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Merge remote-tracking branch 'upstream/master' into fix_python_move

This commit is contained in:
Richard Berger 2017-12-15 13:56:54 -05:00
parent bcc5f49d0b d029cb9002
commit 2a131d1416
176 changed files with 3963 additions and 1199 deletions
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3
doc/src/Section_commands.txt
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@ -1024,7 +1024,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"tri/lj"_pair_tri_lj.html,
"vashishta (ko)"_pair_vashishta.html,
"vashishta/table (o)"_pair_vashishta.html,
"yukawa (go)"_pair_yukawa.html,
"yukawa (gok)"_pair_yukawa.html,
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)
@ -1046,6 +1046,7 @@ package"_Section_start.html#start_3.
"edpd"_pair_meso.html,
"eff/cut"_pair_eff.html,
"exp6/rx"_pair_exp6_rx.html,
"extep"_pair_extep.html,
"gauss/cut"_pair_gauss.html,
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"lennard/mdf"_pair_mdf.html,

22
doc/src/create_atoms.txt
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@ -36,9 +36,9 @@ keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
{set} values = dim name
dim = {x} or {y} or {z}
name = name of variable to set with x, y, or z atom position
{rotate} values = Rx Ry Rz theta
Rx,Ry,Rz = rotation vector for single molecule
{rotate} values = theta Rx Ry Rz
theta = rotation angle for single molecule (degrees)
Rx,Ry,Rz = rotation vector for single molecule
{units} value = {lattice} or {box}
{lattice} = the geometry is defined in lattice units
{box} = the geometry is defined in simulation box units :pre
@ -242,15 +242,15 @@ write_dump all atom sinusoid.lammpstrj :pre
:c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
The {rotate} keyword can be used with the {single} style, when adding
a single molecule to specify the orientation at which the molecule is
inserted. The axis of rotation is determined by the rotation vector
(Rx,Ry,Rz) that goes through the insertion point. The specified
{theta} determines the angle of rotation around that axis. Note that
the direction of rotation for the atoms around the rotation axis is
consistent with the right-hand rule: if your right-hand's thumb points
along {R}, then your fingers wrap around the axis in the direction of
rotation.
The {rotate} keyword can only be used with the {single} style and
when adding a single molecule. It allows to specify the orientation
at which the molecule is inserted. The axis of rotation is
determined by the rotation vector (Rx,Ry,Rz) that goes through the
insertion point. The specified {theta} determines the angle of
rotation around that axis. Note that the direction of rotation for
the atoms around the rotation axis is consistent with the right-hand
rule: if your right-hand's thumb points along {R}, then your fingers
wrap around the axis in the direction of rotation.
The {units} keyword determines the meaning of the distance units used
to specify the coordinates of the one particle created by the {single}

2
doc/src/create_bonds.txt
View File

@ -18,7 +18,7 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
group2-ID = ID of second group, bonds will be between atoms in the 2 groups
btype = bond type of created bonds
rmin = minimum distance between pair of atoms to bond together
rmax = minimum distance between pair of atoms to bond together
rmax = maximum distance between pair of atoms to bond together
{single/bond} args = btype batom1 batom2
btype = bond type of new bond
batom1,batom2 = atom IDs for two atoms in bond

1
doc/src/lammps.book
View File

@ -445,6 +445,7 @@ pair_edip.html
pair_eff.html
pair_eim.html
pair_exp6_rx.html
pair_extep.html
pair_gauss.html
pair_gayberne.html
pair_gran.html

40
doc/src/pair_extep.txt Normal file
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@ -0,0 +1,40 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style extep command :h3
[Syntax:]
pair_style extep :pre
[Examples:]
pair_style extep
pair_coeff * * BN.extep B N :pre
[Description:]
Style {extep} computes the Extended Tersoff Potential (ExTeP)
interactions as described in "(Los2017)"_#Los2017.
:line
[Restrictions:] none
[Related commands:]
"pair_tersoff" pair_tersoff.html
[Default:] none
:line
:link(Los2017)
[(Los2017)] J. H. Los et al. "Extended Tersoff potential for boron nitride:
Energetics and elastic properties of pristine and defective h-BN",
Phys. Rev. B 96 (184108), 2017.

1
doc/src/pair_yukawa.txt
View File

@ -9,6 +9,7 @@
pair_style yukawa command :h3
pair_style yukawa/gpu command :h3
pair_style yukawa/omp command :h3
pair_style yukawa/kk command :h3
[Syntax:]

1
doc/src/pairs.txt
View File

@ -32,6 +32,7 @@ Pair Styles :h1
pair_eff
pair_eim
pair_exp6_rx
pair_extep
pair_gauss
pair_gayberne
pair_gran

116
examples/USER/misc/extep/BN.data Normal file
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@ -0,0 +1,116 @@
info: BN sample with r_BN=1.45
100 atoms
2 atom types
0.0 21.75000000 xlo xhi
0.0 12.55736835 ylo yhi
0.0 50.00000000 zlo zhi
Masses
1 10.811
2 14.0067
Atoms
1 1 0.00000000 0.00000000 0.00000000
2 2 1.45000000 0.00000000 0.00000000
3 1 2.17500000 1.25573684 0.00000000
4 2 3.62500000 1.25573684 0.00000000
5 1 0.00000000 2.51147367 0.00000000
6 2 1.45000000 2.51147367 0.00000000
7 1 2.17500000 3.76721051 0.00000000
8 2 3.62500000 3.76721051 0.00000000
9 1 0.00000000 5.02294734 0.00000000
10 2 1.45000000 5.02294734 0.00000000
11 1 2.17500000 6.27868418 0.00000000
12 2 3.62500000 6.27868418 0.00000000
13 1 0.00000000 7.53442101 0.00000000
14 2 1.45000000 7.53442101 0.00000000
15 1 2.17500000 8.79015785 0.00000000
16 2 3.62500000 8.79015785 0.00000000
17 1 0.00000000 10.04589468 0.00000000
18 2 1.45000000 10.04589468 0.00000000
19 1 2.17500000 11.30163152 0.00000000
20 2 3.62500000 11.30163152 0.00000000
21 1 4.35000000 0.00000000 0.00000000
22 2 5.80000000 0.00000000 0.00000000
23 1 6.52500000 1.25573684 0.00000000
24 2 7.97500000 1.25573684 0.00000000
25 1 4.35000000 2.51147367 0.00000000
26 2 5.80000000 2.51147367 0.00000000
27 1 6.52500000 3.76721051 0.00000000
28 2 7.97500000 3.76721051 0.00000000
29 1 4.35000000 5.02294734 0.00000000
30 2 5.80000000 5.02294734 0.00000000
31 1 6.52500000 6.27868418 0.00000000
32 2 7.97500000 6.27868418 0.00000000
33 1 4.35000000 7.53442101 0.00000000
34 2 5.80000000 7.53442101 0.00000000
35 1 6.52500000 8.79015785 0.00000000
36 2 7.97500000 8.79015785 0.00000000
37 1 4.35000000 10.04589468 0.00000000
38 2 5.80000000 10.04589468 0.00000000
39 1 6.52500000 11.30163152 0.00000000
40 2 7.97500000 11.30163152 0.00000000
41 1 8.70000000 0.00000000 0.00000000
42 2 10.15000000 0.00000000 0.00000000
43 1 10.87500000 1.25573684 0.00000000
44 2 12.32500000 1.25573684 0.00000000
45 1 8.70000000 2.51147367 0.00000000
46 2 10.15000000 2.51147367 0.00000000
47 1 10.87500000 3.76721051 0.00000000
48 2 12.32500000 3.76721051 0.00000000
49 1 8.70000000 5.02294734 0.00000000
50 2 10.15000000 5.02294734 0.00000000
51 1 10.87500000 6.27868418 0.00000000
52 2 12.32500000 6.27868418 0.00000000
53 1 8.70000000 7.53442101 0.00000000
54 2 10.15000000 7.53442101 0.00000000
55 1 10.87500000 8.79015785 0.00000000
56 2 12.32500000 8.79015785 0.00000000
57 1 8.70000000 10.04589468 0.00000000
58 2 10.15000000 10.04589468 0.00000000
59 1 10.87500000 11.30163152 0.00000000
60 2 12.32500000 11.30163152 0.00000000
61 1 13.05000000 0.00000000 0.00000000
62 2 14.50000000 0.00000000 0.00000000
63 1 15.22500000 1.25573684 0.00000000
64 2 16.67500000 1.25573684 0.00000000
65 1 13.05000000 2.51147367 0.00000000
66 2 14.50000000 2.51147367 0.00000000
67 1 15.22500000 3.76721051 0.00000000
68 2 16.67500000 3.76721051 0.00000000
69 1 13.05000000 5.02294734 0.00000000
70 2 14.50000000 5.02294734 0.00000000
71 1 15.22500000 6.27868418 0.00000000
72 2 16.67500000 6.27868418 0.00000000
73 1 13.05000000 7.53442101 0.00000000
74 2 14.50000000 7.53442101 0.00000000
75 1 15.22500000 8.79015785 0.00000000
76 2 16.67500000 8.79015785 0.00000000
77 1 13.05000000 10.04589468 0.00000000
78 2 14.50000000 10.04589468 0.00000000
79 1 15.22500000 11.30163152 0.00000000
80 2 16.67500000 11.30163152 0.00000000
81 1 17.40000000 0.00000000 0.00000000
82 2 18.85000000 0.00000000 0.00000000
83 1 19.57500000 1.25573684 0.00000000
84 2 21.02500000 1.25573684 0.00000000
85 1 17.40000000 2.51147367 0.00000000
86 2 18.85000000 2.51147367 0.00000000
87 1 19.57500000 3.76721051 0.00000000
88 2 21.02500000 3.76721051 0.00000000
89 1 17.40000000 5.02294734 0.00000000
90 2 18.85000000 5.02294734 0.00000000
91 1 19.57500000 6.27868418 0.00000000
92 2 21.02500000 6.27868418 0.00000000
93 1 17.40000000 7.53442101 0.00000000
94 2 18.85000000 7.53442101 0.00000000
95 1 19.57500000 8.79015785 0.00000000
96 2 21.02500000 8.79015785 0.00000000
97 1 17.40000000 10.04589468 0.00000000
98 2 18.85000000 10.04589468 0.00000000
99 1 19.57500000 11.30163152 0.00000000
100 2 21.02500000 11.30163152 0.00000000

29
examples/USER/misc/extep/in.extep-bn Normal file
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@ -0,0 +1,29 @@
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1
# System and atom definition
read_data BN.data # read lammps data file
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Potential
pair_style extep
pair_coeff * * ../../../../potentials/BN.extep B N
# Output
thermo 10
thermo_style custom step time etotal pe temp lx ly lz pxx pyy pzz
thermo_modify line one format float %14.8g
# Setup NPT MD run
timestep 0.0001 # ps
velocity all create 300.0 12345
fix thermos all npt temp 300 300 1.0 x 0 0 1.0 y 0 0 1.0
run 1000

180
examples/USER/misc/extep/log.23Oct17.extep-bn.g++.1 Normal file
View File

@ -0,0 +1,180 @@
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1
# System and atom definition
read_data BN.data # read lammps data file
orthogonal box = (0 0 0) to (21.75 12.5574 50)
1 by 1 by 1 MPI processor grid
reading atoms ...
100 atoms
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Potential
pair_style extep
pair_coeff * * ../../../../potentials/BN.extep B N
Reading potential file ../../../../potentials/BN.extep with DATE: 2017-11-28
# Output
thermo 10
thermo_style custom step time etotal pe temp lx ly lz pxx pyy pzz
thermo_modify line one format float %14.8g
# Setup NPT MD run
timestep 0.0001 # ps
velocity all create 300.0 12345
fix thermos all npt temp 300 300 1.0 x 0 0 1.0 y 0 0 1.0
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.2
ghost atom cutoff = 4.2
binsize = 2.1, bins = 11 6 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair extep, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.97 | 2.97 | 2.97 Mbytes
Step Time TotEng PotEng Temp Lx Ly Lz Pxx Pyy Pzz
0 0 -665.11189 -668.95092 300 21.75 12.557368 50 -1638.8315 -1636.7368 321.73163
10 0.001 -665.11194 -668.81065 289.03491 21.749944 12.557333 50 -1391.3771 -1841.1723 316.66669
20 0.002 -665.1121 -668.4273 259.06599 21.749789 12.557222 50 -1137.0171 -1980.5977 301.79466
30 0.003 -665.11237 -667.90117 217.93027 21.749552 12.557029 50 -912.51949 -2055.822 278.00774
40 0.004 -665.11278 -667.36471 175.97662 21.74925 12.556752 50 -755.38643 -2078.0669 246.62816
50 0.005 -665.11333 -666.94254 142.94321 21.748894 12.556389 50 -694.93153 -2062.1349 209.26356
60 0.006 -665.11405 -666.71476 125.08741 21.748487 12.55594 50 -744.6962 -2019.9093 167.70563
70 0.007 -665.11494 -666.69555 123.51632 21.748026 12.555408 50 -898.67863 -1956.2845 123.88845
80 0.008 -665.116 -666.83408 134.25892 21.7475 12.554796 50 -1132.5952 -1868.738 79.87581
90 0.009 -665.1172 -667.03647 149.98053 21.746893 12.554106 50 -1409.6896 -1750.4875 37.821017
100 0.01 -665.11853 -667.20002 162.65705 21.746185 12.553344 50 -1689.1599 -1595.9411 -0.14399002
110 0.011 -665.11997 -667.24752 166.25742 21.745356 12.552516 50 -1934.6334 -1406.3665 -32.091026
120 0.012 -665.12148 -667.15088 158.58671 21.744389 12.55163 50 -2120.4014 -1193.6117 -56.50543
130 0.013 -665.12306 -666.93754 141.7922 21.743271 12.550694 50 -2234.0841 -980.32815 -72.45885
140 0.014 -665.1247 -666.67903 121.4631 21.741993 12.549719 50 -2275.5656 -796.26701 -79.693692
150 0.015 -665.1264 -666.46562 104.65306 21.740553 12.54871 50 -2253.08 -671.5409 -78.603431
160 0.016 -665.1282 -666.37541 97.462619 21.738952 12.547674 50 -2178.0108 -628.83531 -70.130423
170 0.017 -665.13011 -666.44775 102.96665 21.737195 12.546611 50 -2060.2073 -677.02227 -55.623931
180 0.018 -665.13215 -666.67004 120.17784 21.735292 12.54552 50 -1905.36 -808.22824 -36.699042
190 0.019 -665.13431 -666.98201 144.38814 21.733253 12.544396 50 -1715.2526 -999.2481 -15.117617
200 0.02 -665.13656 -667.29591 168.74214 21.731091 12.543231 50 -1490.6934 -1216.735 7.3107732
210 0.021 -665.13885 -667.52511 186.47391 21.728823 12.542015 50 -1235.9283 -1424.4324 28.822782
220 0.022 -665.14112 -667.61153 193.0492 21.726467 12.540741 50 -962.70697 -1590.2885 47.801678
230 0.023 -665.14332 -667.54317 187.53534 21.724043 12.539402 50 -692.12856 -1691.6537 62.881768
240 0.024 -665.1454 -667.35665 172.79772 21.72157 12.537993 50 -453.02755 -1717.6064 73.041858
250 0.025 -665.14735 -667.12424 154.48373 21.719064 12.536514 50 -276.81709 -1668.3598 77.670868
260 0.026 -665.14918 -666.92939 139.11409 21.716539 12.534967 50 -190.03656 -1552.4049 76.59734
270 0.027 -665.15091 -666.83859 131.88391 21.714 12.533357 50 -206.85537 -1382.4915 70.085105
280 0.028 -665.15258 -666.87889 134.90214 21.711446 12.53169 50 -324.01795 -1171.7578 58.801327
290 0.029 -665.15421 -667.02881 146.49028 21.708869 12.529975 50 -520.0146 -931.26466 43.758636
300 0.03 -665.1558 -667.22646 161.81084 21.706255 12.528222 50 -758.87113 -669.74523 26.225956
310 0.031 -665.15734 -667.39183 174.61368 21.703587 12.526442 50 -997.42782 -395.56111 7.601897
320 0.032 -665.15878 -667.45546 179.47345 21.700849 12.524646 50 -1193.9402 -119.86797 -10.744258
330 0.033 -665.16008 -667.38312 173.71901 21.698026 12.522846 50 -1315.6446 140.7451 -27.638433
340 0.034 -665.16118 -667.18792 158.37888 21.695112 12.521051 50 -1343.5396 363.95099 -42.231049
350 0.035 -665.16207 -666.92571 137.81938 21.692103 12.519271 50 -1273.6625 524.73453 -54.046178
360 0.036 -665.16274 -666.67543 118.20885 21.689004 12.517514 50 -1115.1514 601.37143 -62.932702
370 0.037 -665.1632 -666.5115 105.36258 21.685827 12.515781 50 -886.11568 582.42087 -68.942158
380 0.038 -665.16348 -666.47849 102.76116 21.682589 12.514072 50 -608.71321 472.04732 -72.193259
390 0.039 -665.1636 -666.57728 110.47178 21.679308 12.512382 50 -304.85697 291.41908 -72.787214
400 0.04 -665.16356 -666.76741 125.33244 21.676006 12.510704 50 6.3732307 75.407852 -70.806087
410 0.041 -665.16336 -666.98363 142.24457 21.672705 12.50903 50 309.23046 -134.40319 -66.378966
420 0.042 -665.16298 -667.15939 156.00935 21.669426 12.507351 50 590.16982 -298.16702 -59.767469
430 0.043 -665.16239 -667.24843 163.01313 21.66619 12.50566 50 836.19535 -385.22443 -51.420249
440 0.044 -665.16157 -667.23746 162.2204 21.663014 12.503955 50 1033.943 -378.7816 -41.969885
450 0.045 -665.1605 -667.14707 155.24066 21.659911 12.502234 50 1170.3399 -277.11556 -32.175503
460 0.046 -665.15917 -667.0218 145.55489 21.656891 12.500503 50 1234.9026 -91.620499 -22.833423
470 0.047 -665.15761 -666.91366 137.22578 21.65396 12.498768 50 1222.9519 157.31306 -14.680548
480 0.048 -665.15585 -666.86462 133.53159 21.651114 12.497041 50 1138.5551 445.2926 -8.3071781
490 0.049 -665.15393 -666.89359 135.9458 21.64835 12.495333 50 996.00682 748.51842 -4.0872169
500 0.05 -665.15188 -666.99142 143.75058 21.645657 12.493655 50 819.08561 1046.9785 -2.1306918
510 0.051 -665.14975 -667.12519 154.36991 21.643022 12.49202 50 637.99022 1325.7112 -2.2650822
520 0.052 -665.14756 -667.25 164.29491 21.640432 12.49044 50 484.54509 1574.1916 -4.0528391
530 0.053 -665.14531 -667.32459 170.29969 21.637878 12.488923 50 386.77357 1784.4858 -6.8479114
540 0.054 -665.143 -667.32552 170.55254 21.635352 12.48748 50 364.14599 1949.2189 -9.8841824
550 0.055 -665.14064 -667.25527 165.24765 21.632853 12.486117 50 424.6565 2060.4607 -12.37851
560 0.056 -665.13822 -667.14127 156.52756 21.630385 12.484837 50 564.3912 2110.2547 -13.62742
570 0.057 -665.13576 -667.0259 147.70502 21.627958 12.483643 50 769.54354 2092.8157 -13.082914
580 0.058 -665.13327 -666.95107 142.05154 21.625586 12.482535 50 1020.1218 2007.6508 -10.405617
590 0.059 -665.13079 -666.94279 141.59877 21.623287 12.481508 50 1294.1274 1862.3568 -5.5031153
600 0.06 -665.12832 -667.00189 146.40928 21.621079 12.480557 50 1570.9478 1673.8456 1.4410957
610 0.061 -665.12591 -667.10417 154.59072 21.618982 12.479674 50 1833.1388 1467.2639 9.9561573
620 0.062 -665.12355 -667.20973 163.02368 21.617015 12.478851 50 2066.4951 1272.6732 19.310607
630 0.063 -665.12128 -667.27744 168.49239 21.615193 12.47808 50 2259.0193 1120.2758 28.59477
640 0.064 -665.11911 -667.27898 168.7823 21.613531 12.477355 50 2399.792 1035.3525 36.8539
650 0.065 -665.11707 -667.20773 163.37438 21.612037 12.476673 50 2478.6675 1034.0481 43.239368
660 0.066 -665.11518 -667.0802 153.55598 21.610718 12.476033 50 2487.2505 1120.8274 47.131883
670 0.067 -665.11345 -666.93026 141.97434 21.609573 12.475439 50 2420.9786 1288.0136 48.201717
680 0.068 -665.11191 -666.79864 131.80955 21.608598 12.474897 50 2281.6131 1517.4002 46.399066
690 0.069 -665.11056 -666.72065 125.82027 21.607784 12.474418 50 2079.2055 1783.5346 41.895586
700 0.07 -665.10941 -666.71578 125.5291 21.607116 12.474011 50 1832.7039 2057.9076 35.011051
710 0.071 -665.10848 -666.78203 130.77932 21.606577 12.473687 50 1568.7275 2313.0601 26.153491
720 0.072 -665.10776 -666.89681 139.80468 21.606148 12.473458 50 1318.5189 2525.6808 15.783637
730 0.073 -665.10727 -667.0243 149.80574 21.605812 12.47333 50 1113.5537 2678.1859 4.3967762
740 0.074 -665.10701 -667.12698 157.85016 21.605555 12.473311 50 980.633 2758.9123 -7.4930622
750 0.075 -665.10697 -667.17729 161.78497 21.605368 12.473404 50 937.45086 2761.5936 -19.376492
760 0.076 -665.10714 -667.1654 160.84249 21.605247 12.473609 50 989.5724 2684.9256 -30.776106
770 0.077 -665.1075 -667.10061 155.75086 21.605196 12.473922 50 1129.4775 2532.7048 -41.263677
780 0.078 -665.10803 -667.00654 148.35835 21.605226 12.474338 50 1337.8663 2314.4556 -50.455407
790 0.079 -665.10869 -666.91242 140.9515 21.605349 12.474848 50 1586.9099 2045.9808 -57.988114
800 0.08 -665.10946 -666.84375 135.52533 21.605585 12.475441 50 1844.7038 1749.1281 -63.495405
810 0.081 -665.11032 -666.81538 133.24173 21.60595 12.476105 50 2079.9601 1450.3113 -66.60795
820 0.082 -665.11127 -666.82877 134.21424 21.606461 12.476828 50 2266.0059 1177.7937 -66.990929
830 0.083 -665.1123 -666.87353 137.6312 21.607131 12.477599 50 2383.4351 958.19752 -64.411861
840 0.084 -665.11343 -666.93214 142.12323 21.607968 12.478409 50 2421.1969 812.91475 -58.816538
850 0.085 -665.11467 -666.98597 146.2321 21.608975 12.479253 50 2376.3483 755.06052 -50.389393
860 0.086 -665.11603 -667.02075 148.84448 21.610149 12.480128 50 2252.9811 787.43069 -39.585062
870 0.087 -665.1175 -667.03045 149.48743 21.611481 12.481034 50 2060.884 901.76342 -27.129117
880 0.088 -665.11907 -667.01838 148.42091 21.612958 12.481978 50 1814.3354 1079.4855 -13.988401
890 0.089 -665.12073 -666.99552 146.50471 21.614562 12.482966 50 1531.1565 1293.9709 -1.305884
900 0.09 -665.12247 -666.97639 144.87389 21.616275 12.484007 50 1231.9005 1514.0741 9.7083525
910 0.091 -665.12426 -666.97371 144.52455 21.618074 12.485109 50 938.90089 1708.364 17.929974
920 0.092 -665.12609 -666.99389 145.95889 21.61994 12.486281 50 674.90767 1849.2415 22.497207
930 0.093 -665.12794 -667.03498 149.02559 21.621853 12.487528 50 461.18604 1916.1468 22.971745
940 0.094 -665.12977 -667.08777 153.00718 21.6238 12.488852 50 315.19601 1897.3867 19.43758
950 0.095 -665.13156 -667.13925 156.8903 21.62577 12.490254 50 248.20946 1790.5667 12.504818
960 0.096 -665.13326 -667.17668 159.68273 21.627757 12.491728 50 263.35912 1601.9528 3.2123256
970 0.097 -665.13485 -667.19079 160.6611 21.629764 12.493267 50 354.58496 1345.1489 -7.1487162
980 0.098 -665.13628 -667.17758 159.5175 21.631796 12.494862 50 506.7626 1039.346 -17.249179
990 0.099 -665.13753 -667.13942 156.43758 21.633864 12.496499 50 697.06054 707.26671 -25.92737
1000 0.1 -665.13859 -667.0853 152.12472 21.635982 12.498164 50 897.38498 372.94791 -32.344697
Loop time of 0.463574 on 1 procs for 1000 steps with 100 atoms
Performance: 18.638 ns/day, 1.288 hours/ns, 2157.152 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.44776 | 0.44776 | 0.44776 | 0.0 | 96.59
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0023057 | 0.0023057 | 0.0023057 | 0.0 | 0.50
Output | 0.0015752 | 0.0015752 | 0.0015752 | 0.0 | 0.34
Modify | 0.010602 | 0.010602 | 0.010602 | 0.0 | 2.29
Other | | 0.001331 | | | 0.29
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 360 ave 360 max 360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1800 ave 1800 max 1800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1800
Ave neighs/atom = 18
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

