // user-specified ghost cutoff (mode == SINGLE) + double *cutusermulti; // per collection user ghost cutoff (mode == MULTI) + double *cutusermultiold; // per type user ghost cutoff (mode == MULTIOLD) + int ncollections; // # of collections known by comm, used to test if # has changed + int ncollections_cutoff; // # of collections stored b cutoff/multi int recv_from_partition; // recv proc layout from this partition int send_to_partition; // send my proc layout to this partition // -1 if no recv or send @@ -149,6 +152,7 @@ class Comm : protected Pointers { int ncores; // # of cores per node int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim + int multi_reduce; // 1 if multi cutoff is intra-collection cutoff void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, @@ -195,6 +199,10 @@ E: Use cutoff keyword to set cutoff in single mode Mode is single so cutoff/multi keyword cannot be used. +E: Use cutoff/bytype in mode multi only + +Mode is single so cutoff/bytype keyword cannot be used. + E: Cannot set cutoff/multi before simulation box is defined Self-explanatory. @@ -239,6 +247,10 @@ E: Processor count in z must be 1 for 2d simulation Self-explanatory. +E: Cannot use multi/tiered communication with Newton off + +Self-explanatory. + E: Cannot put data on ring from nullptr pointer W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 8983637e5a..3d80bfceb0 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -30,6 +30,7 @@ #include #include +#include using namespace LAMMPS_NS; @@ -42,12 +43,11 @@ using namespace LAMMPS_NS; CommBrick::CommBrick(LAMMPS *lmp) : Comm(lmp), sendnum(nullptr), recvnum(nullptr), sendproc(nullptr), recvproc(nullptr), - size_forward_recv(nullptr), - size_reverse_send(nullptr), size_reverse_recv(nullptr), + size_forward_recv(nullptr), size_reverse_send(nullptr), size_reverse_recv(nullptr), slablo(nullptr), slabhi(nullptr), multilo(nullptr), multihi(nullptr), - cutghostmulti(nullptr), pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), - sendlist(nullptr), localsendlist(nullptr), maxsendlist(nullptr), - buf_send(nullptr), buf_recv(nullptr) + multioldlo(nullptr), multioldhi(nullptr), cutghostmulti(nullptr), cutghostmultiold(nullptr), + pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), sendlist(nullptr), + localsendlist(nullptr), maxsendlist(nullptr), buf_send(nullptr), buf_recv(nullptr) { style = 0; layout = Comm::LAYOUT_UNIFORM; @@ -65,6 +65,11 @@ CommBrick::~CommBrick() memory->destroy(cutghostmulti); } + if (mode == Comm::MULTIOLD) { + free_multiold(); + memory->destroy(cutghostmultiold); + } + if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]); if (localsendlist) memory->destroy(localsendlist); memory->sfree(sendlist); @@ -101,6 +106,9 @@ void CommBrick::init_buffers() multilo = multihi = nullptr; cutghostmulti = nullptr; + multioldlo = multioldhi = nullptr; + cutghostmultiold = nullptr; + buf_send = buf_recv = nullptr; maxsend = maxrecv = BUFMIN; grow_send(maxsend,2); @@ -128,23 +136,55 @@ void CommBrick::init() init_exchange(); if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); - // memory for multi-style communication + // memory for multi style communication + // allocate in setup - if (mode == Comm::MULTI && multilo == nullptr) { - allocate_multi(maxswap); - memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti"); + if (mode == Comm::MULTI) { + // If inconsitent # of collections, destroy any preexisting arrays (may be missized) + if (ncollections != neighbor->ncollections) { + ncollections = neighbor->ncollections; + if (multilo != nullptr) { + free_multi(); + memory->destroy(cutghostmulti); + } + } + + // delete any old user cutoffs if # of collections chanaged + if (cutusermulti && ncollections != ncollections_cutoff) { + if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined" + " after customizing collections in neigh_modify"); + memory->destroy(cutusermulti); + cutusermulti = nullptr; + } + + if (multilo == nullptr) { + allocate_multi(maxswap); + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + } } - if (mode == Comm::SINGLE && multilo) { + if ((mode == Comm::SINGLE || mode == Comm::MULTIOLD) && multilo) { free_multi(); memory->destroy(cutghostmulti); } + + // memory for multi/old-style communication + + if (mode == Comm::MULTIOLD && multioldlo == nullptr) { + allocate_multiold(maxswap); + memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); + } + if ((mode == Comm::SINGLE || mode == Comm::MULTI) && multioldlo) { + free_multiold(); + memory->destroy(cutghostmultiold); + } } /* ---------------------------------------------------------------------- setup spatial-decomposition communication patterns function of neighbor cutoff(s) & cutghostuser & current box size single mode sets slab boundaries (slablo,slabhi) based on max cutoff - multi mode sets type-dependent slab boundaries (multilo,multihi) + multi mode sets collection-dependent slab boundaries (multilo,multihi) + multi/old mode sets type-dependent slab boundaries (multioldlo,multioldhi) ------------------------------------------------------------------------- */ void CommBrick::setup() @@ -156,9 +196,11 @@ void CommBrick::setup() // neigh->cutghost = distance between tilted planes in box coords // cutghost is in lamda coords = distance between those planes // for multi: - // cutghostmulti = same as cutghost, only for each atom type + // cutghostmulti = same as cutghost, only for each atom collection + // for multi/old: + // cutghostmultiold = same as cutghost, only for each atom type - int i; + int i,j; int ntypes = atom->ntypes; double *prd,*sublo,*subhi; @@ -167,23 +209,51 @@ void CommBrick::setup() error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " "will be generated. Atoms may get lost."); + if (mode == Comm::MULTI) { + double **cutcollectionsq = neighbor->cutcollectionsq; + + // build collection array for atom exchange + neighbor->build_collection(0); + + // If using multi/reduce, communicate particles a distance equal + // to the max cutoff with equally sized or smaller collections + // If not, communicate the maximum cutoff of the entire collection + for (i = 0; i < ncollections; i++) { + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; + } + + for (j = 0; j < ncollections; j++){ + if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); + } + } + } + + if (mode == Comm::MULTIOLD) { + double *cuttype = neighbor->cuttype; + for (i = 1; i <= ntypes; i++) { + double tmp = 0.0; + if (cutusermultiold) tmp = cutusermultiold[i]; + cutghostmultiold[i][0] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][1] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][2] = MAX(tmp,cuttype[i]); + } + } + if (triclinic == 0) { prd = domain->prd; sublo = domain->sublo; subhi = domain->subhi; cutghost[0] = cutghost[1] = cutghost[2] = cut; - - if (mode == Comm::MULTI) { - double *cuttype = neighbor->cuttype; - for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); - } - } - } else { prd = domain->prd_lamda; sublo = domain->sublo_lamda; @@ -196,15 +266,19 @@ void CommBrick::setup() cutghost[1] = cut * length1; length2 = h_inv[2]; cutghost[2] = cut * length2; - if (mode == Comm::MULTI) { - double *cuttype = neighbor->cuttype; + for (i = 0; i < ncollections; i++) { + cutghostmulti[i][0] *= length0; + cutghostmulti[i][1] *= length1; + cutghostmulti[i][2] *= length2; + } + } + + if (mode == Comm::MULTIOLD) { for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = length0 * MAX(cut,cuttype[i]); - cutghostmulti[i][1] = length1 * MAX(cut,cuttype[i]); - cutghostmulti[i][2] = length2 * MAX(cut,cuttype[i]); + cutghostmultiold[i][0] *= length0; + cutghostmultiold[i][1] *= length1; + cutghostmultiold[i][2] *= length2; } } } @@ -350,12 +424,18 @@ void CommBrick::setup() if (ineed < 2) slablo[iswap] = -BIG; else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]); slabhi[iswap] = sublo[dim] + cutghost[dim]; - } else { - for (i = 1; i <= ntypes; i++) { + } else if (mode == Comm::MULTI) { + for (i = 0; i < ncollections; i++) { if (ineed < 2) multilo[iswap][i] = -BIG; else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim]; } + } else { + for (i = 1; i <= ntypes; i++) { + if (ineed < 2) multioldlo[iswap][i] = -BIG; + else multioldlo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); + multioldhi[iswap][i] = sublo[dim] + cutghostmultiold[i][dim]; + } } if (myloc[dim] == 0) { pbc_flag[iswap] = 1; @@ -373,12 +453,18 @@ void CommBrick::setup() slablo[iswap] = subhi[dim] - cutghost[dim]; if (ineed < 2) slabhi[iswap] = BIG; else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]); - } else { - for (i = 1; i <= ntypes; i++) { + } else if (mode == Comm::MULTI) { + for (i = 0; i < ncollections; i++) { multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim]; if (ineed < 2) multihi[iswap][i] = BIG; else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); } + } else { + for (i = 1; i <= ntypes; i++) { + multioldlo[iswap][i] = subhi[dim] - cutghostmultiold[i][dim]; + if (ineed < 2) multioldhi[iswap][i] = BIG; + else multioldhi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]); + } } if (myloc[dim] == procgrid[dim]-1) { pbc_flag[iswap] = 1; @@ -699,15 +785,19 @@ void CommBrick::exchange() void CommBrick::borders() { - int i,n,itype,iswap,dim,ineed,twoneed; - int nsend,nrecv,sendflag,nfirst,nlast,ngroup; + int i,n,itype,icollection,iswap,dim,ineed,twoneed; + int nsend,nrecv,sendflag,nfirst,nlast,ngroup,nprior; double lo,hi; int *type; + int *collection; double **x; double *buf,*mlo,*mhi; MPI_Request request; AtomVec *avec = atom->avec; + // After exchanging/sorting, need to reconstruct collection array for border communication + if (mode == Comm::MULTI) neighbor->build_collection(0); + // do swaps over all 3 dimensions iswap = 0; @@ -728,10 +818,14 @@ void CommBrick::borders() if (mode == Comm::SINGLE) { lo = slablo[iswap]; hi = slabhi[iswap]; - } else { - type = atom->type; + } else if (mode == Comm::MULTI) { + collection = neighbor->collection; mlo = multilo[iswap]; mhi = multihi[iswap]; + } else { + type = atom->type; + mlo = multioldlo[iswap]; + mhi = multioldhi[iswap]; } if (ineed % 2 == 0) { nfirst = nlast; @@ -760,6 +854,14 @@ void CommBrick::borders() if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); sendlist[iswap][nsend++] = i; } + } else if (mode == Comm::MULTI) { + for (i = nfirst; i < nlast; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } } else { for (i = nfirst; i < nlast; i++) { itype = type[i]; @@ -783,6 +885,22 @@ void CommBrick::borders() if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); sendlist[iswap][nsend++] = i; } + } else if (mode == Comm::MULTI) { + ngroup = atom->nfirst; + for (i = 0; i < ngroup; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } + for (i = atom->nlocal; i < nlast; i++) { + icollection = collection[i]; + if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) { + if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend); + sendlist[iswap][nsend++] = i; + } + } } else { ngroup = atom->nfirst; for (i = 0; i < ngroup; i++) { @@ -850,7 +968,10 @@ void CommBrick::borders() size_reverse_send[iswap] = nrecv*size_reverse; size_reverse_recv[iswap] = nsend*size_reverse; firstrecv[iswap] = atom->nlocal + atom->nghost; + nprior = atom->nlocal + atom->nghost; atom->nghost += nrecv; + if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + iswap++; } } @@ -1403,6 +1524,12 @@ void CommBrick::grow_swap(int n) allocate_multi(n); } + if (mode == Comm::MULTIOLD) { + free_multiold(); + allocate_multiold(n); + } + + sendlist = (int **) memory->srealloc(sendlist,n*sizeof(int *),"comm:sendlist"); memory->grow(maxsendlist,n,"comm:maxsendlist"); @@ -1434,15 +1561,26 @@ void CommBrick::allocate_swap(int n) } /* ---------------------------------------------------------------------- - allocation of multi-type swap info + allocation of multi-collection swap info ------------------------------------------------------------------------- */ void CommBrick::allocate_multi(int n) { - multilo = memory->create(multilo,n,atom->ntypes+1,"comm:multilo"); - multihi = memory->create(multihi,n,atom->ntypes+1,"comm:multihi"); + multilo = memory->create(multilo,n,ncollections,"comm:multilo"); + multihi = memory->create(multihi,n,ncollections,"comm:multihi"); } +/* ---------------------------------------------------------------------- + allocation of multi/old-type swap info +------------------------------------------------------------------------- */ + +void CommBrick::allocate_multiold(int n) +{ + multioldlo = memory->create(multioldlo,n,atom->ntypes+1,"comm:multioldlo"); + multioldhi = memory->create(multioldhi,n,atom->ntypes+1,"comm:multioldhi"); +} + + /* ---------------------------------------------------------------------- free memory for swaps ------------------------------------------------------------------------- */ @@ -1464,7 +1602,7 @@ void CommBrick::free_swap() } /* ---------------------------------------------------------------------- - free memory for multi-type swaps + free memory for multi-collection swaps ------------------------------------------------------------------------- */ void CommBrick::free_multi() @@ -1474,6 +1612,17 @@ void CommBrick::free_multi() multilo = multihi = nullptr; } +/* ---------------------------------------------------------------------- + free memory for multi/old-type swaps +------------------------------------------------------------------------- */ + +void CommBrick::free_multiold() +{ + memory->destroy(multioldlo); + memory->destroy(multioldhi); + multioldlo = multioldhi = nullptr; +} + /* ---------------------------------------------------------------------- extract data potentially useful to other classes ------------------------------------------------------------------------- */ diff --git a/src/comm_brick.h b/src/comm_brick.h index 56fb833bab..aa75966249 100644 --- a/src/comm_brick.h +++ b/src/comm_brick.h @@ -61,8 +61,10 @@ class CommBrick : public Comm { int *size_reverse_send; // # to send in each reverse comm int *size_reverse_recv; // # to recv in each reverse comm double *slablo,*slabhi; // bounds of slab to send at each swap - double **multilo,**multihi; // bounds of slabs for multi-type swap - double **cutghostmulti; // cutghost on a per-type basis + double **multilo,**multihi; // bounds of slabs for multi-collection swap + double **multioldlo,**multioldhi; // bounds of slabs for multi-type swap + double **cutghostmulti; // cutghost on a per-collection basis + double **cutghostmultiold; // cutghost on a per-type basis int *pbc_flag; // general flag for sending atoms thru PBC int **pbc; // dimension flags for PBC adjustments @@ -84,11 +86,13 @@ class CommBrick : public Comm { virtual void grow_send(int, int); // reallocate send buffer virtual void grow_recv(int); // free/allocate recv buffer virtual void grow_list(int, int); // reallocate one sendlist - virtual void grow_swap(int); // grow swap and multi arrays + virtual void grow_swap(int); // grow swap, multi, and multi/old arrays virtual void allocate_swap(int); // allocate swap arrays virtual void allocate_multi(int); // allocate multi arrays + virtual void allocate_multiold(int); // allocate multi/old arrays virtual void free_swap(); // free swap arrays virtual void free_multi(); // free multi arrays + virtual void free_multiold(); // free multi/old arrays }; } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 6fa8ef7c37..d5c2244424 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -31,6 +31,7 @@ #include #include +#include using namespace LAMMPS_NS; @@ -53,6 +54,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp) overlap = nullptr; rcbinfo = nullptr; cutghostmulti = nullptr; + cutghostmultiold = nullptr; init_buffers(); } @@ -81,6 +83,7 @@ CommTiled::~CommTiled() deallocate_swap(maxswap); memory->sfree(rcbinfo); memory->destroy(cutghostmulti); + memory->destroy(cutghostmultiold); } /* ---------------------------------------------------------------------- @@ -98,8 +101,11 @@ void CommTiled::init_buffers() overlap = nullptr; rcbinfo = nullptr; cutghostmulti = nullptr; + cutghostmultiold = nullptr; sendbox_multi = nullptr; + sendbox_multiold = nullptr; + // Note this may skip growing multi arrays, will call again in init() maxswap = 6; allocate_swap(maxswap); } @@ -116,8 +122,30 @@ void CommTiled::init() nswap = 2*domain->dimension; memory->destroy(cutghostmulti); - if (mode == Comm::MULTI) - memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti"); + if (mode == Comm::MULTI) { + // If inconsitent # of collections, destroy any preexisting arrays (may be missized) + if (ncollections != neighbor->ncollections) { + ncollections = neighbor->ncollections; + } + + // delete any old user cutoffs if # of collections chanaged + if (cutusermulti && ncollections != ncollections_cutoff) { + if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined" + " after customizing collections in neigh_modify"); + memory->destroy(cutusermulti); + cutusermulti = nullptr; + } + + // grow sendbox_multi now that ncollections is known + for (int i = 0; i < maxswap; i ++) + grow_swap_send_multi(i,DELTA_PROCS); + + memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti"); + } + + memory->destroy(cutghostmultiold); + if (mode == Comm::MULTIOLD) + memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold"); int bufextra_old = bufextra; init_exchange(); @@ -175,14 +203,42 @@ void CommTiled::setup() // check that cutoff < any periodic box length if (mode == Comm::MULTI) { + double **cutcollectionsq = neighbor->cutcollectionsq; + + // build collection array for atom exchange + neighbor->build_collection(0); + + // If using multi/reduce, communicate particles a distance equal + // to the max cutoff with equally sized or smaller collections + // If not, communicate the maximum cutoff of the entire collection + for (i = 0; i < ncollections; i++) { + if (cutusermulti) { + cutghostmulti[i][0] = cutusermulti[i]; + cutghostmulti[i][1] = cutusermulti[i]; + cutghostmulti[i][2] = cutusermulti[i]; + } else { + cutghostmulti[i][0] = 0.0; + cutghostmulti[i][1] = 0.0; + cutghostmulti[i][2] = 0.0; + } + + for (j = 0; j < ncollections; j++){ + if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue; + cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j])); + cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j])); + } + } + } + + if (mode == Comm::MULTIOLD) { double *cuttype = neighbor->cuttype; - double cut; for (i = 1; i <= ntypes; i++) { - cut = 0.0; - if (cutusermulti) cut = cutusermulti[i]; - cutghostmulti[i][0] = MAX(cut,cuttype[i]); - cutghostmulti[i][1] = MAX(cut,cuttype[i]); - cutghostmulti[i][2] = MAX(cut,cuttype[i]); + double tmp = 0.0; + if (cutusermultiold) tmp = cutusermultiold[i]; + cutghostmultiold[i][0] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][1] = MAX(tmp,cuttype[i]); + cutghostmultiold[i][2] = MAX(tmp,cuttype[i]); } } @@ -202,12 +258,20 @@ void CommTiled::setup() length2 = h_inv[2]; cutghost[2] = cut * length2; if (mode == Comm::MULTI) { - for (i = 1; i <= ntypes; i++) { + for (i = 0; i < ncollections; i++) { cutghostmulti[i][0] *= length0; cutghostmulti[i][1] *= length1; cutghostmulti[i][2] *= length2; } } + + if (mode == Comm::MULTIOLD) { + for (i = 1; i <= ntypes; i++) { + cutghostmultiold[i][0] *= length0; + cutghostmultiold[i][1] *= length1; + cutghostmultiold[i][2] *= length2; + } + } } if ((periodicity[0] && cutghost[0] > prd[0]) || @@ -345,7 +409,7 @@ void CommTiled::setup() // extend sbox in those lower dims to include ghost atoms // single mode and multi mode - double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6]; + double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6],sbox_multiold[6]; if (mode == Comm::SINGLE) { for (i = 0; i < noverlap; i++) { @@ -434,7 +498,7 @@ void CommTiled::setup() sbox[5] = MIN(oboxhi[2],hi2[2]); } - for (int itype = 1; itype <= atom->ntypes; itype++) { + for (int icollection = 0; icollection < ncollections; icollection++) { sbox_multi[0] = sbox[0]; sbox_multi[1] = sbox[1]; sbox_multi[2] = sbox[2]; @@ -445,36 +509,112 @@ void CommTiled::setup() sbox_multi[idim] = sublo[idim]; if (i < noverlap1) sbox_multi[3+idim] = - MIN(sbox_multi[3+idim]+cutghostmulti[itype][idim],subhi[idim]); + MIN(sbox_multi[3+idim]+cutghostmulti[icollection][idim],subhi[idim]); else sbox_multi[3+idim] = - MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[itype][idim], + MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[icollection][idim], subhi[idim]); } else { if (i < noverlap1) sbox_multi[idim] = - MAX(sbox_multi[idim]-cutghostmulti[itype][idim],sublo[idim]); + MAX(sbox_multi[idim]-cutghostmulti[icollection][idim],sublo[idim]); else sbox_multi[idim] = - MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[itype][idim], + MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[icollection][idim], sublo[idim]); sbox_multi[3+idim] = subhi[idim]; } if (idim >= 1) { if (sbox_multi[0] == oboxlo[0]) - sbox_multi[0] -= cutghostmulti[itype][idim]; + sbox_multi[0] -= cutghostmulti[icollection][idim]; if (sbox_multi[3] == oboxhi[0]) - sbox_multi[3] += cutghostmulti[itype][idim]; + sbox_multi[3] += cutghostmulti[icollection][idim]; } if (idim == 2) { if (sbox_multi[1] == oboxlo[1]) - sbox_multi[1] -= cutghostmulti[itype][idim]; + sbox_multi[1] -= cutghostmulti[icollection][idim]; if (sbox_multi[4] == oboxhi[1]) - sbox_multi[4] += cutghostmulti[itype][idim]; + sbox_multi[4] += cutghostmulti[icollection][idim]; } - memcpy(sendbox_multi[iswap][i][itype],sbox_multi,6*sizeof(double)); + memcpy(sendbox_multi[iswap][i][icollection],sbox_multi,6*sizeof(double)); + } + } + } + + if (mode == Comm::MULTIOLD) { + for (i = 0; i < noverlap; i++) { + pbc_flag[iswap][i] = 0; + pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] = + pbc[iswap][i][3] = pbc[iswap][i][4] = pbc[iswap][i][5] = 0; + + (this->*box_other)(idim,idir,overlap[i],oboxlo,oboxhi); + + if (i < noverlap1) { + sbox[0] = MAX(oboxlo[0],lo1[0]); + sbox[1] = MAX(oboxlo[1],lo1[1]); + sbox[2] = MAX(oboxlo[2],lo1[2]); + sbox[3] = MIN(oboxhi[0],hi1[0]); + sbox[4] = MIN(oboxhi[1],hi1[1]); + sbox[5] = MIN(oboxhi[2],hi1[2]); + } else { + pbc_flag[iswap][i] = 1; + if (idir == 0) pbc[iswap][i][idim] = 1; + else pbc[iswap][i][idim] = -1; + if (triclinic) { + if (idim == 1) pbc[iswap][i][5] = pbc[iswap][i][idim]; + if (idim == 2) pbc[iswap][i][4] = pbc[iswap][i][3] = pbc[iswap][i][idim]; + } + sbox[0] = MAX(oboxlo[0],lo2[0]); + sbox[1] = MAX(oboxlo[1],lo2[1]); + sbox[2] = MAX(oboxlo[2],lo2[2]); + sbox[3] = MIN(oboxhi[0],hi2[0]); + sbox[4] = MIN(oboxhi[1],hi2[1]); + sbox[5] = MIN(oboxhi[2],hi2[2]); + } + + for (int itype = 1; itype <= atom->ntypes; itype++) { + sbox_multiold[0] = sbox[0]; + sbox_multiold[1] = sbox[1]; + sbox_multiold[2] = sbox[2]; + sbox_multiold[3] = sbox[3]; + sbox_multiold[4] = sbox[4]; + sbox_multiold[5] = sbox[5]; + if (idir == 0) { + sbox_multiold[idim] = sublo[idim]; + if (i < noverlap1) + sbox_multiold[3+idim] = + MIN(sbox_multiold[3+idim]+cutghostmultiold[itype][idim],subhi[idim]); + else + sbox_multiold[3+idim] = + MIN(sbox_multiold[3+idim]-prd[idim]+cutghostmultiold[itype][idim], + subhi[idim]); + } else { + if (i < noverlap1) + sbox_multiold[idim] = + MAX(sbox_multiold[idim]-cutghostmultiold[itype][idim],sublo[idim]); + else + sbox_multiold[idim] = + MAX(sbox_multiold[idim]+prd[idim]-cutghostmultiold[itype][idim], + sublo[idim]); + sbox_multiold[3+idim] = subhi[idim]; + } + + if (idim >= 1) { + if (sbox_multiold[0] == oboxlo[0]) + sbox_multiold[0] -= cutghostmultiold[itype][idim]; + if (sbox_multiold[3] == oboxhi[0]) + sbox_multiold[3] += cutghostmultiold[itype][idim]; + } + if (idim == 2) { + if (sbox_multiold[1] == oboxlo[1]) + sbox_multiold[1] -= cutghostmultiold[itype][idim]; + if (sbox_multiold[4] == oboxhi[1]) + sbox_multiold[4] += cutghostmultiold[itype][idim]; + } + + memcpy(sendbox_multiold[iswap][i][itype],sbox_multiold,6*sizeof(double)); } } } @@ -906,12 +1046,15 @@ void CommTiled::exchange() void CommTiled::borders() { - int i,m,n,nlast,nsend,nrecv,ngroup,ncount,ncountall; + int i,m,n,nlast,nsend,nrecv,ngroup,nprior,ncount,ncountall; double xlo,xhi,ylo,yhi,zlo,zhi; double *bbox; double **x; AtomVec *avec = atom->avec; + // After exchanging, need to reconstruct collection array for border communication + if (mode == Comm::MULTI) neighbor->build_collection(0); + // send/recv max one = max # of atoms in single send/recv for any swap // send/recv max all = max # of atoms in all sends/recvs within any swap @@ -977,6 +1120,56 @@ void CommTiled::borders() smaxone = MAX(smaxone,ncount); ncountall += ncount; + } else if (mode == Comm::MULTI) { + + int* collection=neighbor->collection; + int icollection; + ncount = 0; + + if (!bordergroup) { + for (i = 0; i < nlast; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + } else { + ngroup = atom->nfirst; + for (i = 0; i < ngroup; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + for (i = atom->nlocal; i < nlast; i++) { + icollection=collection[i]; + bbox = sendbox_multi[iswap][m][icollection]; + xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; + xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; + if (x[i][0] >= xlo && x[i][0] < xhi && + x[i][1] >= ylo && x[i][1] < yhi && + x[i][2] >= zlo && x[i][2] < zhi) { + if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount); + sendlist[iswap][m][ncount++] = i; + } + } + } + + sendnum[iswap][m] = ncount; + smaxone = MAX(smaxone,ncount); + ncountall += ncount; } else { int* type=atom->type; @@ -986,7 +1179,7 @@ void CommTiled::borders() if (!bordergroup) { for (i = 0; i < nlast; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1000,7 +1193,7 @@ void CommTiled::borders() ngroup = atom->nfirst; for (i = 0; i < ngroup; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1012,7 +1205,7 @@ void CommTiled::borders() } for (i = atom->nlocal; i < nlast; i++) { itype=type[i]; - bbox = sendbox_multi[iswap][m][itype]; + bbox = sendbox_multiold[iswap][m][itype]; xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2]; xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5]; if (x[i][0] >= xlo && x[i][0] < xhi && @@ -1148,8 +1341,11 @@ void CommTiled::borders() // increment ghost atoms n = nrecvproc[iswap]; - if (n) + if (n) { + nprior = atom->nghost + atom->nlocal; atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1]; + if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior); + } } // For molecular systems we lose some bits for local atom indices due @@ -2089,6 +2285,7 @@ void CommTiled::allocate_swap(int n) pbc = new int**[n]; sendbox = new double**[n]; sendbox_multi = new double***[n]; + sendbox_multiold = new double***[n]; maxsendlist = new int*[n]; sendlist = new int**[n]; @@ -2103,6 +2300,7 @@ void CommTiled::allocate_swap(int n) pbc[i] = nullptr; sendbox[i] = nullptr; sendbox_multi[i] = nullptr; + sendbox_multiold[i] = nullptr; maxsendlist[i] = nullptr; sendlist[i] = nullptr; } @@ -2151,8 +2349,9 @@ void CommTiled::grow_swap_send(int i, int n, int nold) memory->create(pbc[i],n,6,"comm:pbc_flag"); memory->destroy(sendbox[i]); memory->create(sendbox[i],n,6,"comm:sendbox"); - memory->destroy(sendbox_multi[i]); - memory->create(sendbox_multi[i],n,atom->ntypes+1,6,"comm:sendbox_multi"); + grow_swap_send_multi(i,n); + memory->destroy(sendbox_multiold[i]); + memory->create(sendbox_multiold[i],n,atom->ntypes+1,6,"comm:sendbox_multiold"); delete [] maxsendlist[i]; maxsendlist[i] = new int[n]; @@ -2184,6 +2383,19 @@ void CommTiled::grow_swap_recv(int i, int n) size_reverse_send[i] = new int[n]; } + +/* ---------------------------------------------------------------------- + grow info for swap I for multi as ncollections can change +------------------------------------------------------------------------- */ + +void CommTiled::grow_swap_send_multi(int i, int n) +{ + memory->destroy(sendbox_multi[i]); + + if (ncollections > 0) + memory->create(sendbox_multi[i],n,ncollections,6,"comm:sendbox_multi"); +} + /* ---------------------------------------------------------------------- deallocate swap info ------------------------------------------------------------------------- */ @@ -2212,6 +2424,7 @@ void CommTiled::deallocate_swap(int n) memory->destroy(pbc[i]); memory->destroy(sendbox[i]); memory->destroy(sendbox_multi[i]); + memory->destroy(sendbox_multiold[i]); delete [] maxsendlist[i]; @@ -2234,6 +2447,7 @@ void CommTiled::deallocate_swap(int n) delete [] pbc; delete [] sendbox; delete [] sendbox_multi; + delete [] sendbox_multiold; delete [] maxsendlist; delete [] sendlist; diff --git a/src/comm_tiled.h b/src/comm_tiled.h index 45723a1d2d..ed492f4a45 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -77,9 +77,12 @@ class CommTiled : public Comm { double ***sendbox; // bounding box of atoms to send per swap/proc - double **cutghostmulti; // cutghost on a per-type basis + double **cutghostmulti; // cutghost on a per-collection basis + double **cutghostmultiold; // cutghost on a per-type basis double ****sendbox_multi; // bounding box of atoms to send // per swap/proc for multi comm + double ****sendbox_multiold; // bounding box of atoms to send + // per swap/proc for multi/old comm // exchange comm info, proc lists do not include self @@ -148,6 +151,7 @@ class CommTiled : public Comm { void grow_list(int, int, int); // reallocate sendlist for one swap/proc void allocate_swap(int); // allocate swap arrays void grow_swap_send(int, int, int); // grow swap arrays for send and recv + void grow_swap_send_multi(int, int); // grow multi swap arrays for send and recv void grow_swap_recv(int, int); void deallocate_swap(int); // deallocate swap arrays @@ -163,10 +167,6 @@ E: Cannot yet use comm_style tiled with triclinic box Self-explanatory. -E: Cannot yet use comm_style tiled with multi-mode comm - -Self-explanatory. - E: Communication cutoff for comm_style tiled cannot exceed periodic box length Self-explanatory. diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index b7b1d711c3..91d806582b 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -35,7 +35,7 @@ enum{TYPE,RADIUS}; ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - vlocal(nullptr), alocal(nullptr), indices(nullptr), pack_choice(nullptr) + vlocal(NULL), alocal(NULL), indices(NULL), pack_choice(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute property/local command"); @@ -233,7 +233,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : // error check - if (atom->molecular == Atom::TEMPLATE && (kindflag == BOND || kindflag == ANGLE || + if (atom->molecular == 2 && (kindflag == BOND || kindflag == ANGLE || kindflag == DIHEDRAL || kindflag == IMPROPER)) error->all(FLERR,"Compute property/local does not (yet) work " "with atom_style template"); @@ -254,8 +254,8 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute property/local requires atom attribute radius"); nmax = 0; - vlocal = nullptr; - alocal = nullptr; + vlocal = NULL; + alocal = NULL; } /* ---------------------------------------------------------------------- */ @@ -273,7 +273,7 @@ ComputePropertyLocal::~ComputePropertyLocal() void ComputePropertyLocal::init() { if (kindflag == NEIGH || kindflag == PAIR) { - if (force->pair == nullptr) + if (force->pair == NULL) error->all(FLERR,"No pair style is defined for compute property/local"); if (force->pair->single_enable == 0) error->all(FLERR,"Pair style does not support compute property/local"); diff --git a/src/info.cpp b/src/info.cpp index 4a91f41672..b9c320bf2e 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -367,9 +367,24 @@ void Info::command(int narg, char **arg) if (comm->mode == 1) { fputs("Communication mode = multi\n",out); double cut; + for (int i=0; i < neighbor->ncollections; ++i) { + if (comm->cutusermulti) cut = comm->cutusermulti[i]; + else cut = 0.0; + for (int j=0; j < neighbor->ncollections; ++j) { + cut = MAX(cut,sqrt(neighbor->cutcollectionsq[i][j])); + } + + if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); + fmt::print(out,"Communication cutoff for collection {} = {:.8}\n", i, cut); + } + } + + if (comm->mode == 2) { + fputs("Communication mode = multi/old\n",out); + double cut; for (int i=1; i <= atom->ntypes && neighbor->cuttype; ++i) { cut = neighbor->cuttype[i]; - if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]); + if (comm->cutusermultiold) cut = MAX(cut,comm->cutusermultiold[i]); fmt::print(out,"Communication cutoff for type {} = {:.8}\n", i, cut); } } diff --git a/src/nbin.cpp b/src/nbin.cpp index e2024b81f8..7b604ca29d 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -31,6 +31,19 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) bins = nullptr; atom2bin = nullptr; + nbinx_multi = nullptr; nbiny_multi = nullptr; nbinz_multi = nullptr; + mbins_multi = nullptr; + mbinx_multi = nullptr; mbiny_multi = nullptr, mbinz_multi = nullptr; + mbinxlo_multi = nullptr; + mbinylo_multi = nullptr; + mbinzlo_multi = nullptr; + binsizex_multi = nullptr; binsizey_multi = nullptr; binsizez_multi = nullptr; + bininvx_multi = nullptr; bininvy_multi = nullptr; bininvz_multi = nullptr; + binhead_multi = nullptr; + maxbins_multi = nullptr; + + maxcollections = 0; + neighbor->last_setup_bins = -1; // geometry settings @@ -48,6 +61,33 @@ NBin::~NBin() memory->destroy(binhead); memory->destroy(bins); memory->destroy(atom2bin); + + if (!binhead_multi) return; + + memory->destroy(nbinx_multi); + memory->destroy(nbiny_multi); + memory->destroy(nbinz_multi); + memory->destroy(mbins_multi); + memory->destroy(mbinx_multi); + memory->destroy(mbiny_multi); + memory->destroy(mbinz_multi); + memory->destroy(mbinxlo_multi); + memory->destroy(mbinylo_multi); + memory->destroy(mbinzlo_multi); + + memory->destroy(binsizex_multi); + memory->destroy(binsizey_multi); + memory->destroy(binsizez_multi); + memory->destroy(bininvx_multi); + memory->destroy(bininvy_multi); + memory->destroy(bininvz_multi); + + for (int n = 0; n < maxcollections; n++) { + memory->destroy(binhead_multi[n]); + } + delete [] binhead_multi; + + memory->destroy(maxbins_multi); } /* ---------------------------------------------------------------------- */ @@ -72,38 +112,16 @@ void NBin::copy_neighbor_info() bboxlo = neighbor->bboxlo; bboxhi = neighbor->bboxhi; + ncollections = neighbor->ncollections; + cutcollectionsq = neighbor->cutcollectionsq; + // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) if (cutoff_custom > 0.0) cutneighmax = cutoff_custom; } -/* ---------------------------------------------------------------------- - setup for bin_atoms() -------------------------------------------------------------------------- */ -void NBin::bin_atoms_setup(int nall) -{ - // binhead = per-bin vector, mbins in length - // add 1 bin for USER-INTEL package - - if (mbins > maxbin) { - maxbin = mbins; - memory->destroy(binhead); - memory->create(binhead,maxbin,"neigh:binhead"); - } - - // bins and atom2bin = per-atom vectors - // for both local and ghost atoms - - if (nall > maxatom) { - maxatom = nall; - memory->destroy(bins); - memory->create(bins,maxatom,"neigh:bins"); - memory->destroy(atom2bin); - memory->create(atom2bin,maxatom,"neigh:atom2bin"); - } -} /* ---------------------------------------------------------------------- convert atom coords into local bin # @@ -151,12 +169,47 @@ int NBin::coord2bin(double *x) return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo); } -/* ---------------------------------------------------------------------- */ -double NBin::memory_usage() +/* ---------------------------------------------------------------------- + convert atom coords into local bin # for a particular collection +------------------------------------------------------------------------- */ + +int NBin::coord2bin_multi(double *x, int ic) { - double bytes = 0; - bytes += (double)maxbin*sizeof(int); - bytes += (double)2*maxatom*sizeof(int); - return bytes; + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]); + ix = MIN(ix,nbinx_multi[ic]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ic]) + nbiny_multi[ic]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]); + iy = MIN(iy,nbiny_multi[ic]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ic]) + nbinz_multi[ic]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]); + iz = MIN(iz,nbinz_multi[ic]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1; + + + ibin = (iz-mbinzlo_multi[ic])*mbiny_multi[ic]*mbinx_multi[ic] + + (iy-mbinylo_multi[ic])*mbinx_multi[ic] + + (ix-mbinxlo_multi[ic]); + return ibin; } + diff --git a/src/nbin.h b/src/nbin.h index 7bd5414315..06b5f189be 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -22,6 +22,9 @@ class NBin : protected Pointers { public: int istyle; // 1-N index into binnames bigint last_bin; // last timestep atoms were binned + double cutoff_custom; // cutoff set by requestor + + // Variables for NBinStandard int nbinx,nbiny,nbinz; // # of global bins int mbins; // # of local bins and offset on this proc @@ -35,17 +38,26 @@ class NBin : protected Pointers { int *bins; // index of next atom in same bin int *atom2bin; // bin assignment for each atom (local+ghost) - double cutoff_custom; // cutoff set by requestor + // Analogues for NBinMultimulti + + int *nbinx_multi, *nbiny_multi, *nbinz_multi; + int *mbins_multi; + int *mbinx_multi, *mbiny_multi, *mbinz_multi; + int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi; + double *binsizex_multi, *binsizey_multi, *binsizez_multi; + double *bininvx_multi, *bininvy_multi, *bininvz_multi; + + int **binhead_multi; NBin(class LAMMPS *); ~NBin(); void post_constructor(class NeighRequest *); virtual void copy_neighbor_info(); - virtual void bin_atoms_setup(int); - double memory_usage(); + virtual void bin_atoms_setup(int) = 0; virtual void setup_bins(int) = 0; virtual void bin_atoms() = 0; + virtual double memory_usage() {return 0.0;} // Kokkos package @@ -61,18 +73,28 @@ class NBin : protected Pointers { int binsizeflag; double binsize_user; double *bboxlo,*bboxhi; + int ncollections; + double **cutcollectionsq; // data common to all NBin variants int dimension; int triclinic; - int maxbin; // size of binhead array + // data for standard NBin + int maxatom; // size of bins array + int maxbin; // size of binhead array + + // data for multi NBin + + int maxcollections; // size of multi arrays + int * maxbins_multi; // size of 2nd dimension of binhead_multi array // methods int coord2bin(double *); + int coord2bin_multi(double *, int); }; } diff --git a/src/nbin_multi.cpp b/src/nbin_multi.cpp new file mode 100644 index 0000000000..14ea62200c --- /dev/null +++ b/src/nbin_multi.cpp @@ -0,0 +1,349 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nbin_multi.h" +#include "neighbor.h" +#include "atom.h" +#include "group.h" +#include "domain.h" +#include "comm.h" +#include "update.h" +#include "error.h" +#include "memory.h" + +using namespace LAMMPS_NS; + +#define SMALL 1.0e-6 +#define CUT2BIN_RATIO 100 + +/* ---------------------------------------------------------------------- */ + +NBinMulti::NBinMulti(LAMMPS *lmp) : NBin(lmp) {} + +/* ---------------------------------------------------------------------- + setup for bin_atoms() +------------------------------------------------------------------------- */ + +void NBinMulti::bin_atoms_setup(int nall) +{ + // binhead_multi[n] = per-bin vector mbins in length mbins_multi[n] + + for (int n = 0; n < maxcollections; n++) { + if (mbins_multi[n] > maxbins_multi[n]) { + maxbins_multi[n] = mbins_multi[n]; + memory->destroy(binhead_multi[n]); + memory->create(binhead_multi[n], mbins_multi[n], "neigh:mbins_multi"); + } + } + + // bins and atom2bin = per-atom vectors + // for both local and ghost atoms + // for multi, bins and atom2bin correspond to different binlists + + if (nall > maxatom) { + maxatom = nall; + memory->destroy(bins); + memory->create(bins,maxatom,"neigh:bins"); + memory->destroy(atom2bin); + memory->create(atom2bin,maxatom,"neigh:atom2bin"); + } +} + +/* ---------------------------------------------------------------------- + setup neighbor binning geometry + bin numbering in each dimension is global: + 0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc + nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc + -1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc + code will work for any binsize + since next(xyz) and stencil extend as far as necessary + binsize = 1/2 of cutoff is roughly optimal + for orthogonal boxes: + a dim must be filled exactly by integer # of bins + in periodic, procs on both sides of PBC must see same bin boundary + in non-periodic, coord2bin() still assumes this by use of nbin xyz + for triclinic boxes: + tilted simulation box cannot contain integer # of bins + stencil & neigh list built differently to account for this + mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each collection + mbinhi_multi = highest global bin any of my ghost atoms could fall into for each collection + mbin_multi = number of bins I need in a dimension for each collection +------------------------------------------------------------------------- */ + +void NBinMulti::setup_bins(int /*style*/) +{ + int n; + + // Initialize arrays + if (ncollections > maxcollections) { + + // Clear any/all memory for existing groupings + for (n = 0; n < maxcollections; n++) + memory->destroy(binhead_multi[n]); + + delete [] binhead_multi; + + maxcollections = ncollections; + + binhead_multi = new int*[maxcollections](); + + memory->destroy(nbinx_multi); + memory->destroy(nbiny_multi); + memory->destroy(nbinz_multi); + memory->create(nbinx_multi, maxcollections, "neigh:nbinx_multi"); + memory->create(nbiny_multi, maxcollections, "neigh:nbiny_multi"); + memory->create(nbinz_multi, maxcollections, "neigh:nbinz_multi"); + + memory->destroy(mbins_multi); + memory->destroy(mbinx_multi); + memory->destroy(mbiny_multi); + memory->destroy(mbinz_multi); + memory->create(mbins_multi, maxcollections, "neigh:mbins_multi"); + memory->create(mbinx_multi, maxcollections, "neigh:mbinx_multi"); + memory->create(mbiny_multi, maxcollections, "neigh:mbiny_multi"); + memory->create(mbinz_multi, maxcollections, "neigh:mbinz_multi"); + + memory->destroy(mbinxlo_multi); + memory->destroy(mbinylo_multi); + memory->destroy(mbinzlo_multi); + memory->create(mbinxlo_multi, maxcollections, "neigh:mbinxlo_multi"); + memory->create(mbinylo_multi, maxcollections, "neigh:mbinylo_multi"); + memory->create(mbinzlo_multi, maxcollections, "neigh:mbinzlo_multi"); + + memory->destroy(binsizex_multi); + memory->destroy(binsizey_multi); + memory->destroy(binsizez_multi); + memory->create(binsizex_multi, maxcollections, "neigh:binsizex_multi"); + memory->create(binsizey_multi, maxcollections, "neigh:binsizey_multi"); + memory->create(binsizez_multi, maxcollections, "neigh:binsizez_multi"); + + memory->destroy(bininvx_multi); + memory->destroy(bininvy_multi); + memory->destroy(bininvz_multi); + memory->create(bininvx_multi, maxcollections, "neigh:bininvx_multi"); + memory->create(bininvy_multi, maxcollections, "neigh:bininvy_multi"); + memory->create(bininvz_multi, maxcollections, "neigh:bininvz_multi"); + + memory->destroy(maxbins_multi); + memory->create(maxbins_multi, maxcollections, "neigh:maxbins_multi"); + + // ensure