180
examples/USER/misc/extep/log.23Oct17.extep-bn.g++.4 Normal file
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@ -0,0 +1,180 @@
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1
# System and atom definition
read_data BN.data # read lammps data file
orthogonal box = (0 0 0) to (21.75 12.5574 50)
2 by 2 by 1 MPI processor grid
reading atoms ...
100 atoms
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Potential
pair_style extep
pair_coeff * * ../../../../potentials/BN.extep B N
Reading potential file ../../../../potentials/BN.extep with DATE: 2017-11-28
# Output
thermo 10
thermo_style custom step time etotal pe temp lx ly lz pxx pyy pzz
thermo_modify line one format float %14.8g
# Setup NPT MD run
timestep 0.0001 # ps
velocity all create 300.0 12345
fix thermos all npt temp 300 300 1.0 x 0 0 1.0 y 0 0 1.0
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.2
ghost atom cutoff = 4.2
binsize = 2.1, bins = 11 6 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair extep, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.943 | 2.943 | 2.943 Mbytes
Step Time TotEng PotEng Temp Lx Ly Lz Pxx Pyy Pzz
0 0 -665.11189 -668.95092 300 21.75 12.557368 50 -1638.8315 -1636.7368 321.73163
10 0.001 -665.11194 -668.81065 289.03491 21.749944 12.557333 50 -1391.3771 -1841.1723 316.66669
20 0.002 -665.1121 -668.4273 259.06599 21.749789 12.557222 50 -1137.0171 -1980.5977 301.79466
30 0.003 -665.11237 -667.90117 217.93027 21.749552 12.557029 50 -912.51949 -2055.822 278.00774
40 0.004 -665.11278 -667.36471 175.97662 21.74925 12.556752 50 -755.38643 -2078.0669 246.62816
50 0.005 -665.11333 -666.94254 142.94321 21.748894 12.556389 50 -694.93153 -2062.1349 209.26356
60 0.006 -665.11405 -666.71476 125.08741 21.748487 12.55594 50 -744.6962 -2019.9093 167.70563
70 0.007 -665.11494 -666.69555 123.51632 21.748026 12.555408 50 -898.67863 -1956.2845 123.88845
80 0.008 -665.116 -666.83408 134.25892 21.7475 12.554796 50 -1132.5952 -1868.738 79.87581
90 0.009 -665.1172 -667.03647 149.98053 21.746893 12.554106 50 -1409.6896 -1750.4875 37.821017
100 0.01 -665.11853 -667.20002 162.65705 21.746185 12.553344 50 -1689.1599 -1595.9411 -0.14399002
110 0.011 -665.11997 -667.24752 166.25742 21.745356 12.552516 50 -1934.6334 -1406.3665 -32.091026
120 0.012 -665.12148 -667.15088 158.58671 21.744389 12.55163 50 -2120.4014 -1193.6117 -56.50543
130 0.013 -665.12306 -666.93754 141.7922 21.743271 12.550694 50 -2234.0841 -980.32815 -72.45885
140 0.014 -665.1247 -666.67903 121.4631 21.741993 12.549719 50 -2275.5656 -796.26701 -79.693692
150 0.015 -665.1264 -666.46562 104.65306 21.740553 12.54871 50 -2253.08 -671.5409 -78.603431
160 0.016 -665.1282 -666.37541 97.462619 21.738952 12.547674 50 -2178.0108 -628.83531 -70.130423
170 0.017 -665.13011 -666.44775 102.96665 21.737195 12.546611 50 -2060.2073 -677.02227 -55.623931
180 0.018 -665.13215 -666.67004 120.17784 21.735292 12.54552 50 -1905.36 -808.22824 -36.699042
190 0.019 -665.13431 -666.98201 144.38814 21.733253 12.544396 50 -1715.2526 -999.2481 -15.117617
200 0.02 -665.13656 -667.29591 168.74214 21.731091 12.543231 50 -1490.6934 -1216.735 7.3107732
210 0.021 -665.13885 -667.52511 186.47391 21.728823 12.542015 50 -1235.9283 -1424.4324 28.822782
220 0.022 -665.14112 -667.61153 193.0492 21.726467 12.540741 50 -962.70697 -1590.2885 47.801678
230 0.023 -665.14332 -667.54317 187.53534 21.724043 12.539402 50 -692.12856 -1691.6537 62.881768
240 0.024 -665.1454 -667.35665 172.79772 21.72157 12.537993 50 -453.02755 -1717.6064 73.041858
250 0.025 -665.14735 -667.12424 154.48373 21.719064 12.536514 50 -276.81709 -1668.3598 77.670868
260 0.026 -665.14918 -666.92939 139.11409 21.716539 12.534967 50 -190.03656 -1552.4049 76.59734
270 0.027 -665.15091 -666.83859 131.88391 21.714 12.533357 50 -206.85537 -1382.4915 70.085105
280 0.028 -665.15258 -666.87889 134.90214 21.711446 12.53169 50 -324.01795 -1171.7578 58.801327
290 0.029 -665.15421 -667.02881 146.49028 21.708869 12.529975 50 -520.0146 -931.26466 43.758636
300 0.03 -665.1558 -667.22646 161.81084 21.706255 12.528222 50 -758.87113 -669.74523 26.225956
310 0.031 -665.15734 -667.39183 174.61368 21.703587 12.526442 50 -997.42782 -395.56111 7.601897
320 0.032 -665.15878 -667.45546 179.47345 21.700849 12.524646 50 -1193.9402 -119.86797 -10.744258
330 0.033 -665.16008 -667.38312 173.71901 21.698026 12.522846 50 -1315.6446 140.7451 -27.638433
340 0.034 -665.16118 -667.18792 158.37888 21.695112 12.521051 50 -1343.5396 363.95099 -42.231049
350 0.035 -665.16207 -666.92571 137.81938 21.692103 12.519271 50 -1273.6625 524.73453 -54.046178
360 0.036 -665.16274 -666.67543 118.20885 21.689004 12.517514 50 -1115.1514 601.37143 -62.932702
370 0.037 -665.1632 -666.5115 105.36258 21.685827 12.515781 50 -886.11568 582.42087 -68.942158
380 0.038 -665.16348 -666.47849 102.76116 21.682589 12.514072 50 -608.71321 472.04732 -72.193259
390 0.039 -665.1636 -666.57728 110.47178 21.679308 12.512382 50 -304.85697 291.41908 -72.787214
400 0.04 -665.16356 -666.76741 125.33244 21.676006 12.510704 50 6.3732307 75.407852 -70.806087
410 0.041 -665.16336 -666.98363 142.24457 21.672705 12.50903 50 309.23046 -134.40319 -66.378966
420 0.042 -665.16298 -667.15939 156.00935 21.669426 12.507351 50 590.16982 -298.16702 -59.767469
430 0.043 -665.16239 -667.24843 163.01313 21.66619 12.50566 50 836.19535 -385.22443 -51.420249
440 0.044 -665.16157 -667.23746 162.2204 21.663014 12.503955 50 1033.943 -378.7816 -41.969885
450 0.045 -665.1605 -667.14707 155.24066 21.659911 12.502234 50 1170.3399 -277.11556 -32.175503
460 0.046 -665.15917 -667.0218 145.55489 21.656891 12.500503 50 1234.9026 -91.620499 -22.833423
470 0.047 -665.15761 -666.91366 137.22578 21.65396 12.498768 50 1222.9519 157.31306 -14.680548
480 0.048 -665.15585 -666.86462 133.53159 21.651114 12.497041 50 1138.5551 445.2926 -8.3071781
490 0.049 -665.15393 -666.89359 135.9458 21.64835 12.495333 50 996.00682 748.51842 -4.0872169
500 0.05 -665.15188 -666.99142 143.75058 21.645657 12.493655 50 819.08561 1046.9785 -2.1306918
510 0.051 -665.14975 -667.12519 154.36991 21.643022 12.49202 50 637.99022 1325.7112 -2.2650822
520 0.052 -665.14756 -667.25 164.29491 21.640432 12.49044 50 484.54509 1574.1916 -4.0528391
530 0.053 -665.14531 -667.32459 170.29969 21.637878 12.488923 50 386.77357 1784.4858 -6.8479114
540 0.054 -665.143 -667.32552 170.55254 21.635352 12.48748 50 364.14599 1949.2189 -9.8841824
550 0.055 -665.14064 -667.25527 165.24765 21.632853 12.486117 50 424.6565 2060.4607 -12.37851
560 0.056 -665.13822 -667.14127 156.52756 21.630385 12.484837 50 564.3912 2110.2547 -13.62742
570 0.057 -665.13576 -667.0259 147.70502 21.627958 12.483643 50 769.54354 2092.8157 -13.082914
580 0.058 -665.13327 -666.95107 142.05154 21.625586 12.482535 50 1020.1218 2007.6508 -10.405617
590 0.059 -665.13079 -666.94279 141.59877 21.623287 12.481508 50 1294.1274 1862.3568 -5.5031153
600 0.06 -665.12832 -667.00189 146.40928 21.621079 12.480557 50 1570.9478 1673.8456 1.4410957
610 0.061 -665.12591 -667.10417 154.59072 21.618982 12.479674 50 1833.1388 1467.2639 9.9561573
620 0.062 -665.12355 -667.20973 163.02368 21.617015 12.478851 50 2066.4951 1272.6732 19.310607
630 0.063 -665.12128 -667.27744 168.49239 21.615193 12.47808 50 2259.0193 1120.2758 28.59477
640 0.064 -665.11911 -667.27898 168.7823 21.613531 12.477355 50 2399.792 1035.3525 36.8539
650 0.065 -665.11707 -667.20773 163.37438 21.612037 12.476673 50 2478.6675 1034.0481 43.239368
660 0.066 -665.11518 -667.0802 153.55598 21.610718 12.476033 50 2487.2505 1120.8274 47.131883
670 0.067 -665.11345 -666.93026 141.97434 21.609573 12.475439 50 2420.9786 1288.0136 48.201717
680 0.068 -665.11191 -666.79864 131.80955 21.608598 12.474897 50 2281.6131 1517.4002 46.399066
690 0.069 -665.11056 -666.72065 125.82027 21.607784 12.474418 50 2079.2055 1783.5346 41.895586
700 0.07 -665.10941 -666.71578 125.5291 21.607116 12.474011 50 1832.7039 2057.9076 35.011051
710 0.071 -665.10848 -666.78203 130.77932 21.606577 12.473687 50 1568.7275 2313.0601 26.153491
720 0.072 -665.10776 -666.89681 139.80468 21.606148 12.473458 50 1318.5189 2525.6808 15.783637
730 0.073 -665.10727 -667.0243 149.80574 21.605812 12.47333 50 1113.5537 2678.1859 4.3967762
740 0.074 -665.10701 -667.12698 157.85016 21.605555 12.473311 50 980.633 2758.9123 -7.4930622
750 0.075 -665.10697 -667.17729 161.78497 21.605368 12.473404 50 937.45086 2761.5936 -19.376492
760 0.076 -665.10714 -667.1654 160.84249 21.605247 12.473609 50 989.5724 2684.9256 -30.776106
770 0.077 -665.1075 -667.10061 155.75086 21.605196 12.473922 50 1129.4775 2532.7048 -41.263677
780 0.078 -665.10803 -667.00654 148.35835 21.605226 12.474338 50 1337.8663 2314.4556 -50.455407
790 0.079 -665.10869 -666.91242 140.9515 21.605349 12.474848 50 1586.9099 2045.9808 -57.988114
800 0.08 -665.10946 -666.84375 135.52533 21.605585 12.475441 50 1844.7038 1749.1281 -63.495405
810 0.081 -665.11032 -666.81538 133.24173 21.60595 12.476105 50 2079.9601 1450.3113 -66.60795
820 0.082 -665.11127 -666.82877 134.21424 21.606461 12.476828 50 2266.0059 1177.7937 -66.990929
830 0.083 -665.1123 -666.87353 137.6312 21.607131 12.477599 50 2383.4351 958.19752 -64.411861
840 0.084 -665.11343 -666.93214 142.12323 21.607968 12.478409 50 2421.1969 812.91475 -58.816538
850 0.085 -665.11467 -666.98597 146.2321 21.608975 12.479253 50 2376.3483 755.06052 -50.389393
860 0.086 -665.11603 -667.02075 148.84448 21.610149 12.480128 50 2252.9811 787.43069 -39.585062
870 0.087 -665.1175 -667.03045 149.48743 21.611481 12.481034 50 2060.884 901.76342 -27.129117
880 0.088 -665.11907 -667.01838 148.42091 21.612958 12.481978 50 1814.3354 1079.4855 -13.988401
890 0.089 -665.12073 -666.99552 146.50471 21.614562 12.482966 50 1531.1565 1293.9709 -1.305884
900 0.09 -665.12247 -666.97639 144.87389 21.616275 12.484007 50 1231.9005 1514.0741 9.7083525
910 0.091 -665.12426 -666.97371 144.52455 21.618074 12.485109 50 938.90089 1708.364 17.929974
920 0.092 -665.12609 -666.99389 145.95889 21.61994 12.486281 50 674.90767 1849.2415 22.497207
930 0.093 -665.12794 -667.03498 149.02559 21.621853 12.487528 50 461.18604 1916.1468 22.971745
940 0.094 -665.12977 -667.08777 153.00718 21.6238 12.488852 50 315.19601 1897.3867 19.43758
950 0.095 -665.13156 -667.13925 156.8903 21.62577 12.490254 50 248.20946 1790.5667 12.504818
960 0.096 -665.13326 -667.17668 159.68273 21.627757 12.491728 50 263.35912 1601.9528 3.2123256
970 0.097 -665.13485 -667.19079 160.6611 21.629764 12.493267 50 354.58496 1345.1489 -7.1487162
980 0.098 -665.13628 -667.17758 159.5175 21.631796 12.494862 50 506.7626 1039.346 -17.249179
990 0.099 -665.13753 -667.13942 156.43758 21.633864 12.496499 50 697.06054 707.26671 -25.92737
1000 0.1 -665.13859 -667.0853 152.12472 21.635982 12.498164 50 897.38498 372.94791 -32.344697
Loop time of 0.174508 on 4 procs for 1000 steps with 100 atoms
Performance: 49.511 ns/day, 0.485 hours/ns, 5730.393 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12409 | 0.12834 | 0.13408 | 1.1 | 73.54
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.016369 | 0.021358 | 0.025324 | 2.7 | 12.24
Output | 0.0023892 | 0.0025101 | 0.0028272 | 0.4 | 1.44
Modify | 0.01733 | 0.018302 | 0.018958 | 0.5 | 10.49
Other | | 0.003995 | | | 2.29
Nlocal: 25 ave 26 max 24 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 179 ave 180 max 178 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 450 ave 468 max 432 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1800
Ave neighs/atom = 18
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