reallocation occurs in bin_atoms_setup() + for (n = 0; n < maxcollections; n++) { + maxbins_multi[n] = 0; + } + maxatom = 0; + } + + // Identify smallest collection + int icollectionmin = 0; + for (n = 0; n < ncollections; n++) + if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin]) + icollectionmin = n; + + // bbox = size of bbox of entire domain + // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost + // for triclinic: + // bbox bounds all 8 corners of tilted box + // subdomain is in lamda coords + // include dimension-dependent extension via comm->cutghost + // domain->bbox() converts lamda extent to box coords and computes bbox + + double bbox[3],bsubboxlo[3],bsubboxhi[3]; + double *cutghost = comm->cutghost; + + if (triclinic == 0) { + bsubboxlo[0] = domain->sublo[0] - cutghost[0]; + bsubboxlo[1] = domain->sublo[1] - cutghost[1]; + bsubboxlo[2] = domain->sublo[2] - cutghost[2]; + bsubboxhi[0] = domain->subhi[0] + cutghost[0]; + bsubboxhi[1] = domain->subhi[1] + cutghost[1]; + bsubboxhi[2] = domain->subhi[2] + cutghost[2]; + } else { + double lo[3],hi[3]; + lo[0] = domain->sublo_lamda[0] - cutghost[0]; + lo[1] = domain->sublo_lamda[1] - cutghost[1]; + lo[2] = domain->sublo_lamda[2] - cutghost[2]; + hi[0] = domain->subhi_lamda[0] + cutghost[0]; + hi[1] = domain->subhi_lamda[1] + cutghost[1]; + hi[2] = domain->subhi_lamda[2] + cutghost[2]; + domain->bbox(lo,hi,bsubboxlo,bsubboxhi); + } + + bbox[0] = bboxhi[0] - bboxlo[0]; + bbox[1] = bboxhi[1] - bboxlo[1]; + bbox[2] = bboxhi[2] - bboxlo[2]; + + // For each grouping... + + double binsize_optimal, binsizeinv, coord; + int mbinxhi,mbinyhi,mbinzhi; + + for (n = 0; n < ncollections; n++) { + // binsize_user only relates to smallest collection + // optimal bin size is roughly 1/2 the collection-collection cutoff + // special case of all cutoffs = 0.0, binsize = box size + + if (n == icollectionmin && binsizeflag) binsize_optimal = binsize_user; + else binsize_optimal = 0.5*sqrt(cutcollectionsq[n][n]); + if (binsize_optimal == 0.0) binsize_optimal = bbox[0]; + binsizeinv = 1.0/binsize_optimal; + + // test for too many global bins in any dimension due to huge global domain + + if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT || + bbox[2]*binsizeinv > MAXSMALLINT) + error->all(FLERR,"Domain too large for neighbor bins"); + + // create actual bins + // always have one bin even if cutoff > bbox + // for 2d, nbinz_multi[n] = 1 + + nbinx_multi[n] = static_cast (bbox[0]*binsizeinv); + nbiny_multi[n] = static_cast (bbox[1]*binsizeinv); + if (dimension == 3) nbinz_multi[n] = static_cast (bbox[2]*binsizeinv); + else nbinz_multi[n] = 1; + + if (nbinx_multi[n] == 0) nbinx_multi[n] = 1; + if (nbiny_multi[n] == 0) nbiny_multi[n] = 1; + if (nbinz_multi[n] == 0) nbinz_multi[n] = 1; + + // compute actual bin size for nbins to fit into box exactly + // error if actual bin size << cutoff, since will create a zillion bins + // this happens when nbin = 1 and box size << cutoff + // typically due to non-periodic, flat system in a particular dim + // in that extreme case, cannot use multi, should use NSQ not BIN neighbor style + + binsizex_multi[n] = bbox[0]/nbinx_multi[n]; + binsizey_multi[n] = bbox[1]/nbiny_multi[n]; + binsizez_multi[n] = bbox[2]/nbinz_multi[n]; + + bininvx_multi[n] = 1.0 / binsizex_multi[n]; + bininvy_multi[n] = 1.0 / binsizey_multi[n]; + bininvz_multi[n] = 1.0 / binsizez_multi[n]; + + if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO || + binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO) + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); + if ((dimension == 3) && (binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO)) + error->all(FLERR,"Cannot use neighbor bins - box size << cutoff"); + + // mbinlo/hi = lowest and highest global bins my ghost atoms could be in + // coord = lowest and highest values of coords for my ghost atoms + // static_cast(-1.5) = -1, so subract additional -1 + // add in SMALL for round-off safety + + coord = bsubboxlo[0] - SMALL*bbox[0]; + mbinxlo_multi[n] = static_cast ((coord-bboxlo[0])*bininvx_multi[n]); + if (coord < bboxlo[0]) mbinxlo_multi[n] = mbinxlo_multi[n] - 1; + coord = bsubboxhi[0] + SMALL*bbox[0]; + mbinxhi = static_cast ((coord-bboxlo[0])*bininvx_multi[n]); + + coord = bsubboxlo[1] - SMALL*bbox[1]; + mbinylo_multi[n] = static_cast ((coord-bboxlo[1])*bininvy_multi[n]); + if (coord < bboxlo[1]) mbinylo_multi[n] = mbinylo_multi[n] - 1; + coord = bsubboxhi[1] + SMALL*bbox[1]; + mbinyhi = static_cast ((coord-bboxlo[1])*bininvy_multi[n]); + + if (dimension == 3) { + coord = bsubboxlo[2] - SMALL*bbox[2]; + mbinzlo_multi[n] = static_cast ((coord-bboxlo[2])*bininvz_multi[n]); + if (coord < bboxlo[2]) mbinzlo_multi[n] = mbinzlo_multi[n] - 1; + coord = bsubboxhi[2] + SMALL*bbox[2]; + mbinzhi = static_cast ((coord-bboxlo[2])*bininvz_multi[n]); + } + + // extend bins by 1 to insure stencil extent is included + // for 2d, only 1 bin in z + + mbinxlo_multi[n] = mbinxlo_multi[n] - 1; + mbinxhi = mbinxhi + 1; + mbinx_multi[n] = mbinxhi - mbinxlo_multi[n] + 1; + + mbinylo_multi[n] = mbinylo_multi[n] - 1; + mbinyhi = mbinyhi + 1; + mbiny_multi[n] = mbinyhi - mbinylo_multi[n] + 1; + + if (dimension == 3) { + mbinzlo_multi[n] = mbinzlo_multi[n] - 1; + mbinzhi = mbinzhi + 1; + } else mbinzlo_multi[n] = mbinzhi = 0; + mbinz_multi[n] = mbinzhi - mbinzlo_multi[n] + 1; + + bigint bbin = ((bigint) mbinx_multi[n]) + * ((bigint) mbiny_multi[n]) * ((bigint) mbinz_multi[n]) + 1; + if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins"); + mbins_multi[n] = bbin; + } + +} + +/* ---------------------------------------------------------------------- + bin owned and ghost atoms by type +------------------------------------------------------------------------- */ + +void NBinMulti::bin_atoms() +{ + int i,ibin,n; + + last_bin = update->ntimestep; + for (n = 0; n < ncollections; n++) { + for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1; + } + // bin in reverse order so linked list will be in forward order + // also puts ghost atoms at end of list, which is necessary + + int *collection = neighbor->collection; + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + if (includegroup) { + int bitmask = group->bitmask[includegroup]; + for (i = nall-1; i >= nlocal; i--) { + if (mask[i] & bitmask) { + n = collection[i]; + ibin = coord2bin_multi(x[i], n); + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; + } + } + for (i = atom->nfirst-1; i >= 0; i--) { + n = collection[i]; + ibin = coord2bin_multi(x[i], n); + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; + } + } else { + for (i = nall-1; i >= 0; i--) { + n = collection[i]; + ibin = coord2bin_multi(x[i], n); + atom2bin[i] = ibin; + bins[i] = binhead_multi[n][ibin]; + binhead_multi[n][ibin] = i; + } + } +} + +/* ---------------------------------------------------------------------- */ + +double NBinMulti::memory_usage() +{ + double bytes = 0; + for (int m = 0; m < maxcollections; m++) + bytes += (double)maxbins_multi[m]*sizeof(int); + bytes += (double)2*maxatom*sizeof(int); + return bytes; +} diff --git a/src/nbin_multi.h b/src/nbin_multi.h new file mode 100644 index 0000000000..7b79cf9653 --- /dev/null +++ b/src/nbin_multi.h @@ -0,0 +1,63 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NBIN_CLASS + +NBinStyle(multi, + NBinMulti, + NB_MULTI) + +#else + +#ifndef LMP_NBIN_MULTI_H +#define LMP_NBIN_MULTI_H + +#include "nbin.h" + +namespace LAMMPS_NS { + +class NBinMulti : public NBin { + public: + + NBinMulti(class LAMMPS *); + ~NBinMulti() {} + void bin_atoms_setup(int); + void setup_bins(int); + void bin_atoms(); + double memory_usage(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Domain too large for neighbor bins + +UNDOCUMENTED + +E: Cannot use neighbor bins - box size << cutoff + +UNDOCUMENTED + +E: Too many neighbor bins + +UNDOCUMENTED + +E Non-numeric positions - simulation unstable + +UNDOCUMENTED + +*/ diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp index f94e6d37d9..031cdd8b62 100644 --- a/src/nbin_standard.cpp +++ b/src/nbin_standard.cpp @@ -19,6 +19,7 @@ #include "comm.h" #include "update.h" #include "error.h" +#include "memory.h" using namespace LAMMPS_NS; @@ -29,6 +30,33 @@ using namespace LAMMPS_NS; NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {} +/* ---------------------------------------------------------------------- + setup for bin_atoms() +------------------------------------------------------------------------- */ + +void NBinStandard::bin_atoms_setup(int nall) +{ + // binhead = per-bin vector, mbins in length + // add 1 bin for USER-INTEL package + + if (mbins > maxbin) { + maxbin = mbins; + memory->destroy(binhead); + memory->create(binhead,maxbin,"neigh:binhead"); + } + + // bins and atom2bin = per-atom vectors + // for both local and ghost atoms + + if (nall > maxatom) { + maxatom = nall; + memory->destroy(bins); + memory->create(bins,maxatom,"neigh:bins"); + memory->destroy(atom2bin); + memory->create(atom2bin,maxatom,"neigh:atom2bin"); + } +} + /* ---------------------------------------------------------------------- setup neighbor binning geometry bin numbering in each dimension is global: @@ -87,7 +115,7 @@ void NBinStandard::setup_bins(int style) // optimal bin size is roughly 1/2 the cutoff // for BIN style, binsize = 1/2 of max neighbor cutoff - // for MULTI style, binsize = 1/2 of min neighbor cutoff + // for MULTI_OLD style, binsize = 1/2 of min neighbor cutoff // special case of all cutoffs = 0.0, binsize = box size double binsize_optimal; @@ -230,3 +258,13 @@ void NBinStandard::bin_atoms() } } } + +/* ---------------------------------------------------------------------- */ + +double NBinStandard::memory_usage() +{ + double bytes = 0; + bytes += (double)maxbin*sizeof(int); + bytes += (double)2*maxatom*sizeof(int); + return bytes; +} diff --git a/src/nbin_standard.h b/src/nbin_standard.h index 1116653050..54a6cf8358 100644 --- a/src/nbin_standard.h +++ b/src/nbin_standard.h @@ -15,7 +15,7 @@ NBinStyle(standard, NBinStandard, - 0) + NB_STANDARD) #else @@ -30,8 +30,10 @@ class NBinStandard : public NBin { public: NBinStandard(class LAMMPS *); ~NBinStandard() {} + void bin_atoms_setup(int); void setup_bins(int); void bin_atoms(); + double memory_usage(); }; } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index eb4e89e692..357784927b 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -13,6 +13,7 @@ /* ---------------------------------------------------------------------- Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL) + Contributing author (improved multi-neigh) : Joel Clemmer (SNL) ------------------------------------------------------------------------- */ #include "neighbor.h" @@ -43,6 +44,7 @@ #include "style_npair.h" #include "style_nstencil.h" #include "style_ntopo.h" +#include "tokenizer.h" #include "update.h" #include @@ -53,13 +55,14 @@ using namespace NeighConst; #define RQDELTA 1 #define EXDELTA 1 +#define DELTA_PERATOM 64 #define BIG 1.0e20 enum{NONE,ALL,PARTIAL,TEMPLATE}; -static const char cite_neigh_multi[] = - "neighbor multi command:\n\n" +static const char cite_neigh_multi_old[] = + "neighbor multi/old command: doi:10.1016/j.cpc.2008.03.005\n\n" "@Article{Intveld08,\n" " author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton" " and G.{\\,}S.~Grest},\n" @@ -71,6 +74,31 @@ static const char cite_neigh_multi[] = " pages = {320--329}\n" "}\n\n"; +static const char cite_neigh_multi[] = + "neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2\n\n" + "@Article{Intveld08,\n" + " author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton" + " and G.{\\,}S.~Grest},\n" + " title = {Accurate and Efficient Methods for Modeling Colloidal\n" + " Mixtures in an Explicit Solvent using Molecular Dynamics},\n" + " journal = {Comp.~Phys.~Comm.},\n" + " year = 2008,\n" + " volume = 179,\n" + " pages = {320--329}\n" + "}\n\n" + "@article{Stratford2018,\n" + " author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},\n" + " title = {Implementation of multi-level contact detection in LAMMPS},\n" + " year = {2018}\n" + "}\n\n" + "@article{Shire2020,\n" + " author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},\n" + " title = {DEM simulations of polydisperse media: efficient contact\n" + " detection applied to investigate the quasi-static limit},\n" + " journal = {Computational Particle Mechanics},\n" + " year = {2020}\n" + "}\n\n"; + //#define NEIGH_LIST_DEBUG 1 /* ---------------------------------------------------------------------- */ @@ -168,6 +196,16 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr) nex_mol = maxex_mol = 0; ex_mol_group = ex_mol_bit = ex_mol_intra = nullptr; + // Multi data + + type2collection = nullptr; + collection2cut = nullptr; + collection = nullptr; + cutcollectionsq = nullptr; + custom_collection_flag = 0; + interval_collection_flag = 0; + nmax_collection = 0; + // Kokkos setting copymode = 0; @@ -233,6 +271,11 @@ Neighbor::~Neighbor() memory->destroy(ex_mol_group); delete [] ex_mol_bit; memory->destroy(ex_mol_intra); + + memory->destroy(type2collection); + memory->destroy(collection2cut); + memory->destroy(collection); + memory->destroy(cutcollectionsq); } /* ---------------------------------------------------------------------- */ @@ -316,6 +359,101 @@ void Neighbor::init() } cutneighmaxsq = cutneighmax * cutneighmax; + // Define cutoffs for multi + if (style == Neighbor::MULTI) { + int icollection, jcollection; + + // If collections not yet defined, create default map using types + if (not custom_collection_flag) { + ncollections = n; + interval_collection_flag = 0; + if (not type2collection) + memory->create(type2collection,n+1,"neigh:type2collection"); + for (i = 1; i <= n; i++) + type2collection[i] = i-1; + } + + memory->grow(cutcollectionsq, ncollections, ncollections, "neigh:cutcollectionsq"); + + // 3 possible ways of defining collections + // 1) Types are used to define collections + // Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff + // 2) Collections are defined by intervals, point particles + // Types are first sorted into collections based on cutneighsq[i][i] + // Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff + // 3) Collections are defined by intervals, finite particles + // + + // Define collection cutoffs + for (i = 0; i < ncollections; i++) + for (j = 0; j < ncollections; j++) + cutcollectionsq[i][j] = 0.0; + + if (not interval_collection_flag) { + finite_cut_flag = 0; + for (i = 1; i <= n; i++){ + icollection = type2collection[i]; + for (j = 1; j <= n; j++){ + jcollection = type2collection[j]; + if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; + cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; + } + } + } + } else { + if (force->pair->finitecutflag) { + finite_cut_flag = 1; + // If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs + double ri, rj, tmp; + for (i = 0; i < ncollections; i++){ + ri = collection2cut[i]*0.5; + for (j = 0; j < ncollections; j++){ + rj = collection2cut[j]*0.5; + tmp = force->pair->radii2cut(ri, rj) + skin; + cutcollectionsq[i][j] = tmp*tmp; + } + } + } else { + finite_cut_flag = 0; + + // Map types to collections + if (not type2collection) + memory->create(type2collection,n+1,"neigh:type2collection"); + + for (i = 1; i <= n; i++) + type2collection[i] = -1; + + double cuttmp; + for (i = 1; i <= n; i++){ + // Remove skin added to cutneighsq + cuttmp = sqrt(cutneighsq[i][i]) - skin; + for (icollection = 0; icollection < ncollections; icollection ++){ + if (collection2cut[icollection] >= cuttmp) { + type2collection[i] = icollection; + break; + } + } + + if (type2collection[i] == -1) + error->all(FLERR, "Pair cutoff exceeds interval cutoffs for multi"); + } + + // Define cutoffs + for (i = 1; i <= n; i++){ + icollection = type2collection[i]; + for (j = 1; j <= n; j++){ + jcollection = type2collection[j]; + if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) { + cutcollectionsq[icollection][jcollection] = cutneighsq[i][j]; + cutcollectionsq[jcollection][icollection] = cutneighsq[i][j]; + } + } + } + } + } + } + // rRESPA cutoffs int respa = 0; @@ -1621,6 +1759,13 @@ int Neighbor::choose_bin(NeighRequest *rq) if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue; if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue; + // multi neighbor style require multi bin style + if (style == Neighbor::MULTI) { + if (!(mask & NB_MULTI)) continue; + } else { + if (!(mask & NB_STANDARD)) continue; + } + return i+1; } @@ -1653,9 +1798,14 @@ int Neighbor::choose_stencil(NeighRequest *rq) else if (rq->newton == 1) newtflag = 1; else if (rq->newton == 2) newtflag = 0; - //printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d\n", + // request a full stencil if building full neighbor list or newton is off + int fullflag = 0; + if (rq->full) fullflag = 1; + if (!newtflag) fullflag = 1; + + //printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d fullflag %d\n", // rq->half,rq->full,rq->newton,rq->ghost,rq->ssa, - // newtflag); + // newtflag, fullflag); // use request and system settings to match exactly one NStencil class mask // checks are bitwise using NeighConst bit masks @@ -1665,24 +1815,15 @@ int Neighbor::choose_stencil(NeighRequest *rq) for (int i = 0; i < nsclass; i++) { mask = stencilmasks[i]; - //printf("III %d: half %d full %d newton %d newtoff %d ghost %d ssa %d\n", - // i,mask & NS_HALF,mask & NS_FULL,mask & NS_NEWTON, - // mask & NS_NEWTOFF,mask & NS_GHOST,mask & NS_SSA); + //printf("III %d: half %d full %d ghost %d ssa %d\n", + // i,mask & NS_HALF,mask & NS_FULL,mask & NS_GHOST,mask & NS_SSA); // exactly one of half or full is set and must match - if (rq->half) { - if (!(mask & NS_HALF)) continue; - } else if (rq->full) { + if (fullflag) { if (!(mask & NS_FULL)) continue; - } - - // newtflag is on or off and must match - - if (newtflag) { - if (!(mask & NS_NEWTON)) continue; - } else if (!newtflag) { - if (!(mask & NS_NEWTOFF)) continue; + } else { + if (!(mask & NS_HALF)) continue; } // require match of these request flags and mask bits @@ -1691,10 +1832,12 @@ int Neighbor::choose_stencil(NeighRequest *rq) if (!rq->ghost != !(mask & NS_GHOST)) continue; if (!rq->ssa != !(mask & NS_SSA)) continue; - // neighbor style is BIN or MULTI and must match + // neighbor style is one of BIN, MULTI_OLD, or MULTI and must match if (style == Neighbor::BIN) { if (!(mask & NS_BIN)) continue; + } else if (style == Neighbor::MULTI_OLD) { + if (!(mask & NS_MULTI_OLD)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NS_MULTI)) continue; } @@ -1826,12 +1969,14 @@ int Neighbor::choose_pair(NeighRequest *rq) if (!rq->halffull != !(mask & NP_HALF_FULL)) continue; if (!rq->off2on != !(mask & NP_OFF2ON)) continue; - // neighbor style is one of NSQ,BIN,MULTI and must match + // neighbor style is one of NSQ, BIN, MULTI_OLD, or MULTI and must match if (style == Neighbor::NSQ) { if (!(mask & NP_NSQ)) continue; } else if (style == Neighbor::BIN) { if (!(mask & NP_BIN)) continue; + } else if (style == Neighbor::MULTI_OLD) { + if (!(mask & NP_MULTI_OLD)) continue; } else if (style == Neighbor::MULTI) { if (!(mask & NP_MULTI)) continue; } @@ -2030,6 +2175,8 @@ void Neighbor::build(int topoflag) int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; + // rebuild collection array from scratch + if (style == Neighbor::MULTI) build_collection(0); // check that using special bond flags will not overflow neigh lists @@ -2202,9 +2349,13 @@ void Neighbor::set(int narg, char **arg) if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ; else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN; - else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI; + else if (strcmp(arg[1],"multi") == 0) { + style = Neighbor::MULTI; + ncollections = atom->ntypes; + } else if (strcmp(arg[1],"multi/old") == 0) style = Neighbor::MULTI_OLD; else error->all(FLERR,"Illegal neighbor command"); + if (style == Neighbor::MULTI_OLD && lmp->citeme) lmp->citeme->add(cite_neigh_multi_old); if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi); } @@ -2351,7 +2502,97 @@ void Neighbor::modify_params(int narg, char **arg) iarg += 2; } else error->all(FLERR,"Illegal neigh_modify command"); + } else if (strcmp(arg[iarg],"collection/interval") == 0) { + if (style != Neighbor::MULTI) + error->all(FLERR,"Cannot use collection/interval command without multi setting"); + if (iarg+2 > narg) + error->all(FLERR,"Invalid collection/interval command"); + ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if (ncollections < 1) + error->all(FLERR,"Invalid collection/interval command"); + if (iarg+1+ncollections > narg) + error->all(FLERR,"Invalid collection/interval command"); + + int i; + + // Invalidate old user cutoffs + comm->ncollections_cutoff = 0; + interval_collection_flag = 1; + custom_collection_flag = 1; + memory->grow(collection2cut,ncollections,"neigh:collection2cut"); + + // Set upper cutoff for each collection + + double cut_interval; + for (i = 0; i < ncollections; i++){ + cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp); + collection2cut[i] = cut_interval; + + if (i != 0) + if (collection2cut[i-1] >= collection2cut[i]) + error->all(FLERR,"Nonsequential interval cutoffs in collection/interval setting"); + } + + iarg += 2 + ncollections; + } else if (strcmp(arg[iarg],"collection/type") == 0) { + if (style != Neighbor::MULTI) + error->all(FLERR,"Cannot use collection/type command without multi setting"); + + if (iarg+2 > narg) + error->all(FLERR,"Invalid collection/type command"); + ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if (ncollections < 1) + error->all(FLERR,"Invalid collection/interval command"); + if (iarg+1+ncollections > narg) + error->all(FLERR,"Invalid collection/type command"); + + int ntypes = atom->ntypes; + int n, nlo, nhi, i, j, k; + + // Invalidate old user cutoffs + comm->ncollections_cutoff = 0; + interval_collection_flag = 0; + custom_collection_flag = 1; + if (not type2collection) + memory->create(type2collection,ntypes+1,"neigh:type2collection"); + + // Erase previous mapping + for (i = 1; i <= ntypes; i++) + type2collection[i] = -1; + + // For each custom range, define mapping for types in interval + int nfield; + char *str; + for (i = 0; i < ncollections; i++){ + n = strlen(arg[iarg+2+i]) + 1; + str = new char[n]; + strcpy(str,arg[iarg+2+i]); + std::vector words = Tokenizer(str, ",").as_vector(); + nfield = words.size(); + + for (j = 0; j < nfield; j++) { + const char * field = words[j].c_str(); + utils::bounds(FLERR,field,1,ntypes,nlo,nhi,error); + + for (k = nlo; k <= nhi; k++) { + if (type2collection[k] != -1) + error->all(FLERR,"Type specified more than once in collection/type commnd"); + type2collection[k] = i; + } + } + + delete [] str; + } + + // Check for undefined atom type + for (i = 1; i <= ntypes; i++){ + if (type2collection[i] == -1) { + error->all(FLERR,"Type missing in collection/type commnd"); + } + } + + iarg += 2 + ncollections; } else error->all(FLERR,"Illegal neigh_modify command"); } } @@ -2406,6 +2647,59 @@ int Neighbor::exclude_setting() return exclude; } +/* ---------------------------------------------------------------------- + check if any of the old requested neighbor lists are full +------------------------------------------------------------------------- */ + +int Neighbor::any_full() +{ + int any_full = 0; + for (int i = 0; i < old_nrequest; i++) { + if (old_requests[i]->full) any_full = 1; + } + return any_full; +} + +/* ---------------------------------------------------------------------- + populate collection array for multi starting at the index istart +------------------------------------------------------------------------- */ + +void Neighbor::build_collection(int istart) +{ + if (style != Neighbor::MULTI) + error->all(FLERR, "Cannot define atom collections without neighbor style multi"); + + int nmax = atom->nlocal+atom->nghost; + if (nmax > nmax_collection) { + nmax_collection = nmax+DELTA_PERATOM; + memory->grow(collection, nmax_collection, "neigh:collection"); + } + + if (finite_cut_flag) { + double cut; + int icollection; + for (int i = istart; i < nmax; i++){ + cut = force->pair->atom2cut(i); + collection[i] = -1; + + for (icollection = 0; icollection < ncollections; icollection++){ + if (collection2cut[icollection] >= cut) { + collection[i] = icollection; + break; + } + } + + if (collection[i] == -1) + error->one(FLERR, "Atom cutoff exceeds interval cutoffs for multi"); + } + } else { + int *type = atom->type; + for (int i = istart; i < nmax; i++){ + collection[i] = type2collection[type[i]]; + } + } +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/neighbor.h b/src/neighbor.h index 0dd809bcdb..2aa1f203c4 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -20,8 +20,8 @@ namespace LAMMPS_NS { class Neighbor : protected Pointers { public: - enum{NSQ,BIN,MULTI}; - int style; // 0,1,2 = nsq, bin, multi + enum{NSQ,BIN,MULTI_OLD,MULTI}; + int style; // 0,1,2,3 = nsq, bin, multi/old, multi int every; // build every this many steps int delay; // delay build for this many steps int dist_check; // 0 = always build, 1 = only if 1/2 dist @@ -102,6 +102,18 @@ class Neighbor : protected Pointers { int nimproperlist; // list of impropers to compute int **improperlist; + // optional type grouping for multi + + int custom_collection_flag; // 1 if custom collections are defined for multi + int interval_collection_flag; // 1 if custom collections use intervals + int finite_cut_flag; // 1 if multi considers finite atom size + int ncollections; // # of custom collections + int nmax_collection; // maximum atoms stored in collection array + int *type2collection; // ntype array mapping types to custom collections + double *collection2cut; // ncollection array with upper bounds on cutoff intervals + double **cutcollectionsq; // cutoffs for each combination of collections + int *collection; // local per-atom array to store collection id + // public methods Neighbor(class LAMMPS *); @@ -123,6 +135,8 @@ class Neighbor : protected Pointers { void exclusion_group_group_delete(int, int); // rm a group-group exclusion int exclude_setting(); // return exclude value to accelerator pkg class NeighRequest *find_request(void *); // find a neighbor request + int any_full(); // Check if any old requests had full neighbor lists + void build_collection(int); // build peratom collection array starting at the given index double memory_usage(); @@ -240,7 +254,9 @@ namespace NeighConst { NB_INTEL = 1<<0, NB_KOKKOS_DEVICE = 1<<1, NB_KOKKOS_HOST = 1<<2, - NB_SSA = 1<<3 + NB_SSA = 1<<3, + NB_STANDARD = 1<<4, + NB_MULTI = 1<<5 }; enum { @@ -250,12 +266,11 @@ namespace NeighConst { NS_FULL = 1<<3, NS_2D = 1<<4, NS_3D = 1<<5, - NS_NEWTON = 1<<6, - NS_NEWTOFF = 1<<7, - NS_ORTHO = 1<<8, - NS_TRI = 1<<9, - NS_GHOST = 1<<10, - NS_SSA = 1<<11 + NS_ORTHO = 1<<6, + NS_TRI = 1<<7, + NS_GHOST = 1<<8, + NS_SSA = 1<<9, + NS_MULTI_OLD = 1<<10 }; enum { @@ -283,7 +298,8 @@ namespace NeighConst { NP_COPY = 1<<21, NP_SKIP = 1<<22, NP_HALF_FULL = 1<<23, - NP_OFF2ON = 1<<24 + NP_OFF2ON = 1<<24, + NP_MULTI_OLD = 1<<25 }; } diff --git a/src/npair.cpp b/src/npair.cpp index 0fa4136020..1472da512a 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -95,6 +95,11 @@ void NPair::copy_neighbor_info() special_flag = neighbor->special_flag; + // multi info + + ncollections = neighbor->ncollections; + cutcollectionsq = neighbor->cutcollectionsq; + // overwrite per-type Neighbor cutoffs with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -134,6 +139,23 @@ void NPair::copy_bin_info() atom2bin = nb->atom2bin; bins = nb->bins; binhead = nb->binhead; + + nbinx_multi = nb->nbinx_multi; + nbiny_multi = nb->nbiny_multi; + nbinz_multi = nb->nbinz_multi; + mbins_multi = nb->mbins_multi; + mbinx_multi = nb->mbinx_multi; + mbiny_multi = nb->mbiny_multi; + mbinz_multi = nb->mbinz_multi; + mbinxlo_multi = nb->mbinxlo_multi; + mbinylo_multi = nb->mbinylo_multi; + mbinzlo_multi = nb->mbinzlo_multi; + + bininvx_multi = nb->bininvx_multi; + bininvy_multi = nb->bininvy_multi; + bininvz_multi = nb->bininvz_multi; + + binhead_multi = nb->binhead_multi; } /* ---------------------------------------------------------------------- @@ -145,9 +167,12 @@ void NPair::copy_stencil_info() nstencil = ns->nstencil; stencil = ns->stencil; stencilxyz = ns->stencilxyz; + nstencil_multi_old = ns->nstencil_multi_old; + stencil_multi_old = ns->stencil_multi_old; + distsq_multi_old = ns->distsq_multi_old; + nstencil_multi = ns->nstencil_multi; stencil_multi = ns->stencil_multi; - distsq_multi = ns->distsq_multi; } /* ---------------------------------------------------------------------- @@ -160,7 +185,6 @@ void NPair::build_setup() if (ns) copy_stencil_info(); // set here, since build_setup() always called before build() - last_build = update->ntimestep; } @@ -241,3 +265,46 @@ int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) return iz*mbiny*mbinx + iy*mbinx + ix; } + +/* ---------------------------------------------------------------------- + multi version of coord2bin for a given collection +------------------------------------------------------------------------- */ + +int NPair::coord2bin(double *x, int ic) +{ + int ix,iy,iz; + int ibin; + + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) + error->one(FLERR,"Non-numeric positions - simulation unstable"); + + if (x[0] >= bboxhi[0]) + ix = static_cast ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic]; + else if (x[0] >= bboxlo[0]) { + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]); + ix = MIN(ix,nbinx_multi[ic]-1); + } else + ix = static_cast ((x[0]-bboxlo[0])*bininvx_multi[ic]) - 1; + + if (x[1] >= bboxhi[1]) + iy = static_cast ((x[1]-bboxhi[1])*bininvy_multi[ic]) + nbiny_multi[ic]; + else if (x[1] >= bboxlo[1]) { + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]); + iy = MIN(iy,nbiny_multi[ic]-1); + } else + iy = static_cast ((x[1]-bboxlo[1])*bininvy_multi[ic]) - 1; + + if (x[2] >= bboxhi[2]) + iz = static_cast ((x[2]-bboxhi[2])*bininvz_multi[ic]) + nbinz_multi[ic]; + else if (x[2] >= bboxlo[2]) { + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]); + iz = MIN(iz,nbinz_multi[ic]-1); + } else + iz = static_cast ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1; + + ix -= mbinxlo_multi[ic]; + iy -= mbinylo_multi[ic]; + iz -= mbinzlo_multi[ic]; + ibin = iz*mbiny_multi[ic]*mbinx_multi[ic] + iy*mbinx_multi[ic] + ix; + return ibin; +} diff --git a/src/npair.h b/src/npair.h index 54132e6685..5324eea406 100644 --- a/src/npair.h +++ b/src/npair.h @@ -48,6 +48,8 @@ class NPair : protected Pointers { double cut_middle_sq; double cut_middle_inside_sq; double *bboxlo,*bboxhi; + int ncollections; + double **cutcollectionsq; // exclusion data from Neighbor class @@ -79,14 +81,24 @@ class NPair : protected Pointers { int *atom2bin,*bins; int *binhead; + int *nbinx_multi, *nbiny_multi, *nbinz_multi; + int *mbins_multi; + int *mbinx_multi, *mbiny_multi, *mbinz_multi; + int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi; + double *bininvx_multi, *bininvy_multi, *bininvz_multi; + int **binhead_multi; + // data from NStencil class int nstencil; int *stencil; int **stencilxyz; - int *nstencil_multi; - int **stencil_multi; - double **distsq_multi; + int *nstencil_multi_old; + int **stencil_multi_old; + double **distsq_multi_old; + + int ** nstencil_multi; + int *** stencil_multi; // data common to all NPair variants @@ -102,6 +114,9 @@ class NPair : protected Pointers { int coord2bin(double *); // mapping atom coord to a bin int coord2bin(double *, int &, int &, int&); // ditto + int coord2bin(double *, int); // mapping atom coord to group bin + + // find_special: determine if atom j is in special list of atom i // if it is not, return 0 // if it is and special flag is 0 (both coeffs are 0.0), return -1 diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index 79a9c7cec3..c99d6f7a6b 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -12,13 +12,15 @@ ------------------------------------------------------------------------- */ #include "npair_full_multi.h" -#include "neigh_list.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "domain.h" -#include "my_page.h" #include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neighbor.h" +#include "neigh_list.h" using namespace LAMMPS_NS; @@ -28,18 +30,19 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction for all neighbors - multi-type stencil is itype dependent and is distance checked + multi stencil is icollection-jcollection dependent every neighbor pair appears in list of both atoms i and j ------------------------------------------------------------------------- */ void NPairFullMulti::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -67,8 +70,8 @@ void NPairFullMulti::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -78,43 +81,51 @@ void NPairFullMulti::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in other bins in stencil, including self - // skip if i,j neighbor cutoff is less than bin distance - // skip i = j - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (i == j) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } + // loop over all atoms in surrounding bins in stencil including self + // skip i = j + // use full stencil for all collection combinations + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + if (i == j) continue; + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } } diff --git a/src/npair_full_multi_old.cpp b/src/npair_full_multi_old.cpp new file mode 100644 index 0000000000..5b9b451dbc --- /dev/null +++ b/src/npair_full_multi_old.cpp @@ -0,0 +1,132 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_full_multi_old.h" + +#include "atom.h" +#include "atom_vec.h" +#include "domain.h" +#include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neigh_list.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairFullMultiOld::NPairFullMultiOld(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction for all neighbors + multi-type stencil is itype dependent and is distance checked + every neighbor pair appears in list of both atoms i and j +------------------------------------------------------------------------- */ + +void NPairFullMultiOld::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + if (molecular == Atom::TEMPLATE) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in other bins in stencil, including self + // skip if i,j neighbor cutoff is less than bin distance + // skip i = j + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + if (i == j) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; + list->gnum = 0; +} diff --git a/src/nstencil_half_bin_3d_newtoff.h b/src/npair_full_multi_old.h similarity index 61% rename from src/nstencil_half_bin_3d_newtoff.h rename to src/npair_full_multi_old.h index ea04199acd..5344a2f010 100644 --- a/src/nstencil_half_bin_3d_newtoff.h +++ b/src/npair_full_multi_old.h @@ -11,26 +11,26 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifdef NSTENCIL_CLASS +#ifdef NPAIR_CLASS -NStencilStyle(half/bin/3d/newtoff, - NStencilHalfBin3dNewtoff, - NS_HALF | NS_BIN | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI) +NPairStyle(full/multi/old, + NPairFullMultiOld, + NP_FULL | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTOFF_H +#ifndef LMP_NPAIR_FULL_MULTI_OLD_H +#define LMP_NPAIR_FULL_MULTI_OLD_H -#include "nstencil.h" +#include "npair.h" namespace LAMMPS_NS { -class NStencilHalfBin3dNewtoff : public NStencil { +class NPairFullMultiOld : public NPair { public: - NStencilHalfBin3dNewtoff(class LAMMPS *); - ~NStencilHalfBin3dNewtoff() {} - void create(); + NPairFullMultiOld(class LAMMPS *); + ~NPairFullMultiOld() {} + void build(class NeighList *); }; } @@ -40,4 +40,8 @@ class NStencilHalfBin3dNewtoff : public NStencil { /* ERROR/WARNING messages: +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + */ diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 3979e494a9..1efcfe447d 100644 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -12,13 +12,15 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newtoff.h" -#include "neigh_list.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "domain.h" -#include "my_page.h" #include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neighbor.h" +#include "neigh_list.h" using namespace LAMMPS_NS; @@ -28,20 +30,21 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with partial Newton's 3rd law + multi stencil is icollection-jcollection dependent each owned atom i checks own bin and other bins in stencil - multi-type stencil is itype dependent and is distance checked pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ void NPairHalfMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -69,8 +72,8 @@ void NPairHalfMultiNewtoff::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -80,44 +83,52 @@ void NPairHalfMultiNewtoff::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in other bins in stencil including self - // only store pair if i < j - // skip if i,j neighbor cutoff is less than bin distance - // stores own/own pairs only once - // stores own/ghost pairs on both procs - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - if (j <= i) continue; - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + // use full stencil for all collection combinations + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + if (j <= i) continue; + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } } } } diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 7ea58d29ad..a1a0aa07ca 100644 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -12,13 +12,15 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton.h" -#include "neigh_list.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "domain.h" -#include "my_page.h" #include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neighbor.h" +#include "neigh_list.h" using namespace LAMMPS_NS; @@ -28,19 +30,20 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -54,7 +57,7 @@ void NPairHalfMultiNewton::build(NeighList *list) int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; - if (molecular == Atom::TEMPLATE) moltemplate = 1; + if (molecular == 2) moltemplate = 1; else moltemplate = 0; int *ilist = list->ilist; @@ -68,8 +71,8 @@ void NPairHalfMultiNewton::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -79,80 +82,103 @@ void NPairHalfMultiNewton::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over rest of atoms in i's bin, ghosts are at end of linked list - // if j is owned atom, store it, since j is beyond i in linked list - // if j is ghost, only store if j coords are "above and to the right" of i - - for (j = bins[i]; j >= 0; j = bins[j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + // if same collection use own bin + if(icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } + // if same size: uses half stencil so check central bin + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + + if (icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; + + // if same collection, + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + // if different collections, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = js; j >= 0; j = bins[j]) { + if((icollection != jcollection) && (j < i)) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } } + + // for all collections, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } } ilist[inum++] = i; diff --git a/src/npair_half_multi_newton.h b/src/npair_half_multi_newton.h index 3186781357..628f5afa88 100644 --- a/src/npair_half_multi_newton.h +++ b/src/npair_half_multi_newton.h @@ -40,8 +40,4 @@ class NPairHalfMultiNewton : public NPair { /* ERROR/WARNING messages: -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED - */ diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index a1095c3fe2..eb01a91f28 100644 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -12,13 +12,15 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton_tri.h" -#include "neigh_list.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "domain.h" -#include "my_page.h" #include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neighbor.h" +#include "neigh_list.h" using namespace LAMMPS_NS; @@ -28,19 +30,20 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- binned neighbor list construction with Newton's 3rd law for triclinic + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; + int *collection = neighbor->collection; double **x = atom->x; int *type = atom->type; int *mask = atom->mask; @@ -54,7 +57,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; - if (molecular == Atom::TEMPLATE) moltemplate = 1; + if (molecular == 2) moltemplate = 1; else moltemplate = 0; int *ilist = list->ilist; @@ -68,8 +71,8 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -79,55 +82,68 @@ void NPairHalfMultiNewtonTri::build(NeighList *list) tagprev = tag[i] - iatom - 1; } - // loop over all atoms in bins, including self, in stencil - // skip if i,j neighbor cutoff is less than bin distance - // bins below self are excluded from stencil - // pairs for atoms j "below" i are excluded - // below = lower z or (equal z and lower y) or (equal zy and lower x) - // (equal zyx and j <= i) - // latter excludes self-self interaction but allows superposed atoms - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; + + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { + + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + + // if same size (same collection), use half stencil + if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } } - } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; - if (rsq <= cutneighsq[itype][jtype]) { - if (molecular != Atom::ATOMIC) { - if (!moltemplate) - which = find_special(special[i],nspecial[i],tag[j]); - else if (imol >= 0) - which = find_special(onemols[imol]->special[iatom], - onemols[imol]->nspecial[iatom], - tag[j]-tagprev); - else which = 0; - if (which == 0) neighptr[n++] = j; - else if (domain->minimum_image_check(delx,dely,delz)) - neighptr[n++] = j; - else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); - } else neighptr[n++] = j; - } - } + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } } ilist[inum++] = i; diff --git a/src/npair_half_multi_newton_tri.h b/src/npair_half_multi_newton_tri.h index d0967af231..daeb4025a5 100644 --- a/src/npair_half_multi_newton_tri.h +++ b/src/npair_half_multi_newton_tri.h @@ -40,8 +40,4 @@ class NPairHalfMultiNewtonTri : public NPair { /* ERROR/WARNING messages: -E: Neighbor list overflow, boost neigh_modify one - -UNDOCUMENTED - */ diff --git a/src/npair_half_multi_old_newtoff.cpp b/src/npair_half_multi_old_newtoff.cpp new file mode 100644 index 0000000000..58228a3057 --- /dev/null +++ b/src/npair_half_multi_old_newtoff.cpp @@ -0,0 +1,135 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_multi_old_newtoff.h" + +#include "atom.h" +#include "atom_vec.h" +#include "domain.h" +#include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neigh_list.