11
examples/gcmc/in.gcmc.co2
View File

@ -67,6 +67,15 @@ variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
group oxygen dynamic all var oxygen
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@ -74,7 +83,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run

11
examples/gcmc/in.gcmc.h2o
View File

@ -72,6 +72,15 @@ variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
h2omol tfac_insert ${tfac} group h2o shake wshake
# atom counts
variable oxygen atom "type==1"
variable hydrogen atom "type==2"
group oxygen dynamic all var oxygen
group hydrogen dynamic all var hydrogen
variable nO equal count(oxygen)
variable nH equal count(hydrogen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@ -79,7 +88,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run

11
examples/gcmc/in.gcmc.lj
View File

@ -33,6 +33,12 @@ mass * 1.0
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
variable n1 equal count(type1)
# averaging
variable rho equal density
@ -40,10 +46,11 @@ variable p equal press
variable nugget equal 1.0e-8
variable lambda equal 1.0
variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
variable rhoav equal f_ave[1]
variable pav equal f_ave[2]
variable muexav equal f_ave[3]
variable n1av equal f_ave[4]
# output
@ -51,7 +58,7 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
compute_modify thermo_temp dynamic yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
thermo 1000
# run

82
examples/gcmc/log.6Jul17.gcmc.co2.g++.1 → examples/gcmc/log.23Oct17.gcmc.co2.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
@ -46,6 +46,7 @@ Read molecule co2mol:
0 impropers with 0 types
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00196958 secs
# rigid CO2 TraPPE model
@ -87,6 +88,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
dynamic group carbon defined
group oxygen dynamic all var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@ -94,7 +106,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
@ -124,45 +136,45 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0
2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0
3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0
4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0
5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0
6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0
7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0
8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0
9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0
10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0
11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0
12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0
13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0
14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0
15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0
16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0
17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0
18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0
19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0
20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0
Loop time of 20.153 on 1 procs for 20000 steps with 30 atoms
1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16
2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0 9 18
5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0 9 18
6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0 10 20
7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0 12 24
8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0 8 16
9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0 1 2
10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0 13 26
11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0 11 22
12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0 0 0
13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0 2 4
14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0 5 10
15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0 9 18
16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0 12 24
17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0 10 20
18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0 3 6
19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0 8 16
20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0 10 20
Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms
Performance: 85.744 ns/day, 0.280 hours/ns, 992.408 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5352 | 2.5352 | 2.5352 | 0.0 | 12.58
Bond | 0.026112 | 0.026112 | 0.026112 | 0.0 | 0.13
Kspace | 0.25 | 0.25 | 0.25 | 0.0 | 1.24
Neigh | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.51
Comm | 0.22907 | 0.22907 | 0.22907 | 0.0 | 1.14
Output | 0.0013065 | 0.0013065 | 0.0013065 | 0.0 | 0.01
Modify | 16.957 | 16.957 | 16.957 | 0.0 | 84.14
Other | | 0.05061 | | | 0.25
Pair | 2.5462 | 2.5462 | 2.5462 | 0.0 | 12.30
Bond | 0.029783 | 0.029783 | 0.029783 | 0.0 | 0.14
Kspace | 0.26167 | 0.26167 | 0.26167 | 0.0 | 1.26
Neigh | 0.10705 | 0.10705 | 0.10705 | 0.0 | 0.52
Comm | 0.23409 | 0.23409 | 0.23409 | 0.0 | 1.13
Output | 0.0013416 | 0.0013416 | 0.0013416 | 0.0 | 0.01
Modify | 17.458 | 17.458 | 17.458 | 0.0 | 84.37
Other | | 0.05433 | | | 0.26
Nlocal: 30 ave 30 max 30 min
Histogram: 1 0 0 0 0 0 0 0 0 0

84
examples/gcmc/log.6Jul17.gcmc.co2.g++.4 → examples/gcmc/log.23Oct17.gcmc.co2.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
@ -46,6 +46,7 @@ Read molecule co2mol:
0 impropers with 0 types
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00261331 secs
# rigid CO2 TraPPE model
@ -87,6 +88,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
dynamic group carbon defined
group oxygen dynamic all var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@ -94,7 +106,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
@ -124,45 +136,45 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.41 | 15.41 | 15.41 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0
2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0
3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0
4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0
5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0
6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0
7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0
8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0
9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0
10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0
11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0
12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0
13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0
14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0
15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0
16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0
17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0
18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0
19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0
20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0
Loop time of 31.8386 on 4 procs for 20000 steps with 45 atoms
1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10
2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6
3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26
4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28
6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30
7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30
8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26
9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30
10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28
11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30
12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30
13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30
14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28
15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28
16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28
17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28
18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30
19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30
20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30
Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms
Performance: 54.274 ns/day, 0.442 hours/ns, 628.168 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1546 | 1.6687 | 2.1338 | 29.5 | 5.24
Bond | 0.019769 | 0.020369 | 0.02132 | 0.4 | 0.06
Kspace | 0.53392 | 0.99911 | 1.5116 | 37.8 | 3.14
Neigh | 0.06737 | 0.067842 | 0.068412 | 0.2 | 0.21
Comm | 1.9408 | 1.9582 | 1.9733 | 1.1 | 6.15
Output | 0.0019503 | 0.0020472 | 0.0022476 | 0.3 | 0.01
Modify | 26.974 | 26.99 | 27.001 | 0.2 | 84.77
Other | | 0.1322 | | | 0.42
Pair | 1.1687 | 1.6702 | 2.1864 | 30.8 | 5.15
Bond | 0.018828 | 0.020035 | 0.020975 | 0.6 | 0.06
Kspace | 0.57506 | 1.0931 | 1.5898 | 37.7 | 3.37
Neigh | 0.068863 | 0.069524 | 0.070128 | 0.2 | 0.21
Comm | 2.0735 | 2.0865 | 2.0979 | 0.7 | 6.43
Output | 0.0025017 | 0.0025966 | 0.0027781 | 0.2 | 0.01
Modify | 27.335 | 27.344 | 27.363 | 0.2 | 84.27
Other | | 0.1621 | | | 0.50
Nlocal: 11.25 ave 14 max 8 min
Histogram: 1 0 0 0 0 1 1 0 0 1
@ -177,4 +189,4 @@ Ave special neighs/atom = 2
Neighbor list builds = 20394
Dangerous builds = 0
Total wall time: 0:00:31
Total wall time: 0:00:32

124
examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 → examples/gcmc/log.23Oct17.gcmc.h2o.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
@ -51,6 +51,7 @@ Read molecule h2omol:
0 impropers with 0 types
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00201297 secs
# rigid SPC/E water model
@ -100,9 +101,9 @@ Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.1890564 9.2628112e-06 18.98377 739.06991
100 338 -30.182886 0.85607237 -6.1539961 -2535.3207
Loop time of 0.0525794 on 1 procs for 100 steps with 24 atoms
Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
@ -116,14 +117,14 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.044199 | 0.044199 | 0.044199 | 0.0 | 84.06
Bond | 0.00049019 | 0.00049019 | 0.00049019 | 0.0 | 0.93
Kspace | 0.0031631 | 0.0031631 | 0.0031631 | 0.0 | 6.02
Neigh | 0.00046444 | 0.00046444 | 0.00046444 | 0.0 | 0.88
Comm | 0.0034101 | 0.0034101 | 0.0034101 | 0.0 | 6.49
Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.04
Pair | 0.042597 | 0.042597 | 0.042597 | 0.0 | 83.93
Bond | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.94
Kspace | 0.0031135 | 0.0031135 | 0.0031135 | 0.0 | 6.13
Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90
Comm | 0.0032997 | 0.0032997 | 0.0032997 | 0.0 | 6.50
Output | 1.359e-05 | 1.359e-05 | 1.359e-05 | 0.0 | 0.03
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0008333 | | | 1.58
Other | | 0.0007946 | | | 1.57
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -164,22 +165,22 @@ Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -30.182886 0 -7.0100684 993.1985
1000 326.9865 -62.258445 0 -47.638175 -5.3440813
Loop time of 0.14263 on 1 procs for 1000 steps with 24 atoms
Loop time of 0.141449 on 1 procs for 1000 steps with 24 atoms
Performance: 605.764 ns/day, 0.040 hours/ns, 7011.155 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10849 | 0.10849 | 0.10849 | 0.0 | 76.07
Bond | 0.00015426 | 0.00015426 | 0.00015426 | 0.0 | 0.11
Kspace | 0.01205 | 0.01205 | 0.01205 | 0.0 | 8.45
Neigh | 0.0046577 | 0.0046577 | 0.0046577 | 0.0 | 3.27
Comm | 0.011531 | 0.011531 | 0.011531 | 0.0 | 8.08
Output | 1.6212e-05 | 1.6212e-05 | 1.6212e-05 | 0.0 | 0.01
Modify | 0.0037699 | 0.0037699 | 0.0037699 | 0.0 | 2.64
Other | | 0.001957 | | | 1.37
Pair | 0.10788 | 0.10788 | 0.10788 | 0.0 | 76.27
Bond | 0.00018954 | 0.00018954 | 0.00018954 | 0.0 | 0.13
Kspace | 0.011867 | 0.011867 | 0.011867 | 0.0 | 8.39
Neigh | 0.0045254 | 0.0045254 | 0.0045254 | 0.0 | 3.20
Comm | 0.011277 | 0.011277 | 0.011277 | 0.0 | 7.97
Output | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 | 0.0 | 0.01
Modify | 0.00383 | 0.00383 | 0.00383 | 0.0 | 2.71
Other | | 0.001868 | | | 1.32
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -201,6 +202,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
variable oxygen atom "type==1"
variable hydrogen atom "type==2"
group oxygen dynamic all var oxygen
dynamic group oxygen defined
group hydrogen dynamic all var hydrogen
dynamic group hydrogen defined
variable nO equal count(oxygen)
variable nH equal count(hydrogen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@ -208,7 +220,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run
@ -226,44 +238,44 @@ WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0
2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0
3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0
4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0
5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0
6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0
7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0
8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0
9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0
10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0
11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0
12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0
13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0
14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0
15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0
16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0
17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0
18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0
19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0
20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0
21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0
Loop time of 226.155 on 1 procs for 20000 steps with 108 atoms
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0 8 16
2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0 25 50
3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0 30 60
4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0 33 66
5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0 34 68
6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0 34 68
7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0 34 68
8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0 34 68
9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0 34 68
10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0 34 68
11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0 34 68
12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0 34 68
13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0 34 68
14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0 34 68
15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0 35 70
16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0 35 70
17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0 35 70
18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0 35 70
19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0 35 70
20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0 36 72
21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0 36 72
Loop time of 220.662 on 1 procs for 20000 steps with 108 atoms
Performance: 7.641 ns/day, 3.141 hours/ns, 88.435 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 38.053 | 38.053 | 38.053 | 0.0 | 16.83
Bond | 0.089673 | 0.089673 | 0.089673 | 0.0 | 0.04
Kspace | 0.92778 | 0.92778 | 0.92778 | 0.0 | 0.41
Neigh | 1.2619 | 1.2619 | 1.2619 | 0.0 | 0.56
Comm | 0.97483 | 0.97483 | 0.97483 | 0.0 | 0.43
Output | 0.0013306 | 0.0013306 | 0.0013306 | 0.0 | 0.00
Modify | 184.68 | 184.68 | 184.68 | 0.0 | 81.66
Other | | 0.171 | | | 0.08
Pair | 37.459 | 37.459 | 37.459 | 0.0 | 16.98
Bond | 0.087067 | 0.087067 | 0.087067 | 0.0 | 0.04
Kspace | 0.90234 | 0.90234 | 0.90234 | 0.0 | 0.41
Neigh | 1.2299 | 1.2299 | 1.2299 | 0.0 | 0.56
Comm | 0.95437 | 0.95437 | 0.95437 | 0.0 | 0.43
Output | 0.0010636 | 0.0010636 | 0.0010636 | 0.0 | 0.00
Modify | 179.85 | 179.85 | 179.85 | 0.0 | 81.51
Other | | 0.1754 | | | 0.08
Nlocal: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -278,4 +290,4 @@ Ave special neighs/atom = 2
Neighbor list builds = 20439
Dangerous builds = 0
Total wall time: 0:03:46
Total wall time: 0:03:40

120
examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 → examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
@ -51,6 +51,7 @@ Read molecule h2omol:
0 impropers with 0 types
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00174451 secs
# rigid SPC/E water model
@ -100,9 +101,9 @@ Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
100 338 -15.742442 0.14954269 7.579918 -637.49568
Loop time of 0.0828406 on 4 procs for 100 steps with 24 atoms
Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
@ -116,14 +117,14 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.012844 | 0.025471 | 0.047008 | 8.1 | 30.75
Bond | 0.00038934 | 0.00046468 | 0.00054336 | 0.0 | 0.56
Kspace | 0.0061138 | 0.027556 | 0.04014 | 7.8 | 33.26
Pair | 0.0085177 | 0.016083 | 0.026787 | 5.3 | 28.41
Bond | 0.00022459 | 0.00031394 | 0.00037575 | 0.0 | 0.55
Kspace | 0.0049062 | 0.014122 | 0.02044 | 5.0 | 24.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.023276 | 0.023636 | 0.023804 | 0.1 | 28.53
Output | 3.171e-05 | 3.3557e-05 | 3.8147e-05 | 0.0 | 0.04
Comm | 0.018515 | 0.02086 | 0.023246 | 1.2 | 36.84
Output | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 | 0.0 | 0.05
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00568 | | | 6.86
Other | | 0.005213 | | | 9.21
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 1 0 0 0 0 2
@ -164,22 +165,22 @@ Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -15.742442 0 7.4303753 -613.0781
1000 369.81793 -54.202686 0 -37.667331 294.98823
Loop time of 0.199641 on 4 procs for 1000 steps with 24 atoms
Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms
Performance: 432.777 ns/day, 0.055 hours/ns, 5008.996 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.017161 | 0.034988 | 0.05833 | 8.0 | 17.53
Bond | 0.00017357 | 0.00021374 | 0.00027347 | 0.0 | 0.11
Kspace | 0.018025 | 0.044624 | 0.065613 | 8.4 | 22.35
Neigh | 0.0029755 | 0.0033154 | 0.0036366 | 0.6 | 1.66
Comm | 0.059933 | 0.06537 | 0.070709 | 1.5 | 32.74
Output | 3.4571e-05 | 3.6657e-05 | 4.22e-05 | 0.0 | 0.02
Modify | 0.043458 | 0.045628 | 0.04767 | 0.9 | 22.86
Other | | 0.005465 | | | 2.74
Pair | 0.0154 | 0.028993 | 0.040525 | 5.5 | 18.72
Bond | 0.00016999 | 0.0001902 | 0.00023293 | 0.0 | 0.12
Kspace | 0.019093 | 0.028112 | 0.038976 | 4.3 | 18.15
Neigh | 0.0020263 | 0.0022184 | 0.002408 | 0.4 | 1.43
Comm | 0.04947 | 0.053627 | 0.058009 | 1.4 | 34.62
Output | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 | 0.0 | 0.02
Modify | 0.035275 | 0.036815 | 0.038425 | 0.7 | 23.77
Other | | 0.004909 | | | 3.17
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 0 0 1 0 1 1
@ -201,6 +202,17 @@ fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
variable oxygen atom "type==1"
variable hydrogen atom "type==2"
group oxygen dynamic all var oxygen
dynamic group oxygen defined
group hydrogen dynamic all var hydrogen
dynamic group hydrogen defined
variable nO equal count(oxygen)
variable nH equal count(hydrogen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@ -208,7 +220,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run
@ -226,44 +238,44 @@ WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0
2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0
3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0
4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0
5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0
6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0
7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0
8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0
9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0
10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0
11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0
12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0
13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0
14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0
15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0
16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0
17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0
18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0
19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0
20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0
21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0
Loop time of 93.8859 on 4 procs for 20000 steps with 105 atoms
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0 8 16
2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0 29 58
3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0 33 66
4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0 33 66
5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0 33 66
6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0 33 66
7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0 33 66
8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0 33 66
9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0 34 68
10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0 34 68
11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0 34 68
12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0 34 68
13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0 34 68
14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0 34 68
15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0 34 68
16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0 34 68
17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0 34 68
18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0 34 68
19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0 35 70
20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0 35 70
21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0 35 70
Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms
Performance: 18.405 ns/day, 1.304 hours/ns, 213.024 timesteps/s
Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.7882 | 10.264 | 14.758 | 93.2 | 10.93
Bond | 0.028286 | 0.034218 | 0.039038 | 2.5 | 0.04
Kspace | 0.57255 | 5.2227 | 8.8493 | 133.8 | 5.56
Neigh | 0.3635 | 0.36915 | 0.37473 | 0.9 | 0.39
Comm | 2.9961 | 3.2542 | 3.509 | 11.4 | 3.47
Output | 0.0011675 | 0.0012342 | 0.001375 | 0.2 | 0.00
Modify | 74.428 | 74.499 | 74.571 | 0.7 | 79.35
Other | | 0.2411 | | | 0.26
Pair | 6.3571 | 9.7574 | 13.984 | 90.7 | 11.56
Bond | 0.026374 | 0.031321 | 0.035482 | 2.1 | 0.04
Kspace | 0.57402 | 4.7894 | 8.1754 | 129.0 | 5.67
Neigh | 0.34952 | 0.34987 | 0.35021 | 0.1 | 0.41
Comm | 2.4028 | 2.4228 | 2.4372 | 0.9 | 2.87
Output | 0.0012269 | 0.0012826 | 0.0014355 | 0.2 | 0.00
Modify | 66.819 | 66.828 | 66.837 | 0.1 | 79.17
Other | | 0.2281 | | | 0.27
Nlocal: 26.25 ave 31 max 22 min
Histogram: 1 0 1 0 0 0 1 0 0 1
@ -278,4 +290,4 @@ Ave special neighs/atom = 2
Neighbor list builds = 20428
Dangerous builds = 0
Total wall time: 0:01:34
Total wall time: 0:01:24