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMultiOldNewtoff::NPairHalfMultiOldNewtoff(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfMultiOldNewtoff::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + if (molecular == Atom::TEMPLATE) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + if (j <= i) continue; + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_multi_old_newtoff.h b/src/npair_half_multi_old_newtoff.h new file mode 100644 index 0000000000..58b7b4883d --- /dev/null +++ b/src/npair_half_multi_old_newtoff.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi/old/newtoff, + NPairHalfMultiOldNewtoff, + NP_HALF | NP_MULTI_OLD | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMultiOldNewtoff : public NPair { + public: + NPairHalfMultiOldNewtoff(class LAMMPS *); + ~NPairHalfMultiOldNewtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ diff --git a/src/npair_half_multi_old_newton.cpp b/src/npair_half_multi_old_newton.cpp new file mode 100644 index 0000000000..94802ff05d --- /dev/null +++ b/src/npair_half_multi_old_newton.cpp @@ -0,0 +1,168 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_multi_old_newton.h" + +#include "atom.h" +#include "atom_vec.h" +#include "domain.h" +#include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neigh_list.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMultiOldNewton::NPairHalfMultiOldNewton(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfMultiOldNewton::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + if (molecular == Atom::TEMPLATE) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = bins[i]; j >= 0; j = bins[j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_multi_old_newton.h b/src/npair_half_multi_old_newton.h new file mode 100644 index 0000000000..388b2fe69c --- /dev/null +++ b/src/npair_half_multi_old_newton.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi/old/newton, + NPairHalfMultiOldNewton, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMultiOldNewton : public NPair { + public: + NPairHalfMultiOldNewton(class LAMMPS *); + ~NPairHalfMultiOldNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ diff --git a/src/npair_half_multi_old_newton_tri.cpp b/src/npair_half_multi_old_newton_tri.cpp new file mode 100644 index 0000000000..1046b897aa --- /dev/null +++ b/src/npair_half_multi_old_newton_tri.cpp @@ -0,0 +1,143 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_multi_old_newton_tri.h" + +#include "atom.h" +#include "atom_vec.h" +#include "domain.h" +#include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neigh_list.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfMultiOldNewtonTri::NPairHalfMultiOldNewtonTri(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfMultiOldNewtonTri::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + if (molecular == Atom::TEMPLATE) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over all atoms in bins, including self, in stencil + // skip if i,j neighbor cutoff is less than bin distance + // bins below self are excluded from stencil + // pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular != Atom::ATOMIC) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_multi_old_newton_tri.h b/src/npair_half_multi_old_newton_tri.h new file mode 100644 index 0000000000..47502ab392 --- /dev/null +++ b/src/npair_half_multi_old_newton_tri.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/multi/old/newton/tri, + NPairHalfMultiOldNewtonTri, + NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_H +#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfMultiOldNewtonTri : public NPair { + public: + NPairHalfMultiOldNewtonTri(class LAMMPS *); + ~NPairHalfMultiOldNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED + +*/ diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index e419f59d2f..ec1f512fc0 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -5,17 +5,19 @@ Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under +es certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include "npair_half_size_multi_newtoff.h" #include "atom.h" #include "error.h" #include "my_page.h" +#include "neighbor.h" #include "neigh_list.h" using namespace LAMMPS_NS; @@ -27,20 +29,21 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) { /* ---------------------------------------------------------------------- size particles binned neighbor list construction with partial Newton's 3rd law + multi stencil is icollection-jcollection dependent each owned atom i checks own bin and other bins in stencil - multi-type stencil is itype dependent and is distance checked pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewtoff::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; - double *cutsq,*distsq; + int js; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -63,45 +66,53 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - // loop over all atoms in other bins in stencil including self - // only store pair if i < j - // skip if i,j neighbor cutoff is less than bin distance - // stores own/own pairs only once - // stores own/ghost pairs on both procs - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - if (j <= i) continue; - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // stores own/own pairs only once + // stores own/ghost pairs on both procs + // use full stencil for all collection combinations + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + if (j <= i) continue; + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } } } diff --git a/src/npair_half_size_multi_newtoff.h b/src/npair_half_size_multi_newtoff.h index e8df7f1a1a..01b5db4480 100644 --- a/src/npair_half_size_multi_newtoff.h +++ b/src/npair_half_size_multi_newtoff.h @@ -43,4 +43,5 @@ class NPairHalfSizeMultiNewtoff : public NPair { E: Neighbor list overflow, boost neigh_modify one UNDOCUMENTED + */ diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 4e8bc267f7..95f31e1c52 100644 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "error.h" #include "my_page.h" +#include "neighbor.h" #include "neigh_list.h" using namespace LAMMPS_NS; @@ -27,19 +28,19 @@ NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- size particles binned neighbor list construction with full Newton's 3rd law + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in Newton stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewton::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; - double *cutsq,*distsq; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -62,73 +63,96 @@ void NPairHalfSizeMultiNewton::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - // loop over rest of atoms in i's bin, ghosts are at end of linked list - // if j is owned atom, store it, since j is beyond i in linked list - // if j is ghost, only store if j coords are "above and to the right" of i - - for (j = bins[i]; j >= 0; j = bins[j]) { - if (j >= nlocal) { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp && x[j][0] < xtmp) continue; - } - } - - jtype = type[j]; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); - - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } - - // loop over all atoms in other bins in stencil, store every pair - // skip if i,j neighbor cutoff is less than bin distance - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; + // if same size: uses half stencil so check central bin + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + + if (icollection == jcollection) js = bins[i]; + else js = binhead_multi[jcollection][jbin]; + + // if same collection, + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + // if different collections, + // if j is owned atom, store it if j > i + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = js; j >= 0; j = bins[j]) { + if ((icollection != jcollection) && (j < i)) continue; + + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } } } + + // for all collections, loop over all atoms in other bins in stencil, store every pair + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } } ilist[inum++] = i; diff --git a/src/npair_half_size_multi_newton.h b/src/npair_half_size_multi_newton.h index 2bae728057..ad20d2acf3 100644 --- a/src/npair_half_size_multi_newton.h +++ b/src/npair_half_size_multi_newton.h @@ -43,4 +43,5 @@ class NPairHalfSizeMultiNewton : public NPair { E: Neighbor list overflow, boost neigh_modify one UNDOCUMENTED + */ diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 785255f183..904321b697 100644 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "error.h" #include "my_page.h" +#include "neighbor.h" #include "neigh_list.h" using namespace LAMMPS_NS; @@ -25,20 +26,21 @@ using namespace LAMMPS_NS; NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- + size particles binned neighbor list construction with Newton's 3rd law for triclinic + multi stencil is icollection-jcollection dependent each owned atom i checks its own bin and other bins in triclinic stencil - multi-type stencil is itype dependent and is distance checked every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) { - int i,j,k,n,itype,jtype,ibin,ns; + int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; double radi,radsum,cutdistsq; int *neighptr,*s; - double *cutsq,*distsq; + int *collection = neighbor->collection; double **x = atom->x; double *radius = atom->radius; int *type = atom->type; @@ -61,56 +63,68 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list) for (i = 0; i < nlocal; i++) { n = 0; neighptr = ipage->vget(); - itype = type[i]; + icollection = collection[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; radi = radius[i]; - - // loop over all atoms in bins, including self, in stencil - // skip if i,j neighbor cutoff is less than bin distance - // bins below self are excluded from stencil - // pairs for atoms j "below" i are excluded - // below = lower z or (equal z and lower y) or (equal zy and lower x) - // (equal zyx and j <= i) - // latter excludes self-self interaction but allows superposed atoms - ibin = atom2bin[i]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - cutsq = cutneighsq[itype]; - ns = nstencil_multi[itype]; - for (k = 0; k < ns; k++) { - for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { - jtype = type[j]; - if (cutsq[jtype] < distsq[k]) continue; - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp) { - if (x[j][1] < ytmp) continue; - if (x[j][1] == ytmp) { - if (x[j][0] < xtmp) continue; - if (x[j][0] == xtmp && j <= i) continue; + + // loop through stencils for all collections + for (jcollection = 0; jcollection < ncollections; jcollection++) { + + // if same collection use own bin + if (icollection == jcollection) jbin = ibin; + else jbin = coord2bin(x[i], jcollection); + + // loop over all atoms in bins in stencil + // stencil is empty if i larger than j + // stencil is half if i same size as j + // stencil is full if i smaller than j + // if half: pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + s = stencil_multi[icollection][jcollection]; + ns = nstencil_multi[icollection][jcollection]; + + for (k = 0; k < ns; k++) { + js = binhead_multi[jcollection][jbin + s[k]]; + for (j = js; j >= 0; j = bins[j]) { + + // if same size (same collection), use half stencil + if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){ + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } } - } - if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - cutdistsq = (radsum+skin) * (radsum+skin); + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); - if (rsq <= cutdistsq) { - if (history && rsq < radsum*radsum) - neighptr[n++] = j ^ mask_history; - else - neighptr[n++] = j; - } - } + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } } ilist[inum++] = i; diff --git a/src/npair_half_size_multi_newton_tri.h b/src/npair_half_size_multi_newton_tri.h index 6d9be4955b..bac776627a 100644 --- a/src/npair_half_size_multi_newton_tri.h +++ b/src/npair_half_size_multi_newton_tri.h @@ -43,4 +43,5 @@ class NPairHalfSizeMultiNewtonTri : public NPair { E: Neighbor list overflow, boost neigh_modify one UNDOCUMENTED + */ diff --git a/src/npair_half_size_multi_old_newtoff.cpp b/src/npair_half_size_multi_old_newtoff.cpp new file mode 100644 index 0000000000..5bc74325ae --- /dev/null +++ b/src/npair_half_size_multi_old_newtoff.cpp @@ -0,0 +1,118 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_size_multi_old_newtoff.h" + +#include "atom.h" +#include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neigh_list.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiOldNewtoff::NPairHalfSizeMultiOldNewtoff(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + binned neighbor list construction with partial Newton's 3rd law + each owned atom i checks own bin and other bins in stencil + multi-type stencil is itype dependent and is distance checked + pair stored once if i,j are both owned and i < j + pair stored by me if j is ghost (also stored by proc owning j) +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiOldNewtoff::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over all atoms in other bins in stencil including self + // only store pair if i < j + // skip if i,j neighbor cutoff is less than bin distance + // stores own/own pairs only once + // stores own/ghost pairs on both procs + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + if (j <= i) continue; + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_multi_old_newtoff.h b/src/npair_half_size_multi_old_newtoff.h new file mode 100644 index 0000000000..2bb9200989 --- /dev/null +++ b/src/npair_half_size_multi_old_newtoff.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newtoff, + NPairHalfSizeMultiOldNewtoff, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTOFF | NP_ORTHO | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtoff : public NPair { + public: + NPairHalfSizeMultiOldNewtoff(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtoff() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_old_newton.cpp b/src/npair_half_size_multi_old_newton.cpp new file mode 100644 index 0000000000..68d4133d7d --- /dev/null +++ b/src/npair_half_size_multi_old_newton.cpp @@ -0,0 +1,144 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_size_multi_old_newton.h" + +#include "atom.h" +#include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neigh_list.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiOldNewton::NPairHalfSizeMultiOldNewton(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + size particles + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiOldNewton::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + // loop over rest of atoms in i's bin, ghosts are at end of linked list + // if j is owned atom, store it, since j is beyond i in linked list + // if j is ghost, only store if j coords are "above and to the right" of i + + for (j = bins[i]; j >= 0; j = bins[j]) { + if (j >= nlocal) { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + } + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + + // loop over all atoms in other bins in stencil, store every pair + // skip if i,j neighbor cutoff is less than bin distance + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_multi_old_newton.h b/src/npair_half_size_multi_old_newton.h new file mode 100644 index 0000000000..86a9bd8f00 --- /dev/null +++ b/src/npair_half_size_multi_old_newton.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newton, + NPairHalfSizeMultiOldNewton, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_ORTHO) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewton : public NPair { + public: + NPairHalfSizeMultiOldNewton(class LAMMPS *); + ~NPairHalfSizeMultiOldNewton() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_half_size_multi_old_newton_tri.cpp b/src/npair_half_size_multi_old_newton_tri.cpp new file mode 100644 index 0000000000..45576899bc --- /dev/null +++ b/src/npair_half_size_multi_old_newton_tri.cpp @@ -0,0 +1,126 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "npair_half_size_multi_old_newton_tri.h" + +#include "atom.h" +#include "error.h" +#include "molecule.h" +#include "my_page.h" +#include "neigh_list.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NPairHalfSizeMultiOldNewtonTri::NPairHalfSizeMultiOldNewtonTri(LAMMPS *lmp) : NPair(lmp) {} + +/* ---------------------------------------------------------------------- + binned neighbor list construction with Newton's 3rd law for triclinic + each owned atom i checks its own bin and other bins in triclinic stencil + multi-type stencil is itype dependent and is distance checked + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void NPairHalfSizeMultiOldNewtonTri::build(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,ns; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double radi,radsum,cutdistsq; + int *neighptr,*s; + double *cutsq,*distsq; + + double **x = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *molecule = atom->molecule; + int nlocal = atom->nlocal; + if (includegroup) nlocal = atom->nfirst; + + int history = list->history; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int mask_history = 3 << SBBITS; + + int inum = 0; + ipage->reset(); + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + + + // loop over all atoms in bins, including self, in stencil + // skip if i,j neighbor cutoff is less than bin distance + // bins below self are excluded from stencil + // pairs for atoms j "below" i are excluded + // below = lower z or (equal z and lower y) or (equal zy and lower x) + // (equal zyx and j <= i) + // latter excludes self-self interaction but allows superposed atoms + + ibin = atom2bin[i]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; + cutsq = cutneighsq[itype]; + ns = nstencil_multi_old[itype]; + for (k = 0; k < ns; k++) { + for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) { + jtype = type[j]; + if (cutsq[jtype] < distsq[k]) continue; + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp) { + if (x[j][1] < ytmp) continue; + if (x[j][1] == ytmp) { + if (x[j][0] < xtmp) continue; + if (x[j][0] == xtmp && j <= i) continue; + } + } + + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + radsum = radi + radius[j]; + cutdistsq = (radsum+skin) * (radsum+skin); + + if (rsq <= cutdistsq) { + if (history && rsq < radsum*radsum) + neighptr[n++] = j ^ mask_history; + else + neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/npair_half_size_multi_old_newton_tri.h b/src/npair_half_size_multi_old_newton_tri.h new file mode 100644 index 0000000000..ee899a52fd --- /dev/null +++ b/src/npair_half_size_multi_old_newton_tri.