56
examples/gcmc/log.6Jul17.gcmc.lj.g++.1 → examples/gcmc/log.23Oct17.gcmc.lj.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@ -43,6 +43,13 @@ fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
dynamic group type1 defined
variable n1 equal count(type1)
# averaging
variable rho equal density
@ -54,10 +61,11 @@ variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*1+${nugget})
variable muex equal -1.25-2.0*ln(density*1+1e-08)
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
variable rhoav equal f_ave[1]
variable pav equal f_ave[2]
variable muexav equal f_ave[3]
variable n1av equal f_ave[4]
# output
@ -68,7 +76,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
compute_modify thermo_temp dynamic yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
thermo 1000
# run
@ -87,32 +95,32 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
0 0 0 0 -0 0 0 0 0 0 0 0 0
1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094
Loop time of 20.6892 on 1 procs for 10000 steps with 60 atoms
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219 64.98
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004 62.97
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537 63.5
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657 62.17
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777 64.15
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359 64.37
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399 62.33
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766 64.29
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544 62.87
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094 63.2
Loop time of 20.4081 on 1 procs for 10000 steps with 60 atoms
Performance: 208804.611 tau/day, 483.344 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 211680.375 tau/day, 490.001 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47227 | 0.47227 | 0.47227 | 0.0 | 2.28
Neigh | 1.1729 | 1.1729 | 1.1729 | 0.0 | 5.67
Comm | 0.17133 | 0.17133 | 0.17133 | 0.0 | 0.83
Output | 0.00028253 | 0.00028253 | 0.00028253 | 0.0 | 0.00
Modify | 18.852 | 18.852 | 18.852 | 0.0 | 91.12
Other | | 0.02063 | | | 0.10
Pair | 0.46484 | 0.46484 | 0.46484 | 0.0 | 2.28
Neigh | 1.1447 | 1.1447 | 1.1447 | 0.0 | 5.61
Comm | 0.1696 | 0.1696 | 0.1696 | 0.0 | 0.83
Output | 0.000319 | 0.000319 | 0.000319 | 0.0 | 0.00
Modify | 18.607 | 18.607 | 18.607 | 0.0 | 91.17
Other | | 0.02194 | | | 0.11
Nlocal: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0

58
examples/gcmc/log.6Jul17.gcmc.lj.g++.4 → examples/gcmc/log.23Oct17.gcmc.lj.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017)
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@ -43,6 +43,13 @@ fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
dynamic group type1 defined
variable n1 equal count(type1)
# averaging
variable rho equal density
@ -54,10 +61,11 @@ variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
variable muex equal -1.25-2.0*ln(density*1+${nugget})
variable muex equal -1.25-2.0*ln(density*1+1e-08)
fix ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
variable rhoav equal f_ave[1]
variable pav equal f_ave[2]
variable muexav equal f_ave[3]
variable n1av equal f_ave[4]
# output
@ -68,7 +76,7 @@ variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
compute_modify thermo_temp dynamic yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
thermo 1000
# run
@ -87,32 +95,32 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
0 0 0 0 -0 0 0 0 0 0 0 0 0
1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238
Loop time of 24.9916 on 4 procs for 10000 steps with 69 atoms
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24
Loop time of 23.8213 on 4 procs for 10000 steps with 69 atoms
Performance: 172857.936 tau/day, 400.134 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 181350.388 tau/day, 419.793 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11696 | 0.12516 | 0.1321 | 1.7 | 0.50
Neigh | 0.34874 | 0.35644 | 0.36545 | 1.2 | 1.43
Comm | 0.48531 | 0.51366 | 0.54755 | 3.8 | 2.06
Output | 0.0005362 | 0.00069767 | 0.00076008 | 0.0 | 0.00
Modify | 23.956 | 23.972 | 23.988 | 0.3 | 95.92
Other | | 0.02376 | | | 0.10
Pair | 0.10935 | 0.11844 | 0.12741 | 2.1 | 0.50
Neigh | 0.33 | 0.33945 | 0.35091 | 1.6 | 1.42
Comm | 0.49249 | 0.51745 | 0.53856 | 2.7 | 2.17
Output | 0.00053334 | 0.0007208 | 0.0007906 | 0.0 | 0.00
Modify | 22.82 | 22.822 | 22.825 | 0.0 | 95.81
Other | | 0.02289 | | | 0.10
Nlocal: 17.25 ave 23 max 10 min
Histogram: 1 0 0 0 0 0 2 0 0 1
@ -125,4 +133,4 @@ Total # of neighbors = 2823
Ave neighs/atom = 40.913
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:24
Total wall time: 0:00:23

2
lib/atc/Matrix.h
View File

@ -356,7 +356,7 @@ DenseMatrix<T> Matrix<T>::pow(double n) const
int sz=this->size(); for(INDEX i=0; i<sz; i++)
{
double val = R[i];
R[i] = pow(val,n);
R[i] = std::pow(val,n);
}
return R;
}

109
potentials/BN.extep Normal file
View File

@ -0,0 +1,109 @@
# DATE: 2017-11-28 CONTRIBUTOR: J.H. Los, J.M.H. Kroes CITATION: Los et al. Phys. Rev. B 96, 184108 (2017)
# B and N mixture, parameterized for ExTeP potential
# ExTeP parameters for various elements and mixtures
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# these entries are in LAMMPS "metal" units:
# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
# other quantities are unitless
# format of a single entry (one or more lines):
#I J K m, gamma*, lambda3, c, d, h, n, gamma, lambda2, B, R, D, lambda1, A
B B B 3 1.0 0.0 26617.3000 141.2000 -0.1300 1.1422470 0.01498959 2.5211820 2768.7363631 2.0 0.2 2.6857244 3376.3350735
N N N 3 1.0 0.0 23.5000 3.7500 -0.4000 0.6650000 0.01925100 2.6272721 2563.5603417 2.0 0.2 2.8293093 2978.9527928
B B N 3 1.0 0.0 26617.3000 141.2000 -0.1300 1.1422470 0.01498959 2.5211820 2768.7363631 2.0 0.2 2.6857244 3376.3350735
N N B 3 1.0 0.0 23.5000 3.7500 -0.4000 0.6650000 0.01925100 2.6272721 2563.5603417 2.0 0.2 2.8293093 2978.9527928
B N B 3 1.0 0.0d0 306.586555205d0 10.d0 -0.7218d0 0.6576543657d0 0.0027024851d0 2.69335d0 2595.6860833266d0 2.d0 0.2d0 2.95d0 3330.0655849887d0
B N N 3 1.0 0.0d0 306.586555205d0 10.d0 -0.7218d0 0.6576543657d0 0.0027024851d0 2.69335d0 2595.6860833266d0 2.d0 0.2d0 2.95d0 3330.0655849887d0
N B B 3 1.0 0.0d0 306.586555205d0 10.d0 -0.7218d0 0.6576543657d0 0.0027024851d0 2.69335d0 2595.6860833266d0 2.d0 0.2d0 2.95d0 3330.0655849887d0
N B N 3 1.0 0.0d0 306.586555205d0 10.d0 -0.7218d0 0.6576543657d0 0.0027024851d0 2.69335d0 2595.6860833266d0 2.d0 0.2d0 2.95d0 3330.0655849887d0
#
# 1.9925 Bicubic Splines Parameters
#
# F_corr [ B, B]
#
#t1 t2 i j val dx dy dxy
B B 0 0 0.0000 0.0000 0.0000 0.0000
B B 0 1 0.0054 0.0000 0.0000 0.0000
B B 0 2 0.0182 0.0000 0.0000 0.0000
B B 0 3 -0.0034 0.0000 0.0000 0.0000
B B 0 4 -0.0034 0.0000 0.0000 0.0000
B B 1 0 0.0054 0.0000 0.0000 0.0000
B B 1 1 0.0100 0.0000 0.0000 0.0000
B B 1 2 0.0062 0.0000 0.0000 0.0000
B B 1 3 0.0154 0.0000 0.0000 0.0000
B B 1 4 0.0154 0.0000 0.0000 0.0000
B B 2 0 0.0182 0.0000 0.0000 0.0000
B B 2 1 0.0062 0.0000 0.0000 0.0000
B B 2 2 0.0154 0.0000 0.0000 0.0000
B B 2 3 -0.0390 0.0000 -0.0727 0.0000
B B 2 4 -0.0390 0.0000 -0.0727 0.0000
B B 3 0 -0.0034 0.0000 0.0000 0.0000
B B 3 1 0.0154 0.0000 0.0000 0.0000
B B 3 2 -0.0390 -0.0727 0.0000 0.0000
B B 3 3 -0.1300 0.0000 0.0000 0.0000
B B 3 4 -0.1300 0.0000 0.0000 0.0000
B B 4 0 -0.0034 0.0000 0.0000 0.0000
B B 4 1 0.0154 0.0000 0.0000 0.0000
B B 4 2 -0.0390 -0.0727 0.0000 0.0000
B B 4 3 -0.1300 0.0000 0.0000 0.0000
B B 4 4 -0.1300 0.0000 0.0000 0.0000
#
# F_corr [ B, N]
#
#t1 t2 i j val dx dy dxy
B N 0 0 0.0170 0.0000 0.0000 0.0000
B N 0 1 0.0078 0.0000 0.0000 0.0000
B N 0 2 0.0000 0.0000 0.0000 0.0000
B N 0 3 -0.0860 0.0000 0.0000 0.0000
B N 0 4 -0.0860 0.0000 0.0000 0.0000
B N 1 0 -0.0090 0.0000 0.0000 0.0000
B N 1 1 0.0090 0.0000 0.0000 0.0000
B N 1 2 -0.0068 0.0000 -0.0214 0.0000
B N 1 3 -0.0338 0.0000 0.0388 0.0000
B N 1 4 -0.0338 0.0000 0.0388 0.0000
B N 2 0 0.0000 0.0000 0.0000 0.0000
B N 2 1 -0.0198 0.0000 0.0000 0.0000
B N 2 2 0.0000 0.0000 0.0000 0.0000
B N 2 3 -0.0084 0.0000 0.0169 0.0000
B N 2 4 -0.0084 0.0000 0.0169 0.0000
B N 3 0 -0.0750 0.0000 0.0000 0.0000
B N 3 1 -0.0168 0.0306 0.0000 0.0000
B N 3 2 -0.0138 0.0084 0.0000 0.0000
B N 3 3 0.0000 0.0000 0.0000 0.0000
B N 3 4 0.0000 0.0000 0.0000 0.0000
B N 4 0 -0.0750 0.0000 0.0000 0.0000
B N 4 1 -0.0168 0.0306 0.0000 0.0000
B N 4 2 -0.0138 0.0084 0.0000 0.0000
B N 4 3 0.0000 0.0000 0.0000 0.0000
B N 4 4 0.0000 0.0000 0.0000 0.0000
#
# F_corr [ N, N]
#
#t1 t2 i j val dx dy dxy
N N 0 0 0.0000 0.0000 0.0000 0.0000
N N 0 1 -0.0282 0.0000 0.0000 0.0000
N N 0 2 -0.0018 0.0000 0.0000 0.0000
N N 0 3 -0.0004 0.0000 0.0000 0.0000
N N 0 4 -0.0004 0.0000 0.0000 0.0000
N N 1 0 -0.0282 0.0000 0.0000 0.0000
N N 1 1 0.0200 0.0000 0.0000 0.0000
N N 1 2 0.0180 0.0162 -0.0027 0.0000
N N 1 3 0.0146 0.0000 0.0000 0.0000
N N 1 4 0.0146 0.0000 0.0000 0.0000
N N 2 0 -0.0018 0.0000 0.0000 0.0000
N N 2 1 0.0180 -0.0027 0.0162 0.0000
N N 2 2 0.0306 0.0000 0.0000 0.0000
N N 2 3 0.0060 0.0000 -0.0073 0.0000
N N 2 4 0.0060 0.0000 -0.0073 0.0000
N N 3 0 -0.0004 0.0000 0.0000 0.0000
N N 3 1 0.0146 0.0000 0.0000 0.0000
N N 3 2 0.0060 -0.0073 0.0000 0.0000
N N 3 3 0.0000 0.0000 0.0000 0.0000
N N 3 4 0.0000 0.0000 0.0000 0.0000
N N 4 0 -0.0004 0.0000 0.0000 0.0000
N N 4 1 0.0146 0.0000 0.0000 0.0000
N N 4 2 0.0060 -0.0073 0.0000 0.0000
N N 4 3 0.0000 0.0000 0.0000 0.0000
N N 4 4 0.0000 0.0000 0.0000 0.0000

26
python/lammps.py
View File

@ -619,6 +619,30 @@ class Atom2D(Atom):
self.lmp.eval("fy[%d]" % self.index))
class variable_set:
def __init__(self, name, variable_dict):
self._name = name
array_pattern = re.compile(r"(?P<arr>.+)\[(?P<index>[0-9]+)\]")
for key, value in variable_dict.items():
m = array_pattern.match(key)
if m:
g = m.groupdict()
varname = g['arr']
idx = int(g['index'])
if varname not in self.__dict__:
self.__dict__[varname] = {}
self.__dict__[varname][idx] = value
else:
self.__dict__[key] = value
def __str__(self):
return "{}({})".format(self._name, ','.join(["{}={}".format(k, self.__dict__[k]) for k in self.__dict__.keys() if not k.startswith('_')]))
def __repr__(self):
return self.__str__()
def get_thermo_data(output):
""" traverse output of runs and extract thermo data columns """
if isinstance(output, str):
@ -646,7 +670,7 @@ def get_thermo_data(output):
elif line.startswith("Loop time of "):
in_run = False
columns = None
thermo_data = namedtuple('ThermoData', list(current_run.keys()))(*list(current_run.values()))
thermo_data = variable_set('ThermoData', current_run)
r = {'thermo' : thermo_data }
runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
elif in_run and len(columns) > 0:

7
src/.gitignore vendored
View File

@ -25,6 +25,7 @@
/kokkos.h
/kokkos_type.h
/kokkos_few.h
/kokkos_base.h
/manifold*.cpp
/manifold*.h
@ -1085,10 +1086,16 @@
/pair_born_coul_long_cs.h
/pair_born_coul_dsf_cs.cpp
/pair_born_coul_dsf_cs.h
/pair_born_coul_wolf_cs.cpp
/pair_born_coul_wolf_cs.h
/pair_buck_coul_long_cs.cpp
/pair_buck_coul_long_cs.h
/pair_coul_long_cs.cpp
/pair_coul_long_cs.h
/pair_coul_wolf_cs.cpp
/pair_coul_wolf_cs.h
/pair_extep.cpp
/pair_extep.h
/pair_lj_cut_thole_long.cpp
/pair_lj_cut_thole_long.h
/pair_plum_hb.cpp

1
src/GPU/pair_eam_alloy_gpu.cpp
View File

@ -28,6 +28,7 @@
#include "error.h"
#include "neigh_request.h"
#include "gpu_extra.h"
#include "domain.h"
using namespace LAMMPS_NS;

1
src/GPU/pair_eam_fs_gpu.cpp
View File

@ -28,6 +28,7 @@
#include "error.h"
#include "neigh_request.h"
#include "gpu_extra.h"
#include "domain.h"
using namespace LAMMPS_NS;

1
src/GRANULAR/fix_wall_gran.cpp
View File

@ -30,6 +30,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "neighbor.h"
using namespace LAMMPS_NS;
using namespace FixConst;

2
src/GRANULAR/fix_wall_gran_region.cpp
View File

@ -30,6 +30,8 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "comm.h"
#include "neighbor.h"
using namespace LAMMPS_NS;
using namespace FixConst;

21
src/KOKKOS/Install.sh
View File

@ -28,8 +28,20 @@ action () {
# force rebuild of files with LMP_KOKKOS switch
touch ../accelerator_kokkos.h
touch ../memory.h
KOKKOS_INSTALLED=0
if (test -e ../Makefile.package) then
KOKKOS_INSTALLED=`grep DLMP_KOKKOS ../Makefile.package | wc -l`
fi
if (test $mode = 1) then
if (test $KOKKOS_INSTALLED = 0) then
touch ../accelerator_kokkos.h
fi
elif (test $mode = 0) then
if (test $KOKKOS_INSTALLED = 1) then
touch ../accelerator_kokkos.h
fi
fi
# list of files with optional dependcies
@ -125,8 +137,9 @@ action improper_harmonic_kokkos.cpp improper_harmonic.cpp
action improper_harmonic_kokkos.h improper_harmonic.h
action kokkos.cpp
action kokkos.h
action kokkos_type.h
action kokkos_base.h
action kokkos_few.h
action kokkos_type.h
action memory_kokkos.h
action modify_kokkos.cpp
action modify_kokkos.h
@ -229,6 +242,8 @@ action pair_tersoff_mod_kokkos.cpp pair_tersoff_mod.cpp
action pair_tersoff_mod_kokkos.h pair_tersoff_mod.h
action pair_tersoff_zbl_kokkos.cpp pair_tersoff_zbl.cpp
action pair_tersoff_zbl_kokkos.h pair_tersoff_zbl.h
action pair_yukawa_kokkos.cpp
action pair_yukawa_kokkos.h
action pppm_kokkos.cpp pppm.cpp
action pppm_kokkos.h pppm.h
action rand_pool_wrap_kokkos.cpp

14
src/KOKKOS/angle_charmm_kokkos.cpp
View File

@ -24,7 +24,7 @@
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -51,8 +51,8 @@ template<class DeviceType>
AngleCharmmKokkos<DeviceType>::~AngleCharmmKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -71,15 +71,15 @@ void AngleCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (eflag_atom) {
//if(k_eatom.dimension_0()<maxeatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.template view<DeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.dimension_0()<maxvatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
d_vatom = k_vatom.template view<DeviceType>();
//}
}

14
src/KOKKOS/angle_class2_kokkos.cpp
View File

@ -24,7 +24,7 @@
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -51,8 +51,8 @@ template<class DeviceType>
AngleClass2Kokkos<DeviceType>::~AngleClass2Kokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -70,13 +70,13 @@ void AngleClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");
d_eatom = k_eatom.template view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"angle:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"angle:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}

14
src/KOKKOS/angle_harmonic_kokkos.cpp
View File

@ -24,7 +24,7 @@
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -51,8 +51,8 @@ template<class DeviceType>
AngleHarmonicKokkos<DeviceType>::~AngleHarmonicKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -70,13 +70,13 @@ void AngleHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");
d_eatom = k_eatom.template view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"angle:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"angle:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}

134
src/KOKKOS/atom_kokkos.cpp
View File

@ -19,7 +19,7 @@
#include "update.h"
#include "domain.h"
#include "atom_masks.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "kokkos.h"
@ -33,59 +33,59 @@ AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp) {}
AtomKokkos::~AtomKokkos()
{
memory->destroy_kokkos(k_tag, tag);
memory->destroy_kokkos(k_mask, mask);
memory->destroy_kokkos(k_type, type);
memory->destroy_kokkos(k_image, image);
memory->destroy_kokkos(k_molecule, molecule);
memoryKK->destroy_kokkos(k_tag, tag);
memoryKK->destroy_kokkos(k_mask, mask);
memoryKK->destroy_kokkos(k_type, type);
memoryKK->destroy_kokkos(k_image, image);
memoryKK->destroy_kokkos(k_molecule, molecule);
memory->destroy_kokkos(k_x, x);
memory->destroy_kokkos(k_v, v);
memory->destroy_kokkos(k_f, f);
memoryKK->destroy_kokkos(k_x, x);
memoryKK->destroy_kokkos(k_v, v);
memoryKK->destroy_kokkos(k_f, f);
memory->destroy_kokkos(k_mass, mass);
memory->destroy_kokkos(k_q, q);
memoryKK->destroy_kokkos(k_mass, mass);
memoryKK->destroy_kokkos(k_q, q);
memory->destroy_kokkos(k_radius, radius);
memory->destroy_kokkos(k_rmass, rmass);
memory->destroy_kokkos(k_omega, omega);
memory->destroy_kokkos(k_angmom, angmom);
memory->destroy_kokkos(k_torque, torque);
memoryKK->destroy_kokkos(k_radius, radius);
memoryKK->destroy_kokkos(k_rmass, rmass);
memoryKK->destroy_kokkos(k_omega, omega);
memoryKK->destroy_kokkos(k_angmom, angmom);
memoryKK->destroy_kokkos(k_torque, torque);
memory->destroy_kokkos(k_nspecial, nspecial);
memory->destroy_kokkos(k_special, special);
memory->destroy_kokkos(k_num_bond, num_bond);
memory->destroy_kokkos(k_bond_type, bond_type);
memory->destroy_kokkos(k_bond_atom, bond_atom);
memory->destroy_kokkos(k_num_angle, num_angle);
memory->destroy_kokkos(k_angle_type, angle_type);
memory->destroy_kokkos(k_angle_atom1, angle_atom1);
memory->destroy_kokkos(k_angle_atom2, angle_atom2);
memory->destroy_kokkos(k_angle_atom3, angle_atom3);
memory->destroy_kokkos(k_num_dihedral, num_dihedral);
memory->destroy_kokkos(k_dihedral_type, dihedral_type);
memory->destroy_kokkos(k_dihedral_atom1, dihedral_atom1);
memory->destroy_kokkos(k_dihedral_atom2, dihedral_atom2);
memory->destroy_kokkos(k_dihedral_atom3, dihedral_atom3);
memory->destroy_kokkos(k_dihedral_atom4, dihedral_atom4);
memory->destroy_kokkos(k_num_improper, num_improper);
memory->destroy_kokkos(k_improper_type, improper_type);
memory->destroy_kokkos(k_improper_atom1, improper_atom1);
memory->destroy_kokkos(k_improper_atom2, improper_atom2);
memory->destroy_kokkos(k_improper_atom3, improper_atom3);
memory->destroy_kokkos(k_improper_atom4, improper_atom4);
memoryKK->destroy_kokkos(k_nspecial, nspecial);
memoryKK->destroy_kokkos(k_special, special);
memoryKK->destroy_kokkos(k_num_bond, num_bond);
memoryKK->destroy_kokkos(k_bond_type, bond_type);
memoryKK->destroy_kokkos(k_bond_atom, bond_atom);
memoryKK->destroy_kokkos(k_num_angle, num_angle);
memoryKK->destroy_kokkos(k_angle_type, angle_type);
memoryKK->destroy_kokkos(k_angle_atom1, angle_atom1);
memoryKK->destroy_kokkos(k_angle_atom2, angle_atom2);
memoryKK->destroy_kokkos(k_angle_atom3, angle_atom3);
memoryKK->destroy_kokkos(k_num_dihedral, num_dihedral);
memoryKK->destroy_kokkos(k_dihedral_type, dihedral_type);
memoryKK->destroy_kokkos(k_dihedral_atom1, dihedral_atom1);
memoryKK->destroy_kokkos(k_dihedral_atom2, dihedral_atom2);
memoryKK->destroy_kokkos(k_dihedral_atom3, dihedral_atom3);
memoryKK->destroy_kokkos(k_dihedral_atom4, dihedral_atom4);
memoryKK->destroy_kokkos(k_num_improper, num_improper);
memoryKK->destroy_kokkos(k_improper_type, improper_type);
memoryKK->destroy_kokkos(k_improper_atom1, improper_atom1);
memoryKK->destroy_kokkos(k_improper_atom2, improper_atom2);
memoryKK->destroy_kokkos(k_improper_atom3, improper_atom3);
memoryKK->destroy_kokkos(k_improper_atom4, improper_atom4);
// USER-DPD package
memory->destroy_kokkos(k_uCond,uCond);
memory->destroy_kokkos(k_uMech,uMech);
memory->destroy_kokkos(k_uChem,uChem);
memory->destroy_kokkos(k_uCG,uCG);
memory->destroy_kokkos(k_uCGnew,uCGnew);
memory->destroy_kokkos(k_rho,rho);
memory->destroy_kokkos(k_dpdTheta,dpdTheta);
memory->destroy_kokkos(k_duChem,duChem);
memoryKK->destroy_kokkos(k_uCond,uCond);
memoryKK->destroy_kokkos(k_uMech,uMech);
memoryKK->destroy_kokkos(k_uChem,uChem);
memoryKK->destroy_kokkos(k_uCG,uCG);
memoryKK->destroy_kokkos(k_uCGnew,uCGnew);
memoryKK->destroy_kokkos(k_rho,rho);
memoryKK->destroy_kokkos(k_dpdTheta,dpdTheta);
memoryKK->destroy_kokkos(k_duChem,duChem);
memory->destroy_kokkos(k_dvector,dvector);
memoryKK->destroy_kokkos(k_dvector,dvector);
dvector = NULL;
}
@ -232,10 +232,10 @@ void AtomKokkos::sort()
void AtomKokkos::grow(unsigned int mask){
if (mask & SPECIAL_MASK){
memory->destroy_kokkos(k_special, special);
memoryKK->destroy_kokkos(k_special, special);
sync(Device, mask);
modified(Device, mask);
memory->grow_kokkos(k_special,special,nmax,maxspecial,"atom:special");
memoryKK->grow_kokkos(k_special,special,nmax,maxspecial,"atom:special");
avec->grow_reset();
sync(Host, mask);
}
@ -270,7 +270,7 @@ int AtomKokkos::add_custom(const char *name, int flag)
int n = strlen(name) + 1;
dname[index] = new char[n];
strcpy(dname[index],name);
memory->grow_kokkos(k_dvector,dvector,ndvector,nmax,
memoryKK->grow_kokkos(k_dvector,dvector,ndvector,nmax,
"atom:dvector");
}
@ -291,7 +291,7 @@ void AtomKokkos::remove_custom(int flag, int index)
delete [] iname[index];
iname[index] = NULL;
} else {
//memory->destroy_kokkos(dvector);
//memoryKK->destroy_kokkos(dvector);
dvector[index] = NULL;
delete [] dname[index];
dname[index] = NULL;
@ -302,25 +302,25 @@ void AtomKokkos::remove_custom(int flag, int index)
void AtomKokkos::deallocate_topology()
{
memory->destroy_kokkos(k_bond_type, bond_type);
memory->destroy_kokkos(k_bond_atom, bond_atom);
memoryKK->destroy_kokkos(k_bond_type, bond_type);
memoryKK->destroy_kokkos(k_bond_atom, bond_atom);
memory->destroy_kokkos(k_angle_type, angle_type);
memory->destroy_kokkos(k_angle_atom1, angle_atom1);
memory->destroy_kokkos(k_angle_atom2, angle_atom2);
memory->destroy_kokkos(k_angle_atom3, angle_atom3);
memoryKK->destroy_kokkos(k_angle_type, angle_type);
memoryKK->destroy_kokkos(k_angle_atom1, angle_atom1);
memoryKK->destroy_kokkos(k_angle_atom2, angle_atom2);
memoryKK->destroy_kokkos(k_angle_atom3, angle_atom3);
memory->destroy_kokkos(k_dihedral_type, dihedral_type);
memory->destroy_kokkos(k_dihedral_atom1, dihedral_atom1);
memory->destroy_kokkos(k_dihedral_atom2, dihedral_atom2);
memory->destroy_kokkos(k_dihedral_atom3, dihedral_atom3);
memory->destroy_kokkos(k_dihedral_atom4, dihedral_atom4);
memoryKK->destroy_kokkos(k_dihedral_type, dihedral_type);
memoryKK->destroy_kokkos(k_dihedral_atom1, dihedral_atom1);
memoryKK->destroy_kokkos(k_dihedral_atom2, dihedral_atom2);
memoryKK->destroy_kokkos(k_dihedral_atom3, dihedral_atom3);
memoryKK->destroy_kokkos(k_dihedral_atom4, dihedral_atom4);
memory->destroy_kokkos(k_improper_type, improper_type);
memory->destroy_kokkos(k_improper_atom1, improper_atom1);
memory->destroy_kokkos(k_improper_atom2, improper_atom2);
memory->destroy_kokkos(k_improper_atom3, improper_atom3);
memory->destroy_kokkos(k_improper_atom4, improper_atom4);
memoryKK->destroy_kokkos(k_improper_type, improper_type);
memoryKK->destroy_kokkos(k_improper_atom1, improper_atom1);
memoryKK->destroy_kokkos(k_improper_atom2, improper_atom2);
memoryKK->destroy_kokkos(k_improper_atom3, improper_atom3);
memoryKK->destroy_kokkos(k_improper_atom4, improper_atom4);
}
/* ----------------------------------------------------------------------

38
src/KOKKOS/atom_vec_angle_kokkos.cpp
View File

@ -19,7 +19,7 @@
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -68,33 +68,33 @@ void AtomVecAngleKokkos::grow(int n)
sync(Device,ALL_MASK);
modified(Device,ALL_MASK);
memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
memoryKK->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memoryKK->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memoryKK->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
"atom:special");
memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
memoryKK->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memoryKK->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
"atom:bond_type");
memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
memoryKK->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
"atom:bond_atom");
memory->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
memory->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
memoryKK->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
"atom:angle_type");
memory->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
"atom:angle_atom1");
memory->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
"atom:angle_atom2");
memory->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
"atom:angle_atom3");
grow_reset();

16
src/KOKKOS/atom_vec_atomic_kokkos.cpp
View File

@ -19,7 +19,7 @@
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -64,14 +64,14 @@ void AtomVecAtomicKokkos::grow(int n)
sync(Device,ALL_MASK);
modified(Device,ALL_MASK);
memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
grow_reset();
sync(Host,ALL_MASK);

28
src/KOKKOS/atom_vec_bond_kokkos.cpp
View File

@ -19,7 +19,7 @@
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -65,21 +65,21 @@ void AtomVecBondKokkos::grow(int n)
sync(Device,ALL_MASK);
modified(Device,ALL_MASK);
memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,"atom:special");
memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,"atom:bond_type");
memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,"atom:bond_atom");
memoryKK->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memoryKK->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memoryKK->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,"atom:special");
memoryKK->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memoryKK->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,"atom:bond_type");
memoryKK->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,"atom:bond_atom");
grow_reset();
sync(Host,ALL_MASK);

18
src/KOKKOS/atom_vec_charge_kokkos.cpp
View File

@ -19,7 +19,7 @@
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -67,16 +67,16 @@ void AtomVecChargeKokkos::grow(int n)
sync(Device,ALL_MASK);
modified(Device,ALL_MASK);
memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memory->grow_kokkos(atomKK->k_q,atomKK->q,nmax,"atom:q");
memoryKK->grow_kokkos(atomKK->k_q,atomKK->q,nmax,"atom:q");
grow_reset();
sync(Host,ALL_MASK);

32
src/KOKKOS/atom_vec_dpd_kokkos.cpp
View File

@ -19,7 +19,7 @@
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -67,24 +67,24 @@ void AtomVecDPDKokkos::grow(int n)
sync(Device,ALL_MASK);
modified(Device,ALL_MASK);
memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memory->grow_kokkos(atomKK->k_rho,atomKK->rho,nmax,"atom:rho");
memory->grow_kokkos(atomKK->k_dpdTheta,atomKK->dpdTheta,nmax,"atom:dpdTheta");
memory->grow_kokkos(atomKK->k_uCond,atomKK->uCond,nmax,"atom:uCond");
memory->grow_kokkos(atomKK->k_uMech,atomKK->uMech,nmax,"atom:uMech");
memory->grow_kokkos(atomKK->k_uChem,atomKK->uChem,nmax,"atom:uChem");
memory->grow_kokkos(atomKK->k_uCG,atomKK->uCG,nmax,"atom:uCG");
memory->grow_kokkos(atomKK->k_uCGnew,atomKK->uCGnew,nmax,"atom:uCGnew");
memory->grow_kokkos(atomKK->k_duChem,atomKK->duChem,nmax,"atom:duChem");
memoryKK->grow_kokkos(atomKK->k_rho,atomKK->rho,nmax,"atom:rho");
memoryKK->grow_kokkos(atomKK->k_dpdTheta,atomKK->dpdTheta,nmax,"atom:dpdTheta");
memoryKK->grow_kokkos(atomKK->k_uCond,atomKK->uCond,nmax,"atom:uCond");
memoryKK->grow_kokkos(atomKK->k_uMech,atomKK->uMech,nmax,"atom:uMech");
memoryKK->grow_kokkos(atomKK->k_uChem,atomKK->uChem,nmax,"atom:uChem");
memoryKK->grow_kokkos(atomKK->k_uCG,atomKK->uCG,nmax,"atom:uCG");
memoryKK->grow_kokkos(atomKK->k_uCGnew,atomKK->uCGnew,nmax,"atom:uCGnew");
memoryKK->grow_kokkos(atomKK->k_duChem,atomKK->duChem,nmax,"atom:duChem");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)

64
src/KOKKOS/atom_vec_full_kokkos.cpp
View File

@ -19,7 +19,7 @@
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -67,59 +67,59 @@ void AtomVecFullKokkos::grow(int n)
sync(Device,ALL_MASK);
modified(Device,ALL_MASK);
memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memory->grow_kokkos(atomKK->k_q,atomKK->q,nmax,"atom:q");
memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memoryKK->grow_kokkos(atomKK->k_q,atomKK->q,nmax,"atom:q");
memoryKK->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
memoryKK->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memoryKK->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
"atom:special");
memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
memoryKK->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memoryKK->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
"atom:bond_type");
memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
memoryKK->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
"atom:bond_atom");
memory->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
memory->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
memoryKK->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
"atom:angle_type");
memory->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
"atom:angle_atom1");
memory->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
"atom:angle_atom2");
memory->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
"atom:angle_atom3");
memory->grow_kokkos(atomKK->k_num_dihedral,atomKK->num_dihedral,nmax,"atom:num_dihedral");
memory->grow_kokkos(atomKK->k_dihedral_type,atomKK->dihedral_type,nmax,
memoryKK->grow_kokkos(atomKK->k_num_dihedral,atomKK->num_dihedral,nmax,"atom:num_dihedral");
memoryKK->grow_kokkos(atomKK->k_dihedral_type,atomKK->dihedral_type,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_type");
memory->grow_kokkos(atomKK->k_dihedral_atom1,atomKK->dihedral_atom1,nmax,
memoryKK->grow_kokkos(atomKK->k_dihedral_atom1,atomKK->dihedral_atom1,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_atom1");
memory->grow_kokkos(atomKK->k_dihedral_atom2,atomKK->dihedral_atom2,nmax,
memoryKK->grow_kokkos(atomKK->k_dihedral_atom2,atomKK->dihedral_atom2,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_atom2");
memory->grow_kokkos(atomKK->k_dihedral_atom3,atomKK->dihedral_atom3,nmax,
memoryKK->grow_kokkos(atomKK->k_dihedral_atom3,atomKK->dihedral_atom3,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_atom3");
memory->grow_kokkos(atomKK->k_dihedral_atom4,atomKK->dihedral_atom4,nmax,
memoryKK->grow_kokkos(atomKK->k_dihedral_atom4,atomKK->dihedral_atom4,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_atom4");
memory->grow_kokkos(atomKK->k_num_improper,atomKK->num_improper,nmax,"atom:num_improper");
memory->grow_kokkos(atomKK->k_improper_type,atomKK->improper_type,nmax,
memoryKK->grow_kokkos(atomKK->k_num_improper,atomKK->num_improper,nmax,"atom:num_improper");
memoryKK->grow_kokkos(atomKK->k_improper_type,atomKK->improper_type,nmax,
atomKK->improper_per_atom,"atom:improper_type");
memory->grow_kokkos(atomKK->k_improper_atom1,atomKK->improper_atom1,nmax,
memoryKK->grow_kokkos(atomKK->k_improper_atom1,atomKK->improper_atom1,nmax,
atomKK->improper_per_atom,"atom:improper_atom1");
memory->grow_kokkos(atomKK->k_improper_atom2,atomKK->improper_atom2,nmax,
memoryKK->grow_kokkos(atomKK->k_improper_atom2,atomKK->improper_atom2,nmax,
atomKK->improper_per_atom,"atom:improper_atom2");
memory->grow_kokkos(atomKK->k_improper_atom3,atomKK->improper_atom3,nmax,
memoryKK->grow_kokkos(atomKK->k_improper_atom3,atomKK->improper_atom3,nmax,
atomKK->improper_per_atom,"atom:improper_atom3");
memory->grow_kokkos(atomKK->k_improper_atom4,atomKK->improper_atom4,nmax,
memoryKK->grow_kokkos(atomKK->k_improper_atom4,atomKK->improper_atom4,nmax,
atomKK->improper_per_atom,"atom:improper_atom4");
grow_reset();

2
src/KOKKOS/atom_vec_hybrid_kokkos.cpp
View File

@ -18,7 +18,7 @@
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"