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NPAIR_CLASS + +NPairStyle(half/size/multi/old/newton/tri, + NPairHalfSizeMultiOldNewtonTri, + NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_TRI) + +#else + +#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_H +#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_H + +#include "npair.h" + +namespace LAMMPS_NS { + +class NPairHalfSizeMultiOldNewtonTri : public NPair { + public: + NPairHalfSizeMultiOldNewtonTri(class LAMMPS *); + ~NPairHalfSizeMultiOldNewtonTri() {} + void build(class NeighList *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Neighbor list overflow, boost neigh_modify one + +UNDOCUMENTED +*/ diff --git a/src/npair_halffull_newtoff.h b/src/npair_halffull_newtoff.h index ec1d2dcdcc..5126ced648 100644 --- a/src/npair_halffull_newtoff.h +++ b/src/npair_halffull_newtoff.h @@ -15,22 +15,22 @@ NPairStyle(halffull/newtoff, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI) NPairStyle(halffull/newtoff/skip, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP) NPairStyle(halffull/newtoff/ghost, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_GHOST) NPairStyle(halffull/newtoff/skip/ghost, NPairHalffullNewtoff, - NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF | + NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF | NP_ORTHO | NP_TRI | NP_SKIP | NP_GHOST) #else diff --git a/src/npair_halffull_newton.h b/src/npair_halffull_newton.h index 7470d5491d..cd7cd99d66 100644 --- a/src/npair_halffull_newton.h +++ b/src/npair_halffull_newton.h @@ -15,12 +15,12 @@ NPairStyle(halffull/newton, NPairHalffullNewton, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI) NPairStyle(halffull/newton/skip, NPairHalffullNewton, - NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | + NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_ORTHO | NP_TRI | NP_SKIP) #else diff --git a/src/npair_skip.h b/src/npair_skip.h index 6e81286646..1aece9cffd 100644 --- a/src/npair_skip.h +++ b/src/npair_skip.h @@ -16,13 +16,13 @@ NPairStyle(skip, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) NPairStyle(skip/ghost, NPairSkip, NP_SKIP | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_GHOST) #else diff --git a/src/npair_skip_respa.h b/src/npair_skip_respa.h index 2b04f2b0ee..6414211c3f 100644 --- a/src/npair_skip_respa.h +++ b/src/npair_skip_respa.h @@ -16,7 +16,7 @@ NPairStyle(skip/half/respa, NPairSkipRespa, NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size.h b/src/npair_skip_size.h index 61eab9ba4f..7ecabfc5b3 100644 --- a/src/npair_skip_size.h +++ b/src/npair_skip_size.h @@ -15,7 +15,7 @@ NPairStyle(skip/half/size, NPairSkipSize, - NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | + NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size_off2on.h b/src/npair_skip_size_off2on.h index 4e9649496f..bd3b428dfe 100644 --- a/src/npair_skip_size_off2on.h +++ b/src/npair_skip_size_off2on.h @@ -16,7 +16,7 @@ NPairStyle(skip/size/off2on, NPairSkipSizeOff2on, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/npair_skip_size_off2on_oneside.h b/src/npair_skip_size_off2on_oneside.h index 1b83a97aa1..5a95b95fae 100644 --- a/src/npair_skip_size_off2on_oneside.h +++ b/src/npair_skip_size_off2on_oneside.h @@ -16,7 +16,7 @@ NPairStyle(skip/size/off2on/oneside, NPairSkipSizeOff2onOneside, NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | - NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF | + NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI) #else diff --git a/src/nstencil.cpp b/src/nstencil.cpp index 90de8dcf3c..c412c280ef 100644 --- a/src/nstencil.cpp +++ b/src/nstencil.cpp @@ -31,26 +31,36 @@ using namespace LAMMPS_NS; sx,sy,sz = bin bounds = furthest the stencil could possibly extend calculated below in create_setup() 3d creates xyz stencil, 2d creates xy stencil - for half list with newton off: + for full list or half list with newton off + use a full stencil stencil is all surrounding bins including self regardless of triclinic - for half list with newton on: + for half list with newton on + use a half stencil stencil is bins to the "upper right" of central bin stencil does not include self no versions that allow ghost on (no callers need it?) for half list with newton on and triclinic: + use a half stencil stencil is all bins in z-plane of self and above, but not below in 2d is all bins in y-plane of self and above, but not below stencil includes self no versions that allow ghost on (no callers need it?) - for full list: - stencil is all surrounding bins including self - regardless of newton on/off or triclinic - for multi: + for multi/old: create one stencil for each atom type stencil follows same rules for half/full, newton on/off, triclinic cutoff is not cutneighmaxsq, but max cutoff for that atom type no versions that allow ghost on (any need for it?) + for multi: + create one stencil for each icollection-jcollection pairing + the full/half stencil label refers to the same-collection stencil + a half list with newton on has a half same-collection stencil + a full list or half list with newton off has a full same-collection stencil + cross collection stencils are always full to allow small-to-large lookups + for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin + for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above + cutoff is not cutneighmaxsq, but max cutoff for that atom collection + no versions that allow ghost on (any need for it?) ------------------------------------------------------------------------- */ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) @@ -58,12 +68,22 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp) last_stencil = -1; xyzflag = 0; - maxstencil = maxstencil_multi = 0; + maxstencil = maxstencil_multi_old = 0; stencil = nullptr; stencilxyz = nullptr; + nstencil_multi_old = nullptr; + stencil_multi_old = nullptr; + distsq_multi_old = nullptr; + nstencil_multi = nullptr; stencil_multi = nullptr; - distsq_multi = nullptr; + maxstencil_multi = nullptr; + + flag_half_multi = nullptr; + flag_skip_multi = nullptr; + bin_collection_multi = nullptr; + + maxcollections = 0; dimension = domain->dimension; } @@ -75,16 +95,44 @@ NStencil::~NStencil() memory->destroy(stencil); memory->destroy(stencilxyz); - if (!stencil_multi) return; + if (stencil_multi_old) { - int n = atom->ntypes; - for (int i = 1; i <= n; i++) { - memory->destroy(stencil_multi[i]); - memory->destroy(distsq_multi[i]); + int n = atom->ntypes; + for (int i = 1; i <= n; i++) { + memory->destroy(stencil_multi_old[i]); + memory->destroy(distsq_multi_old[i]); + } + delete [] nstencil_multi_old; + delete [] stencil_multi_old; + delete [] distsq_multi_old; + } + + if (maxstencil_multi) { + + memory->destroy(nstencil_multi); + for (int i = 0; i < maxcollections; i++) { + for (int j = 0; j < maxcollections; j++) + memory->destroy(stencil_multi[i][j]); + delete [] stencil_multi[i]; + } + delete [] stencil_multi; + memory->destroy(maxstencil_multi); + memory->destroy(flag_half_multi); + memory->destroy(flag_skip_multi); + memory->destroy(bin_collection_multi); + + memory->destroy(stencil_sx_multi); + memory->destroy(stencil_sy_multi); + memory->destroy(stencil_sz_multi); + + memory->destroy(stencil_mbinx_multi); + memory->destroy(stencil_mbiny_multi); + memory->destroy(stencil_mbinz_multi); + + memory->destroy(stencil_binsizex_multi); + memory->destroy(stencil_binsizey_multi); + memory->destroy(stencil_binsizez_multi); } - delete [] nstencil_multi; - delete [] stencil_multi; - delete [] distsq_multi; } /* ---------------------------------------------------------------------- */ @@ -105,6 +153,11 @@ void NStencil::copy_neighbor_info() cutneighmax = neighbor->cutneighmax; cutneighmaxsq = neighbor->cutneighmaxsq; cuttypesq = neighbor->cuttypesq; + cutneighsq = neighbor->cutneighsq; + + ncollections = neighbor->ncollections; + collection = neighbor->collection; + cutcollectionsq = neighbor->cutcollectionsq; // overwrite Neighbor cutoff with custom value set by requestor // only works for style = BIN (checked by Neighbor class) @@ -132,6 +185,23 @@ void NStencil::copy_bin_info() bininvz = nb->bininvz; } +/* ---------------------------------------------------------------------- + copy needed info for multi from NBin class to this stencil class +------------------------------------------------------------------------- */ + +void NStencil::copy_bin_info_multi() +{ + mbinx_multi = nb->mbinx_multi; + mbiny_multi = nb->mbiny_multi; + mbinz_multi = nb->mbinz_multi; + binsizex_multi = nb->binsizex_multi; + binsizey_multi = nb->binsizey_multi; + binsizez_multi = nb->binsizez_multi; + bininvx_multi = nb->bininvx_multi; + bininvy_multi = nb->bininvy_multi; + bininvz_multi = nb->bininvz_multi; +} + /* ---------------------------------------------------------------------- insure NBin data is current insure stencils are allocated large enough @@ -139,59 +209,188 @@ void NStencil::copy_bin_info() void NStencil::create_setup() { - if (nb) copy_bin_info(); - last_stencil = update->ntimestep; - // sx,sy,sz = max range of stencil in each dim - // smax = max possible size of entire 3d stencil - // stencil will be empty if cutneighmax = 0.0 + if (neighstyle != Neighbor::MULTI) { + if (nb) copy_bin_info(); + last_stencil = update->ntimestep; - sx = static_cast (cutneighmax*bininvx); - if (sx*binsizex < cutneighmax) sx++; - sy = static_cast (cutneighmax*bininvy); - if (sy*binsizey < cutneighmax) sy++; - sz = static_cast (cutneighmax*bininvz); - if (sz*binsizez < cutneighmax) sz++; - if (dimension == 2) sz = 0; + // sx,sy,sz = max range of stencil in each dim + // smax = max possible size of entire 3d stencil + // stencil will be empty if cutneighmax = 0.0 - int smax = (2*sx+1) * (2*sy+1) * (2*sz+1); + sx = static_cast(cutneighmax*bininvx); + if (sx*binsizex < cutneighmax) sx++; + sy = static_cast(cutneighmax*bininvy); + if (sy*binsizey < cutneighmax) sy++; + sz = static_cast(cutneighmax*bininvz); + if (sz*binsizez < cutneighmax) sz++; + if (dimension == 2) sz = 0; - // reallocate stencil structs if necessary - // for BIN and MULTI styles + int smax = (2*sx+1) * (2*sy+1) * (2*sz+1); - if (neighstyle == Neighbor::BIN) { - if (smax > maxstencil) { - maxstencil = smax; - memory->destroy(stencil); - memory->create(stencil,maxstencil,"neighstencil:stencil"); - if (xyzflag) { - memory->destroy(stencilxyz); - memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz"); + // reallocate stencil structs if necessary + // for BIN and MULTI_OLD styles + + if (neighstyle == Neighbor::BIN) { + if (smax > maxstencil) { + maxstencil = smax; + memory->destroy(stencil); + memory->create(stencil,maxstencil,"neighstencil:stencil"); + if (xyzflag) { + memory->destroy(stencilxyz); + memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz"); + } + } + + } else { + int i; + int n = atom->ntypes; + if (maxstencil_multi_old == 0) { + nstencil_multi_old = new int[n+1]; + stencil_multi_old = new int*[n+1]; + distsq_multi_old = new double*[n+1]; + for (i = 1; i <= n; i++) { + nstencil_multi_old[i] = 0; + stencil_multi_old[i] = nullptr; + distsq_multi_old[i] = nullptr; + } + } + if (smax > maxstencil_multi_old) { + maxstencil_multi_old = smax; + for (i = 1; i <= n; i++) { + memory->destroy(stencil_multi_old[i]); + memory->destroy(distsq_multi_old[i]); + memory->create(stencil_multi_old[i],maxstencil_multi_old, + "neighstencil:stencil_multi_old"); + memory->create(distsq_multi_old[i],maxstencil_multi_old, + "neighstencil:distsq_multi_old"); + } } } - } else { - int i; - int n = atom->ntypes; - if (maxstencil_multi == 0) { - nstencil_multi = new int[n+1]; - stencil_multi = new int*[n+1]; - distsq_multi = new double*[n+1]; - for (i = 1; i <= n; i++) { - nstencil_multi[i] = 0; - stencil_multi[i] = nullptr; - distsq_multi[i] = nullptr; + int i, j, bin_collection, smax; + double stencil_range; + int n = ncollections; + + if (nb) copy_bin_info_multi(); + + // Deallocate arrays if previously allocated + if((n > maxcollections) && stencil_multi){ + memory->destroy(nstencil_multi); + for (i = 0; i < maxcollections; i++) { + for (j = 0; j < maxcollections; j++) + memory->destroy(stencil_multi[i][j]); + delete [] stencil_multi[i]; + } + delete [] stencil_multi; + memory->destroy(maxstencil_multi); + memory->destroy(flag_half_multi); + memory->destroy(flag_skip_multi); + memory->destroy(bin_collection_multi); + memory->destroy(stencil_sx_multi); + memory->destroy(stencil_sy_multi); + memory->destroy(stencil_sz_multi); + memory->destroy(stencil_binsizex_multi); + memory->destroy(stencil_binsizey_multi); + memory->destroy(stencil_binsizez_multi); + memory->destroy(stencil_mbinx_multi); + memory->destroy(stencil_mbiny_multi); + memory->destroy(stencil_mbinz_multi); + } + + // Allocate arrays + if (!maxstencil_multi) { + memory->create(flag_half_multi, n, n, + "neighstencil:flag_half_multi"); + memory->create(flag_skip_multi, n, n, + "neighstencil:flag_skip_multi"); + memory->create(bin_collection_multi, n, n, + "neighstencil:bin_collection_multi"); + + memory->create(stencil_sx_multi, n, n, + "neighstencil:stencil_sx_multi"); + memory->create(stencil_sy_multi, n, n, + "neighstencil:stencil_sy_multi"); + memory->create(stencil_sz_multi, n, n, + "neighstencil:stencil_sz_multi"); + + memory->create(stencil_binsizex_multi, n, n, + "neighstencil:stencil_binsizex_multi"); + memory->create(stencil_binsizey_multi, n, n, + "neighstencil:stencil_binsizey_multi"); + memory->create(stencil_binsizez_multi, n, n, + "neighstencil:stencil_binsizez_multi"); + + memory->create(stencil_mbinx_multi, n, n, + "neighstencil:stencil_mbinx_multi"); + memory->create(stencil_mbiny_multi, n, n, + "neighstencil:stencil_mbiny_multi"); + memory->create(stencil_mbinz_multi, n, n, + "neighstencil:stencil_mbinz_multi"); + + memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi"); + memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi"); + stencil_multi = new int**[n](); + for (i = 0; i < n; ++i) { + stencil_multi[i] = new int*[n](); + for (j = 0; j < n; ++j) { + maxstencil_multi[i][j] = 0; + nstencil_multi[i][j] = 0; + stencil_multi[i][j] = nullptr; + } + } + maxcollections = n; + } + + // Skip all stencils by default, initialize smax + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + flag_skip_multi[i][j] = 1; } } - if (smax > maxstencil_multi) { - maxstencil_multi = smax; - for (i = 1; i <= n; i++) { - memory->destroy(stencil_multi[i]); - memory->destroy(distsq_multi[i]); - memory->create(stencil_multi[i],maxstencil_multi, - "neighstencil:stencil_multi"); - memory->create(distsq_multi[i],maxstencil_multi, - "neighstencil:distsq_multi"); + + // Determine which stencils need to be built + set_stencil_properties(); + + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + // Skip creation of unused stencils + if (flag_skip_multi[i][j]) continue; + + // Copy bin info for this pair of atom collections + bin_collection = bin_collection_multi[i][j]; + + stencil_binsizex_multi[i][j] = binsizex_multi[bin_collection]; + stencil_binsizey_multi[i][j] = binsizey_multi[bin_collection]; + stencil_binsizez_multi[i][j] = binsizez_multi[bin_collection]; + + stencil_mbinx_multi[i][j] = mbinx_multi[bin_collection]; + stencil_mbiny_multi[i][j] = mbiny_multi[bin_collection]; + stencil_mbinz_multi[i][j] = mbinz_multi[bin_collection]; + + stencil_range = sqrt(cutcollectionsq[i][j]); + + sx = static_cast (stencil_range*bininvx_multi[bin_collection]); + if (sx*binsizex_multi[bin_collection] < stencil_range) sx++; + sy = static_cast (stencil_range*bininvy_multi[bin_collection]); + if (sy*binsizey_multi[bin_collection] < stencil_range) sy++; + sz = static_cast (stencil_range*bininvz_multi[bin_collection]); + if (sz*binsizez_multi[bin_collection] < stencil_range) sz++; + if (dimension == 2) sz = 0; + + stencil_sx_multi[i][j] = sx; + stencil_sy_multi[i][j] = sy; + stencil_sz_multi[i][j] = sz; + + smax = ((2*sx+1) * (2*sy+1) * (2*sz+1)); + + if (smax > maxstencil_multi[i][j]) { + maxstencil_multi[i][j] = smax; + if(stencil_multi[i][j]) + memory->destroy(stencil_multi[i][j]); + memory->create(stencil_multi[i][j], smax, + "neighstencil::stencil_multi"); + } } } } @@ -220,6 +419,30 @@ double NStencil::bin_distance(int i, int j, int k) return (delx*delx + dely*dely + delz*delz); } + +/* ---------------------------------------------------------------------- + compute closest distance for a given atom collection +------------------------------------------------------------------------- */ + +double NStencil::bin_distance_multi(int i, int j, int k, int ic) +{ + double delx,dely,delz; + + if (i > 0) delx = (i-1)*binsizex_multi[ic]; + else if (i == 0) delx = 0.0; + else delx = (i+1)*binsizex_multi[ic]; + + if (j > 0) dely = (j-1)*binsizey_multi[ic]; + else if (j == 0) dely = 0.0; + else dely = (j+1)*binsizey_multi[ic]; + + if (k > 0) delz = (k-1)*binsizez_multi[ic]; + else if (k == 0) delz = 0.0; + else delz = (k+1)*binsizez_multi[ic]; + + return (delx*delx + dely*dely + delz*delz); +} + /* ---------------------------------------------------------------------- */ double NStencil::memory_usage() @@ -228,9 +451,16 @@ double NStencil::memory_usage() if (neighstyle == Neighbor::BIN) { bytes += memory->usage(stencil,maxstencil); bytes += memory->usage(stencilxyz,maxstencil,3); + } else if (neighstyle == Neighbor::MULTI_OLD) { + bytes += (double)atom->ntypes*maxstencil_multi_old * sizeof(int); + bytes += (double)atom->ntypes*maxstencil_multi_old * sizeof(double); } else if (neighstyle == Neighbor::MULTI) { - bytes += (double)atom->ntypes*maxstencil_multi * sizeof(int); - bytes += (double)atom->ntypes*maxstencil_multi * sizeof(double); + int n = ncollections; + for (int i = 0; i < n; i++) { + for (int j = 0; j < n; j++) { + bytes += (double)maxstencil_multi[i][j] * sizeof(int); + } + } } return bytes; } diff --git a/src/nstencil.h b/src/nstencil.h index d35035eb90..821f9a7e55 100644 --- a/src/nstencil.h +++ b/src/nstencil.h @@ -27,13 +27,26 @@ class NStencil : protected Pointers { int nstencil; // # of bins in stencil int *stencil; // list of bin offsets int **stencilxyz; // bin offsets in xyz dims - int *nstencil_multi; // # bins in each type-based multi stencil - int **stencil_multi; // list of bin offsets in each stencil - double **distsq_multi; // sq distances to bins in each stencil + int *nstencil_multi_old; // # bins in each type-based old multi stencil + int **stencil_multi_old; // list of bin offsets in each stencil + double **distsq_multi_old; // sq distances to bins in each stencil + int ** nstencil_multi; // # bins bins in each igroup-jgroup multi stencil + int *** stencil_multi; // list of bin offsets in each multi stencil + int ** maxstencil_multi; // max stencil size for each multi stencil + int maxcollections; // size of multi arrays + int sx,sy,sz; // extent of stencil in each dim + int **stencil_sx_multi; // analogs for each multi stencil + int **stencil_sy_multi; + int **stencil_sz_multi; double cutoff_custom; // cutoff set by requestor + // Arrays to store options for multi itype-jtype stencils + bool **flag_half_multi; // flag creation of a half stencil for icollection-jcollection + bool **flag_skip_multi; // skip creation of icollection-jcollection stencils (for newton on) + int **bin_collection_multi; // what collection to use for bin information + NStencil(class LAMMPS *); virtual ~NStencil(); void post_constructor(class NeighRequest *); @@ -53,6 +66,10 @@ class NStencil : protected Pointers { double cutneighmax; double cutneighmaxsq; double *cuttypesq; + double **cutneighsq; + double **cutcollectionsq; + int ncollections; + int *collection; // data from NBin class @@ -60,18 +77,45 @@ class NStencil : protected Pointers { double binsizex,binsizey,binsizez; double bininvx,bininvy,bininvz; + // data from NBin class for multi + + int *mbinx_multi; + int *mbiny_multi; + int *mbinz_multi; + double *binsizex_multi; + double *binsizey_multi; + double *binsizez_multi; + double *bininvx_multi; + double *bininvy_multi; + double *bininvz_multi; + + // Stored bin information for each stencil + + int **stencil_mbinx_multi; + int **stencil_mbiny_multi; + int **stencil_mbinz_multi; + double **stencil_binsizex_multi; + double **stencil_binsizey_multi; + double **stencil_binsizez_multi; + // data common to all NStencil variants int xyzflag; // 1 if stencilxyz is allocated int maxstencil; // max size of stencil - int maxstencil_multi; // max sizes of stencils + int maxstencil_multi_old; // max sizes of stencils int dimension; - // methods for all NStencil variants + // methods for standard NStencil variants void copy_bin_info(); // copy info from NBin class double bin_distance(int, int, int); // distance between bin corners + + // methods for multi NStencil + + double bin_distance_multi(int, int, int, int); // distance between bin corners for different collections + void copy_bin_info_multi(); // copy multi info from NBin class + virtual void set_stencil_properties(){} // determine which stencils to build and how }; } diff --git a/src/nstencil_full_bin_2d.h b/src/nstencil_full_bin_2d.h index 25fe7a450e..9e6678f1cb 100644 --- a/src/nstencil_full_bin_2d.h +++ b/src/nstencil_full_bin_2d.h @@ -15,8 +15,7 @@ NStencilStyle(full/bin/2d, NStencilFullBin2d, - NS_FULL | NS_BIN | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_BIN | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_bin_3d.h b/src/nstencil_full_bin_3d.h index 674333fc29..9e61976462 100644 --- a/src/nstencil_full_bin_3d.h +++ b/src/nstencil_full_bin_3d.h @@ -15,8 +15,7 @@ NStencilStyle(full/bin/3d, NStencilFullBin3d, - NS_FULL | NS_BIN | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_BIN | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_ghost_bin_2d.h b/src/nstencil_full_ghost_bin_2d.h index 6f6289d0a4..adfbaab39c 100644 --- a/src/nstencil_full_ghost_bin_2d.h +++ b/src/nstencil_full_ghost_bin_2d.h @@ -15,8 +15,7 @@ NStencilStyle(full/ghost/bin/2d, NStencilFullGhostBin2d, - NS_FULL | NS_GHOST | NS_BIN | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_GHOST | NS_BIN | NS_2D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_ghost_bin_3d.h b/src/nstencil_full_ghost_bin_3d.h index 493c4f7c51..675ba8d567 100644 --- a/src/nstencil_full_ghost_bin_3d.h +++ b/src/nstencil_full_ghost_bin_3d.h @@ -15,8 +15,7 @@ NStencilStyle(full/ghost/bin/3d, NStencilFullGhostBin3d, - NS_FULL | NS_GHOST | NS_BIN | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NS_FULL | NS_GHOST | NS_BIN | NS_3D | NS_ORTHO | NS_TRI) #else diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index b71ca5e55d..ae7bcad52e 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -12,7 +12,12 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_multi_2d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" #include "atom.h" +#include using namespace