62
src/KOKKOS/atom_vec_molecular_kokkos.cpp
View File

@ -19,7 +19,7 @@
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -67,57 +67,57 @@ void AtomVecMolecularKokkos::grow(int n)
sync(Device,ALL_MASK);
modified(Device,ALL_MASK);
memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
memoryKK->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memoryKK->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memoryKK->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
"atom:special");
memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
memoryKK->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memoryKK->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
"atom:bond_type");
memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
memoryKK->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
"atom:bond_atom");
memory->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
memory->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
memoryKK->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
"atom:angle_type");
memory->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
"atom:angle_atom1");
memory->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
"atom:angle_atom2");
memory->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
memoryKK->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
"atom:angle_atom3");
memory->grow_kokkos(atomKK->k_num_dihedral,atomKK->num_dihedral,nmax,"atom:num_dihedral");
memory->grow_kokkos(atomKK->k_dihedral_type,atomKK->dihedral_type,nmax,
memoryKK->grow_kokkos(atomKK->k_num_dihedral,atomKK->num_dihedral,nmax,"atom:num_dihedral");
memoryKK->grow_kokkos(atomKK->k_dihedral_type,atomKK->dihedral_type,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_type");
memory->grow_kokkos(atomKK->k_dihedral_atom1,atomKK->dihedral_atom1,nmax,
memoryKK->grow_kokkos(atomKK->k_dihedral_atom1,atomKK->dihedral_atom1,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_atom1");
memory->grow_kokkos(atomKK->k_dihedral_atom2,atomKK->dihedral_atom2,nmax,
memoryKK->grow_kokkos(atomKK->k_dihedral_atom2,atomKK->dihedral_atom2,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_atom2");
memory->grow_kokkos(atomKK->k_dihedral_atom3,atomKK->dihedral_atom3,nmax,
memoryKK->grow_kokkos(atomKK->k_dihedral_atom3,atomKK->dihedral_atom3,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_atom3");
memory->grow_kokkos(atomKK->k_dihedral_atom4,atomKK->dihedral_atom4,nmax,
memoryKK->grow_kokkos(atomKK->k_dihedral_atom4,atomKK->dihedral_atom4,nmax,
atomKK->dihedral_per_atom,"atom:dihedral_atom4");
memory->grow_kokkos(atomKK->k_num_improper,atomKK->num_improper,nmax,"atom:num_improper");
memory->grow_kokkos(atomKK->k_improper_type,atomKK->improper_type,nmax,
memoryKK->grow_kokkos(atomKK->k_num_improper,atomKK->num_improper,nmax,"atom:num_improper");
memoryKK->grow_kokkos(atomKK->k_improper_type,atomKK->improper_type,nmax,
atomKK->improper_per_atom,"atom:improper_type");
memory->grow_kokkos(atomKK->k_improper_atom1,atomKK->improper_atom1,nmax,
memoryKK->grow_kokkos(atomKK->k_improper_atom1,atomKK->improper_atom1,nmax,
atomKK->improper_per_atom,"atom:improper_atom1");
memory->grow_kokkos(atomKK->k_improper_atom2,atomKK->improper_atom2,nmax,
memoryKK->grow_kokkos(atomKK->k_improper_atom2,atomKK->improper_atom2,nmax,
atomKK->improper_per_atom,"atom:improper_atom2");
memory->grow_kokkos(atomKK->k_improper_atom3,atomKK->improper_atom3,nmax,
memoryKK->grow_kokkos(atomKK->k_improper_atom3,atomKK->improper_atom3,nmax,
atomKK->improper_per_atom,"atom:improper_atom3");
memory->grow_kokkos(atomKK->k_improper_atom4,atomKK->improper_atom4,nmax,
memoryKK->grow_kokkos(atomKK->k_improper_atom4,atomKK->improper_atom4,nmax,
atomKK->improper_per_atom,"atom:improper_atom4");
grow_reset();

14
src/KOKKOS/bond_class2_kokkos.cpp
View File

@ -23,7 +23,7 @@
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -47,8 +47,8 @@ template<class DeviceType>
BondClass2Kokkos<DeviceType>::~BondClass2Kokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -67,15 +67,15 @@ void BondClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (eflag_atom) {
//if(k_eatom.dimension_0()<maxeatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.template view<DeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.dimension_0()<maxvatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
d_vatom = k_vatom.template view<DeviceType>();
//}
}

14
src/KOKKOS/bond_fene_kokkos.cpp
View File

@ -23,7 +23,7 @@
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -56,8 +56,8 @@ template<class DeviceType>
BondFENEKokkos<DeviceType>::~BondFENEKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -75,13 +75,13 @@ void BondFENEKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"bond:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"bond:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"bond:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"bond:vatom");
d_vatom = k_vatom.view<DeviceType>();
}

14
src/KOKKOS/bond_harmonic_kokkos.cpp
View File

@ -23,7 +23,7 @@
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -48,8 +48,8 @@ template<class DeviceType>
BondHarmonicKokkos<DeviceType>::~BondHarmonicKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -68,15 +68,15 @@ void BondHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (eflag_atom) {
//if(k_eatom.dimension_0()<maxeatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.template view<DeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.dimension_0()<maxvatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
d_vatom = k_vatom.template view<DeviceType>();
//}
}

20
src/KOKKOS/comm_kokkos.cpp
View File

@ -20,7 +20,7 @@
#include "domain.h"
#include "atom_masks.h"
#include "error.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "force.h"
#include "pair.h"
#include "fix.h"
@ -28,6 +28,7 @@
#include "dump.h"
#include "output.h"
#include "modify.h"
#include "kokkos_base.h"
using namespace LAMMPS_NS;
@ -71,7 +72,7 @@ CommKokkos::CommKokkos(LAMMPS *lmp) : CommBrick(lmp)
for (int i = 0; i < maxswap; i++) {
maxsendlist[i] = BUFMIN;
}
memory->create_kokkos(k_sendlist,sendlist,maxswap,BUFMIN,"comm:sendlist");
memoryKK->create_kokkos(k_sendlist,sendlist,maxswap,BUFMIN,"comm:sendlist");
max_buf_pair = 0;
k_buf_send_pair = DAT::tdual_xfloat_1d("comm:k_buf_send_pair",1);
@ -82,11 +83,11 @@ CommKokkos::CommKokkos(LAMMPS *lmp) : CommBrick(lmp)
CommKokkos::~CommKokkos()
{
memory->destroy_kokkos(k_sendlist,sendlist);
memoryKK->destroy_kokkos(k_sendlist,sendlist);
sendlist = NULL;
memory->destroy_kokkos(k_buf_send,buf_send);
memoryKK->destroy_kokkos(k_buf_send,buf_send);
buf_send = NULL;
memory->destroy_kokkos(k_buf_recv,buf_recv);
memoryKK->destroy_kokkos(k_buf_recv,buf_recv);
buf_recv = NULL;
}
@ -379,6 +380,7 @@ void CommKokkos::forward_comm_pair_device(Pair *pair)
MPI_Request request;
int nsize = pair->comm_forward;
KokkosBase* pairKKBase = dynamic_cast<KokkosBase*>(pair);
for (iswap = 0; iswap < nswap; iswap++) {
int n = MAX(max_buf_pair,nsize*sendnum[iswap]);
@ -391,7 +393,7 @@ void CommKokkos::forward_comm_pair_device(Pair *pair)
// pack buffer
n = pair->pack_forward_comm_kokkos(sendnum[iswap],k_sendlist,
n = pairKKBase->pack_forward_comm_kokkos(sendnum[iswap],k_sendlist,
iswap,k_buf_send_pair,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
@ -408,7 +410,7 @@ void CommKokkos::forward_comm_pair_device(Pair *pair)
// unpack buffer
pair->unpack_forward_comm_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv_pair);
pairKKBase->unpack_forward_comm_kokkos(recvnum[iswap],firstrecv[iswap],k_buf_recv_pair);
}
}
@ -1067,7 +1069,7 @@ void CommKokkos::grow_list(int iswap, int n)
k_sendlist.modify<LMPHostType>();
}
memory->grow_kokkos(k_sendlist,sendlist,maxswap,size,"comm:sendlist");
memoryKK->grow_kokkos(k_sendlist,sendlist,maxswap,size,"comm:sendlist");
for(int i=0;i<maxswap;i++) {
maxsendlist[i]=size; sendlist[i]=&k_sendlist.view<LMPHostType>()(i,0);
@ -1095,7 +1097,7 @@ void CommKokkos::grow_swap(int n)
k_sendlist.modify<LMPHostType>();
}
memory->grow_kokkos(k_sendlist,sendlist,maxswap,size,"comm:sendlist");
memoryKK->grow_kokkos(k_sendlist,sendlist,maxswap,size,"comm:sendlist");
memory->grow(maxsendlist,n,"comm:maxsendlist");
for (int i=0;i<maxswap;i++) maxsendlist[i]=size;

2
src/KOKKOS/comm_tiled_kokkos.cpp
View File

@ -25,7 +25,7 @@
#include "compute.h"
#include "output.h"
#include "dump.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"

14
src/KOKKOS/dihedral_charmm_kokkos.cpp
View File

@ -25,7 +25,7 @@
#include "force.h"
#include "pair.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -56,8 +56,8 @@ template<class DeviceType>
DihedralCharmmKokkos<DeviceType>::~DihedralCharmmKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -81,8 +81,8 @@ void DihedralCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (eflag_atom) {
//if(k_eatom.dimension_0()<maxeatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
d_eatom = k_eatom.template view<DeviceType>();
k_eatom_pair = Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType>("dihedral:eatom_pair",maxeatom);
d_eatom_pair = k_eatom.template view<DeviceType>();
@ -90,8 +90,8 @@ void DihedralCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
if (vflag_atom) {
//if(k_vatom.dimension_0()<maxvatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom");
d_vatom = k_vatom.template view<DeviceType>();
k_vatom_pair = Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType>("dihedral:vatom_pair",maxvatom);
d_vatom_pair = k_vatom.template view<DeviceType>();

14
src/KOKKOS/dihedral_class2_kokkos.cpp
View File

@ -24,7 +24,7 @@
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -56,8 +56,8 @@ template<class DeviceType>
DihedralClass2Kokkos<DeviceType>::~DihedralClass2Kokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -75,13 +75,13 @@ void DihedralClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
d_eatom = k_eatom.template view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}

14
src/KOKKOS/dihedral_opls_kokkos.cpp
View File

@ -24,7 +24,7 @@
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -56,8 +56,8 @@ template<class DeviceType>
DihedralOPLSKokkos<DeviceType>::~DihedralOPLSKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -75,13 +75,13 @@ void DihedralOPLSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom");
d_vatom = k_vatom.view<DeviceType>();
}

14
src/KOKKOS/fix_eos_table_rx_kokkos.cpp
View File

@ -21,7 +21,7 @@
#include "atom_kokkos.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "comm.h"
#include <math.h>
#include "modify.h"
@ -517,14 +517,14 @@ void FixEOStableRXKokkos<DeviceType>::create_kokkos_tables()
{
const int tlm1 = tablength-1;
memory->create_kokkos(d_table->lo,h_table->lo,ntables,"Table::lo");
memory->create_kokkos(d_table->hi,h_table->hi,ntables,"Table::hi");
memory->create_kokkos(d_table->invdelta,h_table->invdelta,ntables,"Table::invdelta");
memoryKK->create_kokkos(d_table->lo,h_table->lo,ntables,"Table::lo");
memoryKK->create_kokkos(d_table->hi,h_table->hi,ntables,"Table::hi");
memoryKK->create_kokkos(d_table->invdelta,h_table->invdelta,ntables,"Table::invdelta");
if(tabstyle == LINEAR) {
memory->create_kokkos(d_table->r,h_table->r,ntables,tablength,"Table::r");
memory->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
memory->create_kokkos(d_table->de,h_table->de,ntables,tlm1,"Table::de");
memoryKK->create_kokkos(d_table->r,h_table->r,ntables,tablength,"Table::r");
memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
memoryKK->create_kokkos(d_table->de,h_table->de,ntables,tlm1,"Table::de");
}
for(int i=0; i < ntables; i++) {

30
src/KOKKOS/fix_langevin_kokkos.cpp
View File

@ -21,7 +21,7 @@
#include "update.h"
#include "respa.h"
#include "error.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "group.h"
#include "random_mars.h"
#include "compute.h"
@ -49,9 +49,9 @@ FixLangevinKokkos<DeviceType>::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a
int ntypes = atomKK->ntypes;
// allocate per-type arrays for force prefactors
memory->create_kokkos(k_gfactor1,gfactor1,ntypes+1,"langevin:gfactor1");
memory->create_kokkos(k_gfactor2,gfactor2,ntypes+1,"langevin:gfactor2");
memory->create_kokkos(k_ratio,ratio,ntypes+1,"langevin:ratio");
memoryKK->create_kokkos(k_gfactor1,gfactor1,ntypes+1,"langevin:gfactor1");
memoryKK->create_kokkos(k_gfactor2,gfactor2,ntypes+1,"langevin:gfactor2");
memoryKK->create_kokkos(k_ratio,ratio,ntypes+1,"langevin:ratio");
d_gfactor1 = k_gfactor1.template view<DeviceType>();
h_gfactor1 = k_gfactor1.template view<LMPHostType>();
d_gfactor2 = k_gfactor2.template view<DeviceType>();
@ -92,12 +92,12 @@ FixLangevinKokkos<DeviceType>::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a
template<class DeviceType>
FixLangevinKokkos<DeviceType>::~FixLangevinKokkos()
{
memory->destroy_kokkos(k_gfactor1,gfactor1);
memory->destroy_kokkos(k_gfactor2,gfactor2);
memory->destroy_kokkos(k_ratio,ratio);
memory->destroy_kokkos(k_flangevin,flangevin);
if(gjfflag) memory->destroy_kokkos(k_franprev,franprev);
memory->destroy_kokkos(k_tforce,tforce);
memoryKK->destroy_kokkos(k_gfactor1,gfactor1);
memoryKK->destroy_kokkos(k_gfactor2,gfactor2);
memoryKK->destroy_kokkos(k_ratio,ratio);
memoryKK->destroy_kokkos(k_flangevin,flangevin);
if(gjfflag) memoryKK->destroy_kokkos(k_franprev,franprev);
memoryKK->destroy_kokkos(k_tforce,tforce);
}
/* ---------------------------------------------------------------------- */
@ -121,7 +121,7 @@ void FixLangevinKokkos<DeviceType>::init()
template<class DeviceType>
void FixLangevinKokkos<DeviceType>::grow_arrays(int nmax)
{
memory->grow_kokkos(k_franprev,franprev,nmax,3,"langevin:franprev");
memoryKK->grow_kokkos(k_franprev,franprev,nmax,3,"langevin:franprev");
d_franprev = k_franprev.template view<DeviceType>();
h_franprev = k_franprev.template view<LMPHostType>();
}
@ -167,9 +167,9 @@ void FixLangevinKokkos<DeviceType>::post_force(int vflag)
// reallocate flangevin if necessary
if (tallyflag) {
if (nlocal > maxatom1) {
memory->destroy_kokkos(k_flangevin,flangevin);
memoryKK->destroy_kokkos(k_flangevin,flangevin);
maxatom1 = atomKK->nmax;
memory->create_kokkos(k_flangevin,flangevin,maxatom1,3,"langevin:flangevin");
memoryKK->create_kokkos(k_flangevin,flangevin,maxatom1,3,"langevin:flangevin");
d_flangevin = k_flangevin.template view<DeviceType>();
h_flangevin = k_flangevin.template view<LMPHostType>();
}
@ -671,8 +671,8 @@ void FixLangevinKokkos<DeviceType>::compute_target()
} else {
if (atom->nmax > maxatom2) {
maxatom2 = atom->nmax;
memory->destroy_kokkos(k_tforce,tforce);
memory->create_kokkos(k_tforce,tforce,maxatom2,"langevin:tforce");
memoryKK->destroy_kokkos(k_tforce,tforce);
memoryKK->create_kokkos(k_tforce,tforce,maxatom2,"langevin:tforce");
d_tforce = k_tforce.template view<DeviceType>();
h_tforce = k_tforce.template view<LMPHostType>();
}

2
src/KOKKOS/fix_nh_kokkos.cpp
View File

@ -33,7 +33,7 @@
#include "update.h"
#include "respa.h"
#include "domain_kokkos.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "atom_kokkos.h"

4
src/KOKKOS/fix_property_atom_kokkos.cpp
View File

@ -16,7 +16,7 @@
#include "fix_property_atom_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "update.h"
@ -60,7 +60,7 @@ void FixPropertyAtomKokkos::grow_arrays(int nmax)
size_t nbytes = (nmax-nmax_old) * sizeof(int);
memset(&atom->ivector[index[m]][nmax_old],0,nbytes);
} else if (style[m] == DOUBLE) {
memory->grow_kokkos(atomKK->k_dvector,atomKK->dvector,atomKK->k_dvector.dimension_0(),nmax,
memoryKK->grow_kokkos(atomKK->k_dvector,atomKK->dvector,atomKK->k_dvector.dimension_0(),nmax,
"atom:dvector");
//memory->grow(atom->dvector[index[m]],nmax,"atom:dvector");
//size_t nbytes = (nmax-nmax_old) * sizeof(double);

2
src/KOKKOS/fix_qeq_reax_kokkos.cpp
View File

@ -35,7 +35,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "pair_reaxc_kokkos.h"

6
src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "reaxc_list.h"
#include "reaxc_types.h"
@ -95,7 +95,7 @@ void FixReaxCBondsKokkos::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
MPI_Allreduce(&nlocal,&nlocal_max,1,MPI_INT,MPI_MAX,world);
nbuf = 1+(numbonds_max*2+10)*nlocal_max;
memory->create_kokkos(k_buf,buf,nbuf,"reax/c/bonds:buf");
memoryKK->create_kokkos(k_buf,buf,nbuf,"reax/c/bonds:buf");
// Pass information to buffer
if (reaxc->execution_space == Device)
@ -107,7 +107,7 @@ void FixReaxCBondsKokkos::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
// Receive information from buffer for output
RecvBuffer(buf, nbuf, nbuf_local, nlocal_tot, numbonds_max);
memory->destroy_kokkos(k_buf,buf);
memoryKK->destroy_kokkos(k_buf,buf);
}
/* ---------------------------------------------------------------------- */

2
src/KOKKOS/fix_reaxc_species_kokkos.cpp
View File

@ -33,7 +33,7 @@
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "reaxc_list.h"
#include "atom_masks.h"

63
src/KOKKOS/fix_rx_kokkos.cpp
View File

@ -17,7 +17,7 @@
#include "atom_masks.h"
#include "atom_kokkos.h"
#include "force.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
@ -26,6 +26,9 @@
#include "neigh_request.h"
#include "error.h"
#include "math_special_kokkos.h"
#include "comm.h"
#include "domain.h"
#include "kokkos.h"
#include <float.h> // DBL_EPSILON
@ -81,15 +84,15 @@ FixRxKokkos<DeviceType>::~FixRxKokkos()
if (copymode) return;
if (localTempFlag)
memory->destroy_kokkos(k_dpdThetaLocal, dpdThetaLocal);
memoryKK->destroy_kokkos(k_dpdThetaLocal, dpdThetaLocal);
memory->destroy_kokkos(k_sumWeights, sumWeights);
//memory->destroy_kokkos(k_sumWeights);
memoryKK->destroy_kokkos(k_sumWeights, sumWeights);
//memoryKK->destroy_kokkos(k_sumWeights);
//delete [] scratchSpace;
memory->destroy_kokkos(d_scratchSpace);
memoryKK->destroy_kokkos(d_scratchSpace);
memory->destroy_kokkos(k_cutsq);
memoryKK->destroy_kokkos(k_cutsq);
}
/* ---------------------------------------------------------------------- */
@ -1233,9 +1236,9 @@ void FixRxKokkos<DeviceType>::create_kinetics_data(void)
{
//printf("Inside FixRxKokkos::create_kinetics_data\n");
memory->create_kokkos( d_kineticsData.Arr, h_kineticsData.Arr, nreactions, "KineticsType::Arr");
memory->create_kokkos( d_kineticsData.nArr, h_kineticsData.nArr, nreactions, "KineticsType::nArr");
memory->create_kokkos( d_kineticsData.Ea, h_kineticsData.Ea, nreactions, "KineticsType::Ea");
memoryKK->create_kokkos( d_kineticsData.Arr, h_kineticsData.Arr, nreactions, "KineticsType::Arr");
memoryKK->create_kokkos( d_kineticsData.nArr, h_kineticsData.nArr, nreactions, "KineticsType::nArr");
memoryKK->create_kokkos( d_kineticsData.Ea, h_kineticsData.Ea, nreactions, "KineticsType::Ea");
for (int i = 0; i < nreactions; ++i)
{
@ -1251,8 +1254,8 @@ void FixRxKokkos<DeviceType>::create_kinetics_data(void)
if (useSparseKinetics)
{
memory->create_kokkos( d_kineticsData.nu , h_kineticsData.nu , nreactions, sparseKinetics_maxSpecies, "KineticsType::nu");
memory->create_kokkos( d_kineticsData.nuk, h_kineticsData.nuk, nreactions, sparseKinetics_maxSpecies, "KineticsType::nuk");
memoryKK->create_kokkos( d_kineticsData.nu , h_kineticsData.nu , nreactions, sparseKinetics_maxSpecies, "KineticsType::nu");
memoryKK->create_kokkos( d_kineticsData.nuk, h_kineticsData.nuk, nreactions, sparseKinetics_maxSpecies, "KineticsType::nuk");
for (int i = 0; i < nreactions; ++i)
for (int k = 0; k < sparseKinetics_maxSpecies; ++k)
@ -1266,8 +1269,8 @@ void FixRxKokkos<DeviceType>::create_kinetics_data(void)
if (SparseKinetics_enableIntegralReactions)
{
memory->create_kokkos( d_kineticsData.inu, h_kineticsData.inu, nreactions, sparseKinetics_maxSpecies, "KineticsType::inu");
memory->create_kokkos( d_kineticsData.isIntegral, h_kineticsData.isIntegral, nreactions, "KineticsType::isIntegral");
memoryKK->create_kokkos( d_kineticsData.inu, h_kineticsData.inu, nreactions, sparseKinetics_maxSpecies, "KineticsType::inu");
memoryKK->create_kokkos( d_kineticsData.isIntegral, h_kineticsData.isIntegral, nreactions, "KineticsType::isIntegral");
for (int i = 0; i < nreactions; ++i)
{
@ -1286,9 +1289,9 @@ void FixRxKokkos<DeviceType>::create_kinetics_data(void)
//{
// Dense option
memory->create_kokkos( d_kineticsData.stoich, h_kineticsData.stoich, nreactions, nspecies, "KineticsType::stoich");
memory->create_kokkos( d_kineticsData.stoichReactants, h_kineticsData.stoichReactants, nreactions, nspecies, "KineticsType::stoichReactants");
memory->create_kokkos( d_kineticsData.stoichProducts, h_kineticsData.stoichProducts, nreactions, nspecies, "KineticsType::stoichProducts");
memoryKK->create_kokkos( d_kineticsData.stoich, h_kineticsData.stoich, nreactions, nspecies, "KineticsType::stoich");
memoryKK->create_kokkos( d_kineticsData.stoichReactants, h_kineticsData.stoichReactants, nreactions, nspecies, "KineticsType::stoichReactants");
memoryKK->create_kokkos( d_kineticsData.stoichProducts, h_kineticsData.stoichProducts, nreactions, nspecies, "KineticsType::stoichProducts");
for (int i = 0; i < nreactions; ++i)
for (int k = 0; k < nspecies; ++k)
@ -1445,8 +1448,8 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int vflag, const bool isPreF
const int count = nlocal + (newton_pair ? nghost : 0);
if (count > k_dpdThetaLocal.template view<DeviceType>().dimension_0()) {
memory->destroy_kokkos (k_dpdThetaLocal, dpdThetaLocal);
memory->create_kokkos (k_dpdThetaLocal, dpdThetaLocal, count, "FixRxKokkos::dpdThetaLocal");
memoryKK->destroy_kokkos (k_dpdThetaLocal, dpdThetaLocal);
memoryKK->create_kokkos (k_dpdThetaLocal, dpdThetaLocal, count, "FixRxKokkos::dpdThetaLocal");
this->d_dpdThetaLocal = k_dpdThetaLocal.template view<DeviceType>();
this->h_dpdThetaLocal = k_dpdThetaLocal.h_view;
}
@ -1511,8 +1514,8 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int vflag, const bool isPreF
if (odeIntegrationFlag == ODE_LAMMPS_RKF45 && diagnosticFrequency == 1)
{
memory->create_kokkos (k_diagnosticCounterPerODEnSteps, diagnosticCounterPerODEnSteps, nlocal, "FixRxKokkos::diagnosticCounterPerODEnSteps");
memory->create_kokkos (k_diagnosticCounterPerODEnFuncs, diagnosticCounterPerODEnFuncs, nlocal, "FixRxKokkos::diagnosticCounterPerODEnFuncs");
memoryKK->create_kokkos (k_diagnosticCounterPerODEnSteps, diagnosticCounterPerODEnSteps, nlocal, "FixRxKokkos::diagnosticCounterPerODEnSteps");
memoryKK->create_kokkos (k_diagnosticCounterPerODEnFuncs, diagnosticCounterPerODEnFuncs, nlocal, "FixRxKokkos::diagnosticCounterPerODEnFuncs");
d_diagnosticCounterPerODEnSteps = k_diagnosticCounterPerODEnSteps.template view<DeviceType>();
d_diagnosticCounterPerODEnFuncs = k_diagnosticCounterPerODEnFuncs.template view<DeviceType>();
@ -1542,8 +1545,8 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int vflag, const bool isPreF
//typename ArrayTypes<DeviceType>::t_double_1d d_scratchSpace("d_scratchSpace", scratchSpaceSize * nlocal);
if (nlocal*scratchSpaceSize > d_scratchSpace.dimension_0()) {
memory->destroy_kokkos (d_scratchSpace);
memory->create_kokkos (d_scratchSpace, nlocal*scratchSpaceSize, "FixRxKokkos::d_scratchSpace");
memoryKK->destroy_kokkos (d_scratchSpace);
memoryKK->create_kokkos (d_scratchSpace, nlocal*scratchSpaceSize, "FixRxKokkos::d_scratchSpace");
}
#if 0
@ -1811,8 +1814,8 @@ void FixRxKokkos<DeviceType>::odeDiagnostics(void)
my_min[FuncSum] = std::min( my_min[FuncSum], (double)nFuncs );
}
memory->destroy_kokkos( k_diagnosticCounterPerODEnSteps, diagnosticCounterPerODEnSteps );
memory->destroy_kokkos( k_diagnosticCounterPerODEnFuncs, diagnosticCounterPerODEnFuncs );
memoryKK->destroy_kokkos( k_diagnosticCounterPerODEnSteps, diagnosticCounterPerODEnSteps );
memoryKK->destroy_kokkos( k_diagnosticCounterPerODEnFuncs, diagnosticCounterPerODEnFuncs );
MPI_Reduce (my_sum_sq, sum_sq, 2*numCounters, MPI_DOUBLE, MPI_SUM, 0, world);
@ -2022,10 +2025,10 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
{
const int ntypes = atom->ntypes;
//memory->create_kokkos (k_cutsq, h_cutsq, ntypes+1, ntypes+1, "pair:cutsq");
//memoryKK->create_kokkos (k_cutsq, h_cutsq, ntypes+1, ntypes+1, "pair:cutsq");
if (ntypes+1 > k_cutsq.dimension_0()) {
memory->destroy_kokkos (k_cutsq);
memory->create_kokkos (k_cutsq, ntypes+1, ntypes+1, "FixRxKokkos::k_cutsq");
memoryKK->destroy_kokkos (k_cutsq);
memoryKK->create_kokkos (k_cutsq, ntypes+1, ntypes+1, "FixRxKokkos::k_cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
}
@ -2043,10 +2046,10 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
// Initialize the local temperature weight array
int sumWeightsCt = nlocal + (NEWTON_PAIR ? nghost : 0);
//memory->create_kokkos (k_sumWeights, sumWeights, sumWeightsCt, "FixRxKokkos::sumWeights");
//memoryKK->create_kokkos (k_sumWeights, sumWeights, sumWeightsCt, "FixRxKokkos::sumWeights");
if (sumWeightsCt > k_sumWeights.template view<DeviceType>().dimension_0()) {
memory->destroy_kokkos(k_sumWeights, sumWeights);
memory->create_kokkos (k_sumWeights, sumWeightsCt, "FixRxKokkos::sumWeights");
memoryKK->destroy_kokkos(k_sumWeights, sumWeights);
memoryKK->create_kokkos (k_sumWeights, sumWeightsCt, "FixRxKokkos::sumWeights");
d_sumWeights = k_sumWeights.template view<DeviceType>();
h_sumWeights = k_sumWeights.h_view;
}

14
src/KOKKOS/fix_setforce_kokkos.cpp
View File

@ -22,10 +22,11 @@
#include "respa.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "force.h"
#include "atom_masks.h"
#include "kokkos_base.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -45,7 +46,7 @@ FixSetForceKokkos<DeviceType>::FixSetForceKokkos(LAMMPS *lmp, int narg, char **a
datamask_modify = EMPTY_MASK;
memory->destroy(sforce);
memory->create_kokkos(k_sforce,sforce,maxatom,3,"setforce:sforce");
memoryKK->create_kokkos(k_sforce,sforce,maxatom,3,"setforce:sforce");
}
/* ---------------------------------------------------------------------- */
@ -55,7 +56,7 @@ FixSetForceKokkos<DeviceType>::~FixSetForceKokkos()
{
if (copymode) return;
memory->destroy_kokkos(k_sforce,sforce);
memoryKK->destroy_kokkos(k_sforce,sforce);
sforce = NULL;
}
@ -90,7 +91,8 @@ void FixSetForceKokkos<DeviceType>::post_force(int vflag)
region = domain->regions[iregion];
region->prematch();
DAT::tdual_int_1d k_match = DAT::tdual_int_1d("setforce:k_match",nlocal);
region->match_all_kokkos(groupbit,k_match);
KokkosBase* regionKKBase = dynamic_cast<KokkosBase*>(region);
regionKKBase->match_all_kokkos(groupbit,k_match);
k_match.template sync<DeviceType>();
d_match = k_match.template view<DeviceType>();
}
@ -99,8 +101,8 @@ void FixSetForceKokkos<DeviceType>::post_force(int vflag)
if (varflag == ATOM && atom->nmax > maxatom) {
maxatom = atom->nmax;
memory->destroy_kokkos(k_sforce,sforce);
memory->create_kokkos(k_sforce,sforce,maxatom,3,"setforce:sforce");
memoryKK->destroy_kokkos(k_sforce,sforce);
memoryKK->create_kokkos(k_sforce,sforce,maxatom,3,"setforce:sforce");
}
foriginal[0] = foriginal[1] = foriginal[2] = 0.0;

2
src/KOKKOS/fix_shardlow_kokkos.cpp
View File

@ -50,7 +50,7 @@
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "neigh_request.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "domain.h"
#include "modify.h"
// #include "pair_dpd_fdt.h"

23
src/KOKKOS/gridcomm_kokkos.cpp
View File

@ -15,8 +15,9 @@
#include "gridcomm_kokkos.h"
#include "comm.h"
#include "kspace.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "kokkos_base.h"
using namespace LAMMPS_NS;
@ -126,8 +127,8 @@ template<class DeviceType>
GridCommKokkos<DeviceType>::~GridCommKokkos()
{
for (int i = 0; i < nswap; i++) {
//memory->destroy_kokkos(swap[i].k_packlist,swap[i].packlist);
//memory->destroy_kokkos(swap[i].k_unpacklist,swap[i].unpacklist);
//memoryKK->destroy_kokkos(swap[i].k_packlist,swap[i].packlist);
//memoryKK->destroy_kokkos(swap[i].k_unpacklist,swap[i].unpacklist);
}
memory->sfree(swap);
@ -515,11 +516,13 @@ void GridCommKokkos<DeviceType>::forward_comm(KSpace *kspace, int which)
k_packlist.sync<DeviceType>();
k_unpacklist.sync<DeviceType>();
KokkosBase* kspaceKKBase = dynamic_cast<KokkosBase*>(kspace);
for (int m = 0; m < nswap; m++) {
if (swap[m].sendproc == me)
kspace->pack_forward_kokkos(which,k_buf2,swap[m].npack,k_packlist,m);
kspaceKKBase->pack_forward_kspace_kokkos(which,k_buf2,swap[m].npack,k_packlist,m);
else
kspace->pack_forward_kokkos(which,k_buf1,swap[m].npack,k_packlist,m);
kspaceKKBase->pack_forward_kspace_kokkos(which,k_buf1,swap[m].npack,k_packlist,m);
if (swap[m].sendproc != me) {
MPI_Irecv(k_buf2.view<DeviceType>().ptr_on_device(),nforward*swap[m].nunpack,MPI_FFT_SCALAR,
@ -529,7 +532,7 @@ void GridCommKokkos<DeviceType>::forward_comm(KSpace *kspace, int which)
MPI_Wait(&request,MPI_STATUS_IGNORE);
}
kspace->unpack_forward_kokkos(which,k_buf2,swap[m].nunpack,k_unpacklist,m);
kspaceKKBase->unpack_forward_kspace_kokkos(which,k_buf2,swap[m].nunpack,k_unpacklist,m);
}
}
@ -544,11 +547,13 @@ void GridCommKokkos<DeviceType>::reverse_comm(KSpace *kspace, int which)
k_packlist.sync<DeviceType>();
k_unpacklist.sync<DeviceType>();
KokkosBase* kspaceKKBase = dynamic_cast<KokkosBase*>(kspace);
for (int m = nswap-1; m >= 0; m--) {
if (swap[m].recvproc == me)
kspace->pack_reverse_kokkos(which,k_buf2,swap[m].nunpack,k_unpacklist,m);
kspaceKKBase->pack_reverse_kspace_kokkos(which,k_buf2,swap[m].nunpack,k_unpacklist,m);
else
kspace->pack_reverse_kokkos(which,k_buf1,swap[m].nunpack,k_unpacklist,m);
kspaceKKBase->pack_reverse_kspace_kokkos(which,k_buf1,swap[m].nunpack,k_unpacklist,m);
if (swap[m].recvproc != me) {
MPI_Irecv(k_buf2.view<DeviceType>().ptr_on_device(),nreverse*swap[m].npack,MPI_FFT_SCALAR,
@ -558,7 +563,7 @@ void GridCommKokkos<DeviceType>::reverse_comm(KSpace *kspace, int which)
MPI_Wait(&request,MPI_STATUS_IGNORE);
}
kspace->unpack_reverse_kokkos(which,k_buf2,swap[m].npack,k_packlist,m);
kspaceKKBase->unpack_reverse_kspace_kokkos(which,k_buf2,swap[m].npack,k_packlist,m);
}
}

14
src/KOKKOS/improper_class2_kokkos.cpp
View File

@ -26,7 +26,7 @@
#include "force.h"
#include "update.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -58,8 +58,8 @@ template<class DeviceType>
ImproperClass2Kokkos<DeviceType>::~ImproperClass2Kokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -78,15 +78,15 @@ void ImproperClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (eflag_atom) {
//if(k_eatom.dimension_0()<maxeatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.template view<DeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.dimension_0()<maxvatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
d_vatom = k_vatom.template view<DeviceType>();
//}
}

14
src/KOKKOS/improper_harmonic_kokkos.cpp
View File

@ -26,7 +26,7 @@
#include "force.h"
#include "update.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -58,8 +58,8 @@ template<class DeviceType>
ImproperHarmonicKokkos<DeviceType>::~ImproperHarmonicKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -78,15 +78,15 @@ void ImproperHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (eflag_atom) {
//if(k_eatom.dimension_0()<maxeatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.template view<DeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.dimension_0()<maxvatom) { // won't work without adding zero functor
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"improper:vatom");
d_vatom = k_vatom.template view<DeviceType>();
//}
}

5
src/KOKKOS/kokkos.cpp
View File

@ -23,6 +23,7 @@
#include "neighbor_kokkos.h"
#include "neigh_list_kokkos.h"
#include "error.h"
#include "memory_kokkos.h"
using namespace LAMMPS_NS;
@ -33,6 +34,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
kokkos_exists = 1;
lmp->kokkos = this;
delete memory;
memory = new MemoryKokkos(lmp);
memoryKK = (MemoryKokkos*) memory;
auto_sync = 1;
int me = 0;

47
src/KOKKOS/kokkos_base.h Normal file
View File

@ -0,0 +1,47 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://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.
------------------------------------------------------------------------- */
#ifndef KOKKOS_BASE_H
#define KOKKOS_BASE_H
#include "kokkos_type.h"
namespace LAMMPS_NS {
class KokkosBase {
public:
KokkosBase() {}
//Kspace
virtual void pack_forward_kspace_kokkos(int, DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {};
virtual void unpack_forward_kspace_kokkos(int, DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {};
virtual void pack_reverse_kspace_kokkos(int, DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {};
virtual void unpack_reverse_kspace_kokkos(int, DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {};
// Pair
virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d,
int, DAT::tdual_xfloat_1d &,
int, int *) {return 0;};
virtual void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d &) {}
// Region
virtual void match_all_kokkos(int, DAT::tdual_int_1d) {}
};
}
#endif
/* ERROR/WARNING messages:
*/

19
src/KOKKOS/memory_kokkos.h
View File

@ -11,6 +11,18 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_MEMORY_KOKKOS_H
#define LMP_MEMORY_KOKKOS_H
#include "memory.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
class MemoryKokkos : public Memory {
public:
MemoryKokkos(class LAMMPS *lmp) : Memory(lmp) {}
/* ----------------------------------------------------------------------
Kokkos versions of create/grow/destroy multi-dimensional arrays
------------------------------------------------------------------------- */
@ -279,3 +291,10 @@ void destroy_kokkos(TYPE data, typename TYPE::value_type** &array)
sfree(array);
array = NULL;
}
};
}
#endif

2
src/KOKKOS/nbin_ssa_kokkos.cpp
View File

@ -26,7 +26,7 @@
#include "error.h"
#include "atom_masks.h"
// #include "memory.h"
// #include "memory_kokkos.h"
using namespace LAMMPS_NS;