LAMMPS_NS; @@ -20,31 +25,60 @@ using namespace LAMMPS_NS; NStencilFullMulti2d::NStencilFullMulti2d(LAMMPS *lmp) : NStencil(lmp) {} +/* ---------------------------------------------------------------------- */ + +void NStencilFullMulti2d::set_stencil_properties() +{ + int n = ncollections; + int i, j; + + // Always look up neighbor using full stencil and neighbor's bin + + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + flag_half_multi[i][j] = 0; + flag_skip_multi[i][j] = 0; + bin_collection_multi[i][j] = j; + } + } +} + /* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff + create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ void NStencilFullMulti2d::create() { - int i,j,n; - double rsq,typesq; - int *s; - double *distsq; + int icollection, jcollection, bin_collection, i, j, ns; + int n = ncollections; + double cutsq; - int ntypes = atom->ntypes; - for (int itype = 1; itype <= ntypes; itype++) { - typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - n = 0; - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) { - rsq = bin_distance(i,j,0); - if (rsq < typesq) { - distsq[n] = rsq; - s[n++] = j*mbinx + i; - } + + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; } - nstencil_multi[itype] = n; + + ns = 0; + + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + + bin_collection = bin_collection_multi[icollection][jcollection]; + + cutsq = cutcollectionsq[icollection][jcollection]; + + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; + + nstencil_multi[icollection][jcollection] = ns; + } } } diff --git a/src/nstencil_full_multi_2d.h b/src/nstencil_full_multi_2d.h index 4bef4f6349..ba6cd22a39 100644 --- a/src/nstencil_full_multi_2d.h +++ b/src/nstencil_full_multi_2d.h @@ -14,9 +14,7 @@ #ifdef NSTENCIL_CLASS NStencilStyle(full/multi/2d, - NStencilFullMulti2d, - NS_FULL | NS_MULTI | NS_2D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NStencilFullMulti2d, NS_FULL | NS_MULTI | NS_2D | NS_ORTHO | NS_TRI) #else @@ -32,6 +30,10 @@ class NStencilFullMulti2d : public NStencil { NStencilFullMulti2d(class LAMMPS *); ~NStencilFullMulti2d() {} void create(); + + protected: + void set_stencil_properties(); + }; } diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index 2c63476ae6..7bdf9561f1 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -12,7 +12,12 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_multi_3d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" #include "atom.h" +#include using namespace LAMMPS_NS; @@ -20,32 +25,65 @@ using namespace LAMMPS_NS; NStencilFullMulti3d::NStencilFullMulti3d(LAMMPS *lmp) : NStencil(lmp) {} +/* ---------------------------------------------------------------------- */ + +void NStencilFullMulti3d::set_stencil_properties() +{ + int n = ncollections; + int i, j; + + // Always look up neighbor using full stencil and neighbor's bin + // Stencil cutoff set by i-j cutoff + + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + flag_half_multi[i][j] = 0; + flag_skip_multi[i][j] = 0; + bin_collection_multi[i][j] = j; + } + } +} + /* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff + create stencils based on bin geometry and cutoff ------------------------------------------------------------------------- */ void NStencilFullMulti3d::create() { - int i,j,k,n; - double rsq,typesq; - int *s; - double *distsq; + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; + double cutsq; - int ntypes = atom->ntypes; - for (int itype = 1; itype <= ntypes; itype++) { - typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; - n = 0; - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) { - rsq = bin_distance(i,j,k); - if (rsq < typesq) { - distsq[n] = rsq; - s[n++] = k*mbiny*mbinx + j*mbinx + i; - } - } - nstencil_multi[itype] = n; + + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } + + ns = 0; + + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; + + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; + + bin_collection = bin_collection_multi[icollection][jcollection]; + + cutsq = cutcollectionsq[icollection][jcollection]; + + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = + k*mbiny*mbinx + j*mbinx + i; + + nstencil_multi[icollection][jcollection] = ns; + } } } diff --git a/src/nstencil_full_multi_3d.h b/src/nstencil_full_multi_3d.h index 520e33389a..d02a8b3588 100644 --- a/src/nstencil_full_multi_3d.h +++ b/src/nstencil_full_multi_3d.h @@ -14,9 +14,7 @@ #ifdef NSTENCIL_CLASS NStencilStyle(full/multi/3d, - NStencilFullMulti3d, - NS_FULL | NS_MULTI | NS_3D | - NS_NEWTON | NS_NEWTOFF | NS_ORTHO | NS_TRI) + NStencilFullMulti3d, NS_FULL | NS_MULTI | NS_3D | NS_ORTHO | NS_TRI) #else @@ -30,8 +28,12 @@ namespace LAMMPS_NS { class NStencilFullMulti3d : public NStencil { public: NStencilFullMulti3d(class LAMMPS *); - ~NStencilFullMulti3d() {} + ~NStencilFullMulti3d(){} void create(); + + protected: + void set_stencil_properties(); + }; } diff --git a/src/nstencil_half_multi_2d_newtoff.cpp b/src/nstencil_full_multi_old_2d.cpp similarity index 83% rename from src/nstencil_half_multi_2d_newtoff.cpp rename to src/nstencil_full_multi_old_2d.cpp index 9b6ea08862..ec2dba322e 100644 --- a/src/nstencil_half_multi_2d_newtoff.cpp +++ b/src/nstencil_full_multi_old_2d.cpp @@ -11,21 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_newtoff.h" +#include "nstencil_full_multi_old_2d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dNewtoff:: -NStencilHalfMulti2dNewtoff(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMultiOld2d::NStencilFullMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dNewtoff::create() +void NStencilFullMultiOld2d::create() { int i,j,n; double rsq,typesq; @@ -35,8 +34,8 @@ void NStencilHalfMulti2dNewtoff::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = -sy; j <= sy; j++) for (i = -sx; i <= sx; i++) { @@ -46,6 +45,6 @@ void NStencilHalfMulti2dNewtoff::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_bin_2d_newton.h b/src/nstencil_full_multi_old_2d.h similarity index 69% rename from src/nstencil_half_bin_2d_newton.h rename to src/nstencil_full_multi_old_2d.h index 4d45321281..69829f47f1 100644 --- a/src/nstencil_half_bin_2d_newton.h +++ b/src/nstencil_full_multi_old_2d.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/2d/newton, - NStencilHalfBin2dNewton, - NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_ORTHO) +NStencilStyle(full/multi/old/2d, + NStencilFullMultiOld2d, + NS_FULL | NS_MULTI_OLD | NS_2D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_H -#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_H +#ifndef LMP_NSTENCIL_FULL_MULTI_OLD_2D_H +#define LMP_NSTENCIL_FULL_MULTI_OLD_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBin2dNewton : public NStencil { +class NStencilFullMultiOld2d : public NStencil { public: - NStencilHalfBin2dNewton(class LAMMPS *); - ~NStencilHalfBin2dNewton() {} + NStencilFullMultiOld2d(class LAMMPS *); + ~NStencilFullMultiOld2d() {} void create(); }; diff --git a/src/nstencil_half_multi_3d_newtoff.cpp b/src/nstencil_full_multi_old_3d.cpp similarity index 84% rename from src/nstencil_half_multi_3d_newtoff.cpp rename to src/nstencil_full_multi_old_3d.cpp index 533ba21c3a..2bfd962261 100644 --- a/src/nstencil_half_multi_3d_newtoff.cpp +++ b/src/nstencil_full_multi_old_3d.cpp @@ -11,21 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_newtoff.h" +#include "nstencil_full_multi_old_3d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dNewtoff:: -NStencilHalfMulti3dNewtoff(LAMMPS *lmp) : NStencil(lmp) {} +NStencilFullMultiOld3d::NStencilFullMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dNewtoff::create() +void NStencilFullMultiOld3d::create() { int i,j,k,n; double rsq,typesq; @@ -35,8 +34,8 @@ void NStencilHalfMulti3dNewtoff::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = -sz; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -47,6 +46,6 @@ void NStencilHalfMulti3dNewtoff::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_bin_3d_newton.h b/src/nstencil_full_multi_old_3d.h similarity index 69% rename from src/nstencil_half_bin_3d_newton.h rename to src/nstencil_full_multi_old_3d.h index cd854f6128..9c760682d0 100644 --- a/src/nstencil_half_bin_3d_newton.h +++ b/src/nstencil_full_multi_old_3d.h @@ -13,23 +13,23 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/bin/3d/newton, - NStencilHalfBin3dNewton, - NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_ORTHO) +NStencilStyle(full/multi/old/3d, + NStencilFullMultiOld3d, + NS_FULL | NS_MULTI_OLD | NS_3D | NS_ORTHO | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_H +#ifndef LMP_NSTENCIL_FULL_MULTI_OLD_3D_H +#define LMP_NSTENCIL_FULL_MULTI_OLD_3D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfBin3dNewton : public NStencil { +class NStencilFullMultiOld3d : public NStencil { public: - NStencilHalfBin3dNewton(class LAMMPS *); - ~NStencilHalfBin3dNewton() {} + NStencilFullMultiOld3d(class LAMMPS *); + ~NStencilFullMultiOld3d() {} void create(); }; diff --git a/src/nstencil_half_bin_2d_newton.cpp b/src/nstencil_half_bin_2d.cpp similarity index 87% rename from src/nstencil_half_bin_2d_newton.cpp rename to src/nstencil_half_bin_2d.cpp index f7bf4ffff6..e74e26e89b 100644 --- a/src/nstencil_half_bin_2d_newton.cpp +++ b/src/nstencil_half_bin_2d.cpp @@ -11,19 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton.h" +#include "nstencil_half_bin_2d.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewton::NStencilHalfBin2dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfBin2d::NStencilHalfBin2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewton::create() +void NStencilHalfBin2d::create() { int i,j; diff --git a/src/nstencil_half_bin_2d.h b/src/nstencil_half_bin_2d.h new file mode 100644 index 0000000000..fe5f4cf2da --- /dev/null +++ b/src/nstencil_half_bin_2d.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/bin/2d, + NStencilHalfBin2d, + NS_HALF | NS_BIN | NS_2D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_BIN_2D_H +#define LMP_NSTENCIL_HALF_BIN_2D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBin2d : public NStencil { + public: + NStencilHalfBin2d(class LAMMPS *); + ~NStencilHalfBin2d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp deleted file mode 100644 index 09c74d8b69..0000000000 --- a/src/nstencil_half_bin_2d_newtoff.cpp +++ /dev/null @@ -1,37 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_bin_2d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBin2dNewtoff::NStencilHalfBin2dNewtoff(LAMMPS *lmp) : - NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBin2dNewtoff::create() -{ - int i,j; - - nstencil = 0; - - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutneighmaxsq) - stencil[nstencil++] = j*mbinx + i; -} diff --git a/src/nstencil_half_bin_2d_newton_tri.cpp b/src/nstencil_half_bin_2d_tri.cpp similarity index 87% rename from src/nstencil_half_bin_2d_newton_tri.cpp rename to src/nstencil_half_bin_2d_tri.cpp index b335ec1b34..914a0f4f3d 100644 --- a/src/nstencil_half_bin_2d_newton_tri.cpp +++ b/src/nstencil_half_bin_2d_tri.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_2d_newton_tri.h" +#include "nstencil_half_bin_2d_tri.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin2dNewtonTri::NStencilHalfBin2dNewtonTri(LAMMPS *lmp) : +NStencilHalfBin2dTri::NStencilHalfBin2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin2dNewtonTri::create() +void NStencilHalfBin2dTri::create() { int i,j; diff --git a/src/nstencil_half_bin_2d_tri.h b/src/nstencil_half_bin_2d_tri.h new file mode 100644 index 0000000000..1826e8807c --- /dev/null +++ b/src/nstencil_half_bin_2d_tri.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/bin/2d/tri, + NStencilHalfBin2dTri, + NS_HALF | NS_BIN | NS_2D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_BIN_2D_TRI_H +#define LMP_NSTENCIL_HALF_BIN_2D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBin2dTri : public NStencil { + public: + NStencilHalfBin2dTri(class LAMMPS *); + ~NStencilHalfBin2dTri() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bin_3d_newton.cpp b/src/nstencil_half_bin_3d.cpp similarity index 88% rename from src/nstencil_half_bin_3d_newton.cpp rename to src/nstencil_half_bin_3d.cpp index d09affd83f..227a3af163 100644 --- a/src/nstencil_half_bin_3d_newton.cpp +++ b/src/nstencil_half_bin_3d.cpp @@ -11,19 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton.h" +#include "nstencil_half_bin_3d.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewton::NStencilHalfBin3dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfBin3d::NStencilHalfBin3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewton::create() +void NStencilHalfBin3d::create() { int i,j,k; diff --git a/src/nstencil_half_bin_3d.h b/src/nstencil_half_bin_3d.h new file mode 100644 index 0000000000..ae0f0d89f1 --- /dev/null +++ b/src/nstencil_half_bin_3d.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/bin/3d, + NStencilHalfBin3d, + NS_HALF | NS_BIN | NS_3D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_BIN_3D_H +#define LMP_NSTENCIL_HALF_BIN_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBin3d : public NStencil { + public: + NStencilHalfBin3d(class LAMMPS *); + ~NStencilHalfBin3d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp deleted file mode 100644 index 36b2a11c66..0000000000 --- a/src/nstencil_half_bin_3d_newtoff.cpp +++ /dev/null @@ -1,38 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_bin_3d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfBin3dNewtoff::NStencilHalfBin3dNewtoff(LAMMPS *lmp) : - NStencil(lmp) {} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfBin3dNewtoff::create() -{ - int i,j,k; - - nstencil = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutneighmaxsq) - stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; -} diff --git a/src/nstencil_half_bin_3d_newton_tri.h b/src/nstencil_half_bin_3d_newton_tri.h deleted file mode 100644 index 9a2e7a31e0..0000000000 --- a/src/nstencil_half_bin_3d_newton_tri.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/bin/3d/newton/tri, - NStencilHalfBin3dNewtonTri, - NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_TRI_H -#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfBin3dNewtonTri : public NStencil { - public: - NStencilHalfBin3dNewtonTri(class LAMMPS *); - ~NStencilHalfBin3dNewtonTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_bin_3d_newton_tri.cpp b/src/nstencil_half_bin_3d_tri.cpp similarity index 88% rename from src/nstencil_half_bin_3d_newton_tri.cpp rename to src/nstencil_half_bin_3d_tri.cpp index 08c540e8b2..9f2002e0a8 100644 --- a/src/nstencil_half_bin_3d_newton_tri.cpp +++ b/src/nstencil_half_bin_3d_tri.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_bin_3d_newton_tri.h" +#include "nstencil_half_bin_3d_tri.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfBin3dNewtonTri::NStencilHalfBin3dNewtonTri(LAMMPS *lmp) : +NStencilHalfBin3dTri::NStencilHalfBin3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfBin3dNewtonTri::create() +void NStencilHalfBin3dTri::create() { int i,j,k; diff --git a/src/nstencil_half_bin_3d_tri.h b/src/nstencil_half_bin_3d_tri.h new file mode 100644 index 0000000000..324182ed73 --- /dev/null +++ b/src/nstencil_half_bin_3d_tri.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/bin/3d/tri, + NStencilHalfBin3dTri, + NS_HALF | NS_BIN | NS_3D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_BIN_3D_TRI_H +#define LMP_NSTENCIL_HALF_BIN_3D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfBin3dTri : public NStencil { + public: + NStencilHalfBin3dTri(class LAMMPS *); + ~NStencilHalfBin3dTri() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp deleted file mode 100644 index 0aa5202da8..0000000000 --- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp +++ /dev/null @@ -1,44 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_ghost_bin_2d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfGhostBin2dNewtoff:: -NStencilHalfGhostBin2dNewtoff(LAMMPS *lmp) : NStencil(lmp) -{ - xyzflag = 1; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfGhostBin2dNewtoff::create() -{ - int i,j; - - nstencil = 0; - - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,0) < cutneighmaxsq) { - stencilxyz[nstencil][0] = i; - stencilxyz[nstencil][1] = j; - stencilxyz[nstencil][2] = 0; - stencil[nstencil++] = j*mbinx + i; - } -} diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.h b/src/nstencil_half_ghost_bin_2d_newtoff.h deleted file mode 100644 index 37aee019ba..0000000000 --- a/src/nstencil_half_ghost_bin_2d_newtoff.h +++ /dev/null @@ -1,44 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/ghost/bin/2d/newtoff, - NStencilHalfGhostBin2dNewtoff, - NS_HALF | NS_GHOST | NS_BIN | NS_2D | - NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_GHOST_BIN_2D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_GHOST_BIN_2D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfGhostBin2dNewtoff : public NStencil { - public: - NStencilHalfGhostBin2dNewtoff(class LAMMPS *); - ~NStencilHalfGhostBin2dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp deleted file mode 100644 index 95016108e4..0000000000 --- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp +++ /dev/null @@ -1,45 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "nstencil_half_ghost_bin_3d_newtoff.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -NStencilHalfGhostBin3dNewtoff:: -NStencilHalfGhostBin3dNewtoff(LAMMPS *lmp) : NStencil(lmp) -{ - xyzflag = 1; -} - -/* ---------------------------------------------------------------------- - create stencil based on bin geometry and cutoff -------------------------------------------------------------------------- */ - -void NStencilHalfGhostBin3dNewtoff::create() -{ - int i,j,k; - - nstencil = 0; - - for (k = -sz; k <= sz; k++) - for (j = -sy; j <= sy; j++) - for (i = -sx; i <= sx; i++) - if (bin_distance(i,j,k) < cutneighmaxsq) { - stencilxyz[nstencil][0] = i; - stencilxyz[nstencil][1] = j; - stencilxyz[nstencil][2] = k; - stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; - } -} diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.h b/src/nstencil_half_ghost_bin_3d_newtoff.h deleted file mode 100644 index b22d397290..0000000000 --- a/src/nstencil_half_ghost_bin_3d_newtoff.h +++ /dev/null @@ -1,44 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/ghost/bin/3d/newtoff, - NStencilHalfGhostBin3dNewtoff, - NS_HALF | NS_GHOST | NS_BIN | NS_3D | - NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_GHOST_BIN_3D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_GHOST_BIN_3D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfGhostBin3dNewtoff : public NStencil { - public: - NStencilHalfGhostBin3dNewtoff(class LAMMPS *); - ~NStencilHalfGhostBin3dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_2d.cpp b/src/nstencil_half_multi_2d.cpp new file mode 100644 index 0000000000..6754ddb658 --- /dev/null +++ b/src/nstencil_half_multi_2d.cpp @@ -0,0 +1,106 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_multi_2d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfMulti2d::NStencilHalfMulti2d(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti2d::set_stencil_properties() +{ + int n = ncollections; + int i, j; + + // Cross collections: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil + + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; + + flag_skip_multi[i][j] = 0; + + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ + flag_half_multi[i][j] = 1; + bin_collection_multi[i][j] = i; + } else { + flag_half_multi[i][j] = 0; + bin_collection_multi[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti2d::create() +{ + int icollection, jcollection, bin_collection, i, j, ns; + int n = ncollections; + double cutsq; + + + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } + + ns = 0; + + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + + bin_collection = bin_collection_multi[icollection][jcollection]; + + cutsq = cutcollectionsq[icollection][jcollection]; + + if (flag_half_multi[icollection][jcollection]) { + for (j = 0; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (j > 0 || (j == 0 && i > 0)) { + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; + } + } else { + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; + } + + nstencil_multi[icollection][jcollection] = ns; + } + } +} + diff --git a/src/nstencil_half_multi_2d_newton.h b/src/nstencil_half_multi_2d.h similarity index 68% rename from src/nstencil_half_multi_2d_newton.h rename to src/nstencil_half_multi_2d.h index 4cba552cf3..1e10e50411 100644 --- a/src/nstencil_half_multi_2d_newton.h +++ b/src/nstencil_half_multi_2d.h @@ -13,24 +13,27 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/2d/newton, - NStencilHalfMulti2dNewton, - NS_HALF | NS_MULTI | NS_2D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/multi/2d, + NStencilHalfMulti2d, NS_HALF | NS_MULTI | NS_2D | NS_ORTHO) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_H -#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_H +#define LMP_NSTENCIL_HALF_MULTI_2D_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti2dNewton : public NStencil { +class NStencilHalfMulti2d : public NStencil { public: - NStencilHalfMulti2dNewton(class LAMMPS *); - ~NStencilHalfMulti2dNewton() {} + NStencilHalfMulti2d(class LAMMPS *); + ~NStencilHalfMulti2d() {} void create(); + + protected: + void set_stencil_properties(); + }; } diff --git a/src/nstencil_half_multi_2d_newtoff.h b/src/nstencil_half_multi_2d_newtoff.h deleted file mode 100644 index bba992725e..0000000000 --- a/src/nstencil_half_multi_2d_newtoff.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/2d/newtoff, - NStencilHalfMulti2dNewtoff, - NS_HALF | NS_MULTI | NS_2D | NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti2dNewtoff : public NStencil { - public: - NStencilHalfMulti2dNewtoff(class LAMMPS *); - ~NStencilHalfMulti2dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_2d_newton_tri.h b/src/nstencil_half_multi_2d_newton_tri.h deleted file mode 100644 index e129704ae8..0000000000 --- a/src/nstencil_half_multi_2d_newton_tri.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/2d/newton/tri, - NStencilHalfMulti2dNewtonTri, - NS_HALF | NS_MULTI | NS_2D | NS_NEWTON | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_TRI_H -#define LMP_NSTENCIL_HALF_MULTI_2D_NEWTON_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti2dNewtonTri : public NStencil { - public: - NStencilHalfMulti2dNewtonTri(class LAMMPS *); - ~NStencilHalfMulti2dNewtonTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_2d_tri.cpp b/src/nstencil_half_multi_2d_tri.cpp new file mode 100644 index 0000000000..cd215ee384 --- /dev/null +++ b/src/nstencil_half_multi_2d_tri.cpp @@ -0,0 +1,103 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_multi_2d_tri.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfMulti2dTri::NStencilHalfMulti2dTri(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti2dTri::set_stencil_properties() +{ + int n = ncollections; + int i, j; + + // Cross collections: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil + + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; + + flag_skip_multi[i][j] = 0; + + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ + flag_half_multi[i][j] = 1; + bin_collection_multi[i][j] = i; + } else { + flag_half_multi[i][j] = 0; + bin_collection_multi[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti2dTri::create() +{ + int icollection, jcollection, bin_collection, i, j, ns; + int n = ncollections; + double cutsq; + + + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } + + ns = 0; + + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + + bin_collection = bin_collection_multi[icollection][jcollection]; + + cutsq = cutcollectionsq[icollection][jcollection]; + + if (flag_half_multi[icollection][jcollection]) { + for (j = 0; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; + } else { + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance_multi(i,j,0,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = j*mbinx + i; + } + + nstencil_multi[icollection][jcollection] = ns; + } + } +} diff --git a/src/nstencil_half_multi_3d_newton.h b/src/nstencil_half_multi_2d_tri.h similarity index 68% rename from src/nstencil_half_multi_3d_newton.h rename to src/nstencil_half_multi_2d_tri.h index 32642ca8ab..d04424478a 100644 --- a/src/nstencil_half_multi_3d_newton.h +++ b/src/nstencil_half_multi_2d_tri.h @@ -13,24 +13,26 @@ #ifdef NSTENCIL_CLASS -NStencilStyle(half/multi/3d/newton, - NStencilHalfMulti3dNewton, - NS_HALF | NS_MULTI | NS_3D | NS_NEWTON | NS_ORTHO) +NStencilStyle(half/multi/2d/tri, + NStencilHalfMulti2dTri, NS_HALF | NS_MULTI | NS_2D | NS_TRI) #else -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_H -#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_H +#ifndef LMP_NSTENCIL_HALF_MULTI_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_2D_TRI_H #include "nstencil.h" namespace LAMMPS_NS { -class NStencilHalfMulti3dNewton : public NStencil { +class NStencilHalfMulti2dTri : public NStencil { public: - NStencilHalfMulti3dNewton(class LAMMPS *); - ~NStencilHalfMulti3dNewton() {} + NStencilHalfMulti2dTri(class LAMMPS *); + ~NStencilHalfMulti2dTri() {} void create(); + + protected: + void set_stencil_properties(); }; } diff --git a/src/nstencil_half_multi_3d.cpp b/src/nstencil_half_multi_3d.cpp new file mode 100644 index 0000000000..6e60c34343 --- /dev/null +++ b/src/nstencil_half_multi_3d.cpp @@ -0,0 +1,112 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_multi_3d.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfMulti3d::NStencilHalfMulti3d(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti3d::set_stencil_properties() +{ + int n = ncollections; + int i, j; + + // Cross collections: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil + + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; + + flag_skip_multi[i][j] = 0; + + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ + flag_half_multi[i][j] = 1; + bin_collection_multi[i][j] = i; + } else { + flag_half_multi[i][j] = 0; + bin_collection_multi[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti3d::create() +{ + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; + double cutsq; + + + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } + + ns = 0; + + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; + + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; + + bin_collection = bin_collection_multi[icollection][jcollection]; + + cutsq = cutcollectionsq[icollection][jcollection]; + + if (flag_half_multi[icollection][jcollection]) { + for (k = 0; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (k > 0 || j > 0 || (j == 0 && i > 0)) { + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + } else { + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + + nstencil_multi[icollection][jcollection] = ns; + } + } +} + diff --git a/src/nstencil_half_multi_3d.h b/src/nstencil_half_multi_3d.h new file mode 100644 index 0000000000..b86d7a3ad8 --- /dev/null +++ b/src/nstencil_half_multi_3d.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/3d, + NStencilHalfMulti3d, NS_HALF | NS_MULTI | NS_3D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_H +#define LMP_NSTENCIL_HALF_MULTI_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti3d : public NStencil { + public: + NStencilHalfMulti3d(class LAMMPS *); + ~NStencilHalfMulti3d() {} + void create(); + + protected: + void set_stencil_properties(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_3d_newtoff.h b/src/nstencil_half_multi_3d_newtoff.h deleted file mode 100644 index 64c42f4e7a..0000000000 --- a/src/nstencil_half_multi_3d_newtoff.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/3d/newtoff, - NStencilHalfMulti3dNewtoff, - NS_HALF | NS_MULTI | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTOFF_H -#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTOFF_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti3dNewtoff : public NStencil { - public: - NStencilHalfMulti3dNewtoff(class LAMMPS *); - ~NStencilHalfMulti3dNewtoff() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_3d_newton_tri.h b/src/nstencil_half_multi_3d_newton_tri.h deleted file mode 100644 index fb8a957ce9..0000000000 --- a/src/nstencil_half_multi_3d_newton_tri.h +++ /dev/null @@ -1,43 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - https://lammps.sandia.gov/, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef NSTENCIL_CLASS - -NStencilStyle(half/multi/3d/newton/tri, - NStencilHalfMulti3dNewtonTri, - NS_HALF | NS_MULTI | NS_3D | NS_NEWTON | NS_TRI) - -#else - -#ifndef LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_TRI_H -#define LMP_NSTENCIL_HALF_MULTI_3D_NEWTON_TRI_H - -#include "nstencil.h" - -namespace LAMMPS_NS { - -class NStencilHalfMulti3dNewtonTri : public NStencil { - public: - NStencilHalfMulti3dNewtonTri(class LAMMPS *); - ~NStencilHalfMulti3dNewtonTri() {} - void create(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/nstencil_half_multi_3d_tri.cpp b/src/nstencil_half_multi_3d_tri.cpp new file mode 100644 index 0000000000..632ca5f0ed --- /dev/null +++ b/src/nstencil_half_multi_3d_tri.cpp @@ -0,0 +1,109 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "nstencil_half_multi_3d_tri.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "nbin.h" +#include "memory.h" +#include "atom.h" +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +NStencilHalfMulti3dTri::NStencilHalfMulti3dTri(LAMMPS *lmp) : + NStencil(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void NStencilHalfMulti3dTri::set_stencil_properties() +{ + int n = ncollections; + int i, j; + + // Cross collections: use full stencil, looking one way through hierarchy + // smaller -> larger => use full stencil in larger bin + // larger -> smaller => no nstencil required + // If cut offs are same, use half stencil + + for (i = 0; i < n; i++) { + for (j = 0; j < n; j++) { + if(cutcollectionsq[i][i] > cutcollectionsq[j][j]) continue; + + flag_skip_multi[i][j] = 0; + + if(cutcollectionsq[i][i] == cutcollectionsq[j][j]){ + flag_half_multi[i][j] = 1; + bin_collection_multi[i][j] = i; + } else { + flag_half_multi[i][j] = 0; + bin_collection_multi[i][j] = j; + } + } + } +} + +/* ---------------------------------------------------------------------- + create stencils based on bin geometry and cutoff +------------------------------------------------------------------------- */ + +void NStencilHalfMulti3dTri::create() +{ + int icollection, jcollection, bin_collection, i, j, k, ns; + int n = ncollections; + double cutsq; + + + for (icollection = 0; icollection < n; icollection++) { + for (jcollection = 0; jcollection < n; jcollection++) { + if (flag_skip_multi[icollection][jcollection]) { + nstencil_multi[icollection][jcollection] = 0; + continue; + } + + ns = 0; + + sx = stencil_sx_multi[icollection][jcollection]; + sy = stencil_sy_multi[icollection][jcollection]; + sz = stencil_sz_multi[icollection][jcollection]; + + mbinx = stencil_mbinx_multi[icollection][jcollection]; + mbiny = stencil_mbiny_multi[icollection][jcollection]; + mbinz = stencil_mbinz_multi[icollection][jcollection]; + + bin_collection = bin_collection_multi[icollection][jcollection]; + + cutsq = cutcollectionsq[icollection][jcollection]; + + if (flag_half_multi[icollection][jcollection]) { + for (k = 0; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } else { + for (k = -sz; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance_multi(i,j,k,bin_collection) < cutsq) + stencil_multi[icollection][jcollection][ns++] = + k*mbiny*mbinx + j*mbinx + i; + } + + nstencil_multi[icollection][jcollection] = ns; + } + } +} diff --git a/src/nstencil_half_multi_3d_tri.h b/src/nstencil_half_multi_3d_tri.h new file mode 100644 index 0000000000..59e66a0530 --- /dev/null +++ b/src/nstencil_half_multi_3d_tri.h @@ -0,0 +1,45 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/3d/tri, + NStencilHalfMulti3dTri, NS_HALF | NS_MULTI | NS_3D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_3D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMulti3dTri : public NStencil { + public: + NStencilHalfMulti3dTri(class LAMMPS *); + ~NStencilHalfMulti3dTri() {} + void create(); + + protected: + void set_stencil_properties(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_2d_newton.cpp b/src/nstencil_half_multi_old_2d.cpp similarity index 84% rename from src/nstencil_half_multi_2d_newton.cpp rename to src/nstencil_half_multi_old_2d.cpp index 21a082bca0..18efc14703 100644 --- a/src/nstencil_half_multi_2d_newton.cpp +++ b/src/nstencil_half_multi_old_2d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_newton.h" +#include "nstencil_half_multi_old_2d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dNewton:: -NStencilHalfMulti2dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld2d:: +NStencilHalfMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dNewton::create() +void NStencilHalfMultiOld2d::create() { int i,j,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti2dNewton::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) @@ -47,6 +47,6 @@ void NStencilHalfMulti2dNewton::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_multi_old_2d.h b/src/nstencil_half_multi_old_2d.h new file mode 100644 index 0000000000..c64e805ca1 --- /dev/null +++ b/src/nstencil_half_multi_old_2d.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/old/2d, + NStencilHalfMultiOld2d, NS_HALF | NS_MULTI_OLD | NS_2D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_2D_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_2D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMultiOld2d : public NStencil { + public: + NStencilHalfMultiOld2d(class LAMMPS *); + ~NStencilHalfMultiOld2d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_2d_newton_tri.cpp b/src/nstencil_half_multi_old_2d_tri.cpp similarity index 82% rename from src/nstencil_half_multi_2d_newton_tri.cpp rename to src/nstencil_half_multi_old_2d_tri.cpp index ad12a6934d..24056c2ada 100644 --- a/src/nstencil_half_multi_2d_newton_tri.cpp +++ b/src/nstencil_half_multi_old_2d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_2d_newton_tri.h" +#include "nstencil_half_multi_old_2d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti2dNewtonTri:: -NStencilHalfMulti2dNewtonTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld2dTri:: +NStencilHalfMultiOld2dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti2dNewtonTri::create() +void NStencilHalfMultiOld2dTri::create() { int i,j,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti2dNewtonTri::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (j = 0; j <= sy; j++) for (i = -sx; i <= sx; i++) { @@ -46,6 +46,6 @@ void NStencilHalfMulti2dNewtonTri::create() s[n++] = j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_multi_old_2d_tri.h b/src/nstencil_half_multi_old_2d_tri.h new file mode 100644 index 0000000000..23765b9167 --- /dev/null +++ b/src/nstencil_half_multi_old_2d_tri.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/old/2d/tri, + NStencilHalfMultiOld2dTri, NS_HALF | NS_MULTI_OLD | NS_2D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_2D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_2D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMultiOld2dTri : public NStencil { + public: + NStencilHalfMultiOld2dTri(class LAMMPS *); + ~NStencilHalfMultiOld2dTri() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_3d_newton.cpp b/src/nstencil_half_multi_old_3d.cpp similarity index 84% rename from src/nstencil_half_multi_3d_newton.cpp rename to src/nstencil_half_multi_old_3d.cpp index 2ac1bb0b4d..ebdd09674d 100644 --- a/src/nstencil_half_multi_3d_newton.cpp +++ b/src/nstencil_half_multi_old_3d.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_newton.h" +#include "nstencil_half_multi_old_3d.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dNewton:: -NStencilHalfMulti3dNewton(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld3d:: +NStencilHalfMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dNewton::create() +void NStencilHalfMultiOld3d::create() { int i,j,k,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti3dNewton::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -48,6 +48,6 @@ void NStencilHalfMulti3dNewton::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_multi_old_3d.h b/src/nstencil_half_multi_old_3d.h new file mode 100644 index 0000000000..1c49216f82 --- /dev/null +++ b/src/nstencil_half_multi_old_3d.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi_old/3d, + NStencilHalfMultiOld3d, NS_HALF | NS_MULTI_OLD | NS_3D | NS_ORTHO) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_3D_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_3D_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMultiOld3d : public NStencil { + public: + NStencilHalfMultiOld3d(class LAMMPS *); + ~NStencilHalfMultiOld3d() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/nstencil_half_multi_3d_newton_tri.cpp b/src/nstencil_half_multi_old_3d_tri.cpp similarity index 83% rename from src/nstencil_half_multi_3d_newton_tri.cpp rename to src/nstencil_half_multi_old_3d_tri.cpp index 8f4c3005bf..27dd320c6b 100644 --- a/src/nstencil_half_multi_3d_newton_tri.cpp +++ b/src/nstencil_half_multi_old_3d_tri.cpp @@ -11,21 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "nstencil_half_multi_3d_newton_tri.h" +#include "nstencil_half_multi_old_3d_tri.h" #include "atom.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -NStencilHalfMulti3dNewtonTri:: -NStencilHalfMulti3dNewtonTri(LAMMPS *lmp) : NStencil(lmp) {} +NStencilHalfMultiOld3dTri:: +NStencilHalfMultiOld3dTri(LAMMPS *lmp) : NStencil(lmp) {} /* ---------------------------------------------------------------------- create stencil based on bin geometry and cutoff ------------------------------------------------------------------------- */ -void NStencilHalfMulti3dNewtonTri::create() +void NStencilHalfMultiOld3dTri::create() { int i,j,k,n; double rsq,typesq; @@ -35,8 +35,8 @@ void NStencilHalfMulti3dNewtonTri::create() int ntypes = atom->ntypes; for (int itype = 1; itype <= ntypes; itype++) { typesq = cuttypesq[itype]; - s = stencil_multi[itype]; - distsq = distsq_multi[itype]; + s = stencil_multi_old[itype]; + distsq = distsq_multi_old[itype]; n = 0; for (k = 0; k <= sz; k++) for (j = -sy; j <= sy; j++) @@ -47,6 +47,6 @@ void NStencilHalfMulti3dNewtonTri::create() s[n++] = k*mbiny*mbinx + j*mbinx + i; } } - nstencil_multi[itype] = n; + nstencil_multi_old[itype] = n; } } diff --git a/src/nstencil_half_multi_old_3d_tri.h b/src/nstencil_half_multi_old_3d_tri.h new file mode 100644 index 0000000000..d365f28e56 --- /dev/null +++ b/src/nstencil_half_multi_old_3d_tri.h @@ -0,0 +1,42 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef NSTENCIL_CLASS + +NStencilStyle(half/multi/old/3d/tri, + NStencilHalfMultiOld3dTri, NS_HALF | NS_MULTI_OLD | NS_3D | NS_TRI) + +#else + +#ifndef LMP_NSTENCIL_HALF_MULTI_OLD_3D_TRI_H +#define LMP_NSTENCIL_HALF_MULTI_OLD_3D_TRI_H + +#include "nstencil.h" + +namespace LAMMPS_NS { + +class NStencilHalfMultiOld3dTri : public NStencil { + public: + NStencilHalfMultiOld3dTri(class LAMMPS *); + ~NStencilHalfMultiOld3dTri() {} + void create(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/pair.cpp b/src/pair.cpp index 7f41114fc0..a8ea29b302 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -64,6 +64,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) one_coeff = 0; no_virial_fdotr_compute = 0; writedata = 0; + finitecutflag = 0; ghostneigh = 0; unit_convert_flag = utils::NOCONVERT; diff --git a/src/pair.h b/src/pair.h index aa89f316f6..ac0e5e7390 100644 --- a/src/pair.h +++ b/src/pair.h @@ -56,6 +56,7 @@ class Pair : protected Pointers { int unit_convert_flag; // value != 0 indicates support for unit conversion. int no_virial_fdotr_compute; // 1 if does not invoke virial_fdotr_compute() int writedata; // 1 if writes coeffs to data file + int finitecutflag; // 1 if cut depends on finite atom size int ghostneigh; // 1 if pair style needs neighbors of ghosts double **cutghost; // cutoff for each ghost pair @@ -205,6 +206,8 @@ class Pair : protected Pointers { virtual void min_xf_get(int) {} virtual void min_x_set(int) {} virtual void transfer_history(double *, double*) {} + virtual double atom2cut(int) {return 0.0;} + virtual double radii2cut(double,double) {return 0.0;} // management of callbacks to be run from ev_tally() diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index c96859a6a5..14d58f9414 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -400,6 +400,7 @@ void PairHybrid::flags() if (styles[m]->dispersionflag) dispersionflag = 1; if (styles[m]->tip4pflag) tip4pflag = 1; if (styles[m]->compute_flag) compute_flag = 1; + if (styles[m]->finitecutflag) finitecutflag = 1; } single_enable = (single_enable == nstyles) ? 1 : 0; respa_enable = (respa_enable == nstyles) ? 1 : 0; @@ -1077,6 +1078,42 @@ int PairHybrid::check_ijtype(int itype, int jtype, char *substyle) return 0; } +/* ---------------------------------------------------------------------- + check if substyles calculate self-interaction range of particle +------------------------------------------------------------------------- */ + +double PairHybrid::atom2cut(int i) +{ + double temp, cut; + + cut = 0.0; + for (int m = 0; m < nstyles; m++) { + if (styles[m]->finitecutflag) { + temp = styles[m]->atom2cut(i); + if (temp > cut) cut = temp; + } + } + return cut; +} + +/* ---------------------------------------------------------------------- + check if substyles calculate maximum interaction range for two finite particles +------------------------------------------------------------------------- */ + +double PairHybrid::radii2cut(double r1, double r2) +{ + double temp, cut; + + cut = 0.0; + for (int m = 0; m < nstyles; m++) { + if (styles[m]->finitecutflag) { + temp = styles[m]->radii2cut(r1,r2); + if (temp > cut) cut = temp; + } + } + return cut; +} + /* ---------------------------------------------------------------------- memory usage of each sub-style ------------------------------------------------------------------------- */ diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 51df379568..68b08f3302 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -60,6 +60,8 @@ class PairHybrid : public Pair { virtual void add_tally_callback(class Compute *); virtual void del_tally_callback(class Compute *); + double atom2cut(int); + double radii2cut(double,double); protected: int nstyles; // # of sub-styles