26
src/KOKKOS/neigh_bond_kokkos.cpp
View File

@ -24,7 +24,7 @@
#include "domain_kokkos.h"
#include "output.h"
#include "thermo.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "modify.h"
#include "fix.h"
@ -80,27 +80,27 @@ void NeighBondKokkos<DeviceType>::init_topology_kk() {
if (atom->molecular && atom->nbonds && maxbond == 0) {
if (nprocs == 1) maxbond = atom->nbonds;
else maxbond = static_cast<int> (LB_FACTOR * atom->nbonds / nprocs);
memory->create_kokkos(k_bondlist,neighbor->bondlist,maxbond,3,"neigh:neighbor->bondlist");
memoryKK->create_kokkos(k_bondlist,neighbor->bondlist,maxbond,3,"neigh:neighbor->bondlist");
}
if (atom->molecular && atom->nangles && maxangle == 0) {
if (nprocs == 1) maxangle = atom->nangles;
else maxangle = static_cast<int> (LB_FACTOR * atom->nangles / nprocs);
memory->create_kokkos(k_anglelist,neighbor->anglelist,maxangle,4,"neigh:neighbor->anglelist");
memoryKK->create_kokkos(k_anglelist,neighbor->anglelist,maxangle,4,"neigh:neighbor->anglelist");
}
if (atom->molecular && atom->ndihedrals && maxdihedral == 0) {
if (nprocs == 1) maxdihedral = atom->ndihedrals;
else maxdihedral = static_cast<int>
(LB_FACTOR * atom->ndihedrals / nprocs);
memory->create_kokkos(k_dihedrallist,neighbor->dihedrallist,maxdihedral,5,"neigh:neighbor->dihedrallist");
memoryKK->create_kokkos(k_dihedrallist,neighbor->dihedrallist,maxdihedral,5,"neigh:neighbor->dihedrallist");
}
if (atom->molecular && atom->nimpropers && maximproper == 0) {
if (nprocs == 1) maximproper = atom->nimpropers;
else maximproper = static_cast<int>
(LB_FACTOR * atom->nimpropers / nprocs);
memory->create_kokkos(k_improperlist,neighbor->improperlist,maximproper,5,"neigh:neighbor->improperlist");
memoryKK->create_kokkos(k_improperlist,neighbor->improperlist,maximproper,5,"neigh:neighbor->improperlist");
}
// set flags that determine which topology neighboring routines to use
@ -283,7 +283,7 @@ void NeighBondKokkos<DeviceType>::bond_all()
k_fail_flag.template sync<LMPHostType>();
if (h_fail_flag()) {
maxbond = neighbor->nbondlist + BONDDELTA;
memory->grow_kokkos(k_bondlist,neighbor->bondlist,maxbond,3,"neighbor:neighbor->bondlist");
memoryKK->grow_kokkos(k_bondlist,neighbor->bondlist,maxbond,3,"neighbor:neighbor->bondlist");
v_bondlist = k_bondlist.view<DeviceType>();
}
} while (h_fail_flag());
@ -378,7 +378,7 @@ void NeighBondKokkos<DeviceType>::bond_partial()
k_fail_flag.template sync<LMPHostType>();
if (h_fail_flag()) {
maxbond = neighbor->nbondlist + BONDDELTA;
memory->grow_kokkos(k_bondlist,neighbor->bondlist,maxbond,3,"neighbor:neighbor->bondlist");
memoryKK->grow_kokkos(k_bondlist,neighbor->bondlist,maxbond,3,"neighbor:neighbor->bondlist");
v_bondlist = k_bondlist.view<DeviceType>();
}
} while (h_fail_flag());
@ -500,7 +500,7 @@ void NeighBondKokkos<DeviceType>::angle_all()
k_fail_flag.template sync<LMPHostType>();
if (h_fail_flag()) {
maxangle = neighbor->nanglelist + BONDDELTA;
memory->grow_kokkos(k_anglelist,neighbor->anglelist,maxangle,4,"neighbor:neighbor->anglelist");
memoryKK->grow_kokkos(k_anglelist,neighbor->anglelist,maxangle,4,"neighbor:neighbor->anglelist");
v_anglelist = k_anglelist.view<DeviceType>();
}
} while (h_fail_flag());
@ -602,7 +602,7 @@ void NeighBondKokkos<DeviceType>::angle_partial()
k_fail_flag.template sync<LMPHostType>();
if (h_fail_flag()) {
maxangle = neighbor->nanglelist + BONDDELTA;
memory->grow_kokkos(k_anglelist,neighbor->anglelist,maxangle,4,"neighbor:neighbor->anglelist");
memoryKK->grow_kokkos(k_anglelist,neighbor->anglelist,maxangle,4,"neighbor:neighbor->anglelist");
v_anglelist = k_anglelist.view<DeviceType>();
}
} while (h_fail_flag());
@ -744,7 +744,7 @@ void NeighBondKokkos<DeviceType>::dihedral_all()
k_fail_flag.template sync<LMPHostType>();
if (h_fail_flag()) {
maxdihedral = neighbor->ndihedrallist + BONDDELTA;
memory->grow_kokkos(k_dihedrallist,neighbor->dihedrallist,maxdihedral,5,"neighbor:neighbor->dihedrallist");
memoryKK->grow_kokkos(k_dihedrallist,neighbor->dihedrallist,maxdihedral,5,"neighbor:neighbor->dihedrallist");
v_dihedrallist = k_dihedrallist.view<DeviceType>();
}
} while (h_fail_flag());
@ -851,7 +851,7 @@ void NeighBondKokkos<DeviceType>::dihedral_partial()
k_fail_flag.template sync<LMPHostType>();
if (h_fail_flag()) {
maxdihedral = neighbor->ndihedrallist + BONDDELTA;
memory->grow_kokkos(k_dihedrallist,neighbor->dihedrallist,maxdihedral,5,"neighbor:neighbor->dihedrallist");
memoryKK->grow_kokkos(k_dihedrallist,neighbor->dihedrallist,maxdihedral,5,"neighbor:neighbor->dihedrallist");
v_dihedrallist = k_dihedrallist.view<DeviceType>();
}
} while (h_fail_flag());
@ -1015,7 +1015,7 @@ void NeighBondKokkos<DeviceType>::improper_all()
k_fail_flag.template sync<LMPHostType>();
if (h_fail_flag()) {
maximproper = neighbor->nimproperlist + BONDDELTA;
memory->grow_kokkos(k_improperlist,neighbor->improperlist,maximproper,5,"neighbor:neighbor->improperlist");
memoryKK->grow_kokkos(k_improperlist,neighbor->improperlist,maximproper,5,"neighbor:neighbor->improperlist");
v_improperlist = k_improperlist.view<DeviceType>();
}
} while (h_fail_flag());
@ -1122,7 +1122,7 @@ void NeighBondKokkos<DeviceType>::improper_partial()
k_fail_flag.template sync<LMPHostType>();
if (h_fail_flag()) {
maximproper = neighbor->nimproperlist + BONDDELTA;
memory->grow_kokkos(k_improperlist,neighbor->improperlist,maximproper,5,"neighbor:neighbor->improperlist");
memoryKK->grow_kokkos(k_improperlist,neighbor->improperlist,maximproper,5,"neighbor:neighbor->improperlist");
v_improperlist = k_improperlist.view<DeviceType>();
}
} while (h_fail_flag());

2
src/KOKKOS/neigh_list_kokkos.cpp
View File

@ -13,7 +13,7 @@
#include "neigh_list_kokkos.h"
#include "atom.h"
#include "memory.h"
#include "memory_kokkos.h"
using namespace LAMMPS_NS;

58
src/KOKKOS/neighbor_kokkos.cpp
View File

@ -12,11 +12,11 @@
------------------------------------------------------------------------- */
#include "neighbor_kokkos.h"
#include "atom.h"
#include "atom_kokkos.h"
#include "pair.h"
#include "fix.h"
#include "neigh_request.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "update.h"
#include "atom_masks.h"
#include "error.h"
@ -52,24 +52,24 @@ NeighborKokkos::NeighborKokkos(LAMMPS *lmp) : Neighbor(lmp),
NeighborKokkos::~NeighborKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_cutneighsq,cutneighsq);
memoryKK->destroy_kokkos(k_cutneighsq,cutneighsq);
cutneighsq = NULL;
memory->destroy_kokkos(k_ex_type,ex_type);
memory->destroy_kokkos(k_ex1_type,ex1_type);
memory->destroy_kokkos(k_ex2_type,ex2_type);
memory->destroy_kokkos(k_ex1_group,ex1_group);
memory->destroy_kokkos(k_ex2_group,ex2_group);
memory->destroy_kokkos(k_ex_mol_group,ex_mol_group);
memory->destroy_kokkos(k_ex1_bit,ex1_bit);
memory->destroy_kokkos(k_ex2_bit,ex2_bit);
memory->destroy_kokkos(k_ex_mol_bit,ex_mol_bit);
memory->destroy_kokkos(k_ex_mol_intra,ex_mol_intra);
memoryKK->destroy_kokkos(k_ex_type,ex_type);
memoryKK->destroy_kokkos(k_ex1_type,ex1_type);
memoryKK->destroy_kokkos(k_ex2_type,ex2_type);
memoryKK->destroy_kokkos(k_ex1_group,ex1_group);
memoryKK->destroy_kokkos(k_ex2_group,ex2_group);
memoryKK->destroy_kokkos(k_ex_mol_group,ex_mol_group);
memoryKK->destroy_kokkos(k_ex1_bit,ex1_bit);
memoryKK->destroy_kokkos(k_ex2_bit,ex2_bit);
memoryKK->destroy_kokkos(k_ex_mol_bit,ex_mol_bit);
memoryKK->destroy_kokkos(k_ex_mol_intra,ex_mol_intra);
memory->destroy_kokkos(k_bondlist,bondlist);
memory->destroy_kokkos(k_anglelist,anglelist);
memory->destroy_kokkos(k_dihedrallist,dihedrallist);
memory->destroy_kokkos(k_improperlist,improperlist);
memoryKK->destroy_kokkos(k_bondlist,bondlist);
memoryKK->destroy_kokkos(k_anglelist,anglelist);
memoryKK->destroy_kokkos(k_dihedrallist,dihedrallist);
memoryKK->destroy_kokkos(k_improperlist,improperlist);
}
}
@ -90,7 +90,7 @@ void NeighborKokkos::init()
void NeighborKokkos::init_cutneighsq_kokkos(int n)
{
memory->create_kokkos(k_cutneighsq,cutneighsq,n+1,n+1,"neigh:cutneighsq");
memoryKK->create_kokkos(k_cutneighsq,cutneighsq,n+1,n+1,"neigh:cutneighsq");
k_cutneighsq.modify<LMPHostType>();
}
@ -112,7 +112,7 @@ void NeighborKokkos::create_kokkos_list(int i)
void NeighborKokkos::init_ex_type_kokkos(int n)
{
memory->create_kokkos(k_ex_type,ex_type,n+1,n+1,"neigh:ex_type");
memoryKK->create_kokkos(k_ex_type,ex_type,n+1,n+1,"neigh:ex_type");
k_ex_type.modify<LMPHostType>();
}
@ -120,9 +120,9 @@ void NeighborKokkos::init_ex_type_kokkos(int n)
void NeighborKokkos::init_ex_bit_kokkos()
{
memory->create_kokkos(k_ex1_bit, ex1_bit, nex_group, "neigh:ex1_bit");
memoryKK->create_kokkos(k_ex1_bit, ex1_bit, nex_group, "neigh:ex1_bit");
k_ex1_bit.modify<LMPHostType>();
memory->create_kokkos(k_ex2_bit, ex2_bit, nex_group, "neigh:ex2_bit");
memoryKK->create_kokkos(k_ex2_bit, ex2_bit, nex_group, "neigh:ex2_bit");
k_ex2_bit.modify<LMPHostType>();
}
@ -130,7 +130,7 @@ void NeighborKokkos::init_ex_bit_kokkos()
void NeighborKokkos::init_ex_mol_bit_kokkos()
{
memory->create_kokkos(k_ex_mol_bit, ex_mol_bit, nex_mol, "neigh:ex_mol_bit");
memoryKK->create_kokkos(k_ex_mol_bit, ex_mol_bit, nex_mol, "neigh:ex_mol_bit");
k_ex_mol_bit.modify<LMPHostType>();
}
@ -138,7 +138,7 @@ void NeighborKokkos::init_ex_mol_bit_kokkos()
void NeighborKokkos::grow_ex_mol_intra_kokkos()
{
memory->grow_kokkos(k_ex_mol_intra, ex_mol_intra, maxex_mol, "neigh:ex_mol_intra");
memoryKK->grow_kokkos(k_ex_mol_intra, ex_mol_intra, maxex_mol, "neigh:ex_mol_intra");
k_ex_mol_intra.modify<LMPHostType>();
}
@ -335,29 +335,29 @@ void NeighborKokkos::operator()(TagNeighborXhold<DeviceType>, const int &i) cons
/* ---------------------------------------------------------------------- */
void NeighborKokkos::modify_ex_type_grow_kokkos(){
memory->grow_kokkos(k_ex1_type,ex1_type,maxex_type,"neigh:ex1_type");
memoryKK->grow_kokkos(k_ex1_type,ex1_type,maxex_type,"neigh:ex1_type");
k_ex1_type.modify<LMPHostType>();
memory->grow_kokkos(k_ex2_type,ex2_type,maxex_type,"neigh:ex2_type");
memoryKK->grow_kokkos(k_ex2_type,ex2_type,maxex_type,"neigh:ex2_type");
k_ex2_type.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::modify_ex_group_grow_kokkos(){
memory->grow_kokkos(k_ex1_group,ex1_group,maxex_group,"neigh:ex1_group");
memoryKK->grow_kokkos(k_ex1_group,ex1_group,maxex_group,"neigh:ex1_group");
k_ex1_group.modify<LMPHostType>();
memory->grow_kokkos(k_ex2_group,ex2_group,maxex_group,"neigh:ex2_group");
memoryKK->grow_kokkos(k_ex2_group,ex2_group,maxex_group,"neigh:ex2_group");
k_ex2_group.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::modify_mol_group_grow_kokkos(){
memory->grow_kokkos(k_ex_mol_group,ex_mol_group,maxex_mol,"neigh:ex_mol_group");
memoryKK->grow_kokkos(k_ex_mol_group,ex_mol_group,maxex_mol,"neigh:ex_mol_group");
k_ex_mol_group.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::modify_mol_intra_grow_kokkos(){
memory->grow_kokkos(k_ex_mol_intra,ex_mol_intra,maxex_mol,"neigh:ex_mol_intra");
memoryKK->grow_kokkos(k_ex_mol_intra,ex_mol_intra,maxex_mol,"neigh:ex_mol_intra");
k_ex_mol_intra.modify<LMPHostType>();
}

20
src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -65,8 +65,8 @@ PairBuckCoulCutKokkos<DeviceType>::~PairBuckCoulCutKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
k_cut_ljsq = DAT::tdual_ffloat_2d();
k_cut_coulsq = DAT::tdual_ffloat_2d();
@ -98,13 +98,13 @@ void PairBuckCoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -252,13 +252,13 @@ void PairBuckCoulCutKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->destroy(cut_coulsq);
memory->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_buck_coul**,Kokkos::LayoutRight,DeviceType>("PairBuckCoulCut::params",n+1,n+1);
params = k_params.template view<DeviceType>();

20
src/KOKKOS/pair_buck_coul_long_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -73,8 +73,8 @@ template<class DeviceType>
PairBuckCoulLongKokkos<DeviceType>::~PairBuckCoulLongKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
k_cut_ljsq = DAT::tdual_ffloat_2d();
k_cut_coulsq = DAT::tdual_ffloat_2d();
@ -117,13 +117,13 @@ void PairBuckCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -308,14 +308,14 @@ void PairBuckCoulLongKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_buck_coul**,Kokkos::LayoutRight,DeviceType>("PairBuckCoulLong::params",n+1,n+1);

16
src/KOKKOS/pair_buck_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -61,8 +61,8 @@ template<class DeviceType>
PairBuckKokkos<DeviceType>::~PairBuckKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
memory->sfree(cutsq);
eatom = NULL;
@ -87,13 +87,13 @@ void PairBuckKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -194,7 +194,7 @@ void PairBuckKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_buck**,Kokkos::LayoutRight,DeviceType>("PairBuck::params",n+1,n+1);
params = k_params.template view<DeviceType>();

14
src/KOKKOS/pair_coul_cut_kokkos.cpp
View File

@ -27,7 +27,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -55,7 +55,7 @@ template<class DeviceType>
PairCoulCutKokkos<DeviceType>::~PairCoulCutKokkos()
{
if (allocated)
memory->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
}
/* ---------------------------------------------------------------------- */
@ -86,13 +86,13 @@ void PairCoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -190,7 +190,7 @@ void PairCoulCutKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_cut_ljsq = typename ArrayTypes<DeviceType>::tdual_ffloat_2d("pair:cut_ljsq",n+1,n+1);

14
src/KOKKOS/pair_coul_debye_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -62,7 +62,7 @@ template<class DeviceType>
PairCoulDebyeKokkos<DeviceType>::~PairCoulDebyeKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
}
}
@ -93,13 +93,13 @@ void PairCoulDebyeKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -218,7 +218,7 @@ void PairCoulDebyeKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_coul**,Kokkos::LayoutRight,DeviceType>("PairCoulDebye::params",n+1,n+1);
params = k_params.template view<DeviceType>();

14
src/KOKKOS/pair_coul_dsf_kokkos.cpp
View File

@ -27,7 +27,7 @@
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "neigh_request.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
@ -65,8 +65,8 @@ template<class DeviceType>
PairCoulDSFKokkos<DeviceType>::~PairCoulDSFKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -86,13 +86,13 @@ void PairCoulDSFKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}

18
src/KOKKOS/pair_coul_long_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -72,8 +72,8 @@ template<class DeviceType>
PairCoulLongKokkos<DeviceType>::~PairCoulLongKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
k_cut_coulsq = DAT::tdual_ffloat_2d();
memory->sfree(cutsq);
@ -110,13 +110,13 @@ void PairCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -272,10 +272,10 @@ void PairCoulLongKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_coul**,Kokkos::LayoutRight,DeviceType>("PairCoulLong::params",n+1,n+1);

14
src/KOKKOS/pair_coul_wolf_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -60,8 +60,8 @@ template<class DeviceType>
PairCoulWolfKokkos<DeviceType>::~PairCoulWolfKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -81,13 +81,13 @@ void PairCoulWolfKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}

35
src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
View File

@ -28,11 +28,12 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "modify.h"
#include "pair_dpd_fdt_energy_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "kokkos.h"
using namespace LAMMPS_NS;
@ -62,15 +63,15 @@ PairDPDfdtEnergyKokkos<DeviceType>::~PairDPDfdtEnergyKokkos()
{
if (copymode) return;
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
if (allocated) {
memory->destroy_kokkos(k_duCond,duCond);
memory->destroy_kokkos(k_duMech,duMech);
memoryKK->destroy_kokkos(k_duCond,duCond);
memoryKK->destroy_kokkos(k_duMech,duMech);
}
memory->destroy_kokkos(k_cutsq,cutsq);
memoryKK->destroy_kokkos(k_cutsq,cutsq);
#ifdef DPD_USE_RAN_MARS
rand_pool.destroy();
@ -167,13 +168,13 @@ void PairDPDfdtEnergyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.template view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}
@ -274,11 +275,11 @@ void PairDPDfdtEnergyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// Allocate memory for duCond and duMech
if (allocated) {
memory->destroy_kokkos(k_duCond,duCond);
memory->destroy_kokkos(k_duMech,duMech);
memoryKK->destroy_kokkos(k_duCond,duCond);
memoryKK->destroy_kokkos(k_duMech,duMech);
}
memory->create_kokkos(k_duCond,duCond,nlocal+nghost,"pair:duCond");
memory->create_kokkos(k_duMech,duMech,nlocal+nghost,"pair:duMech");
memoryKK->create_kokkos(k_duCond,duCond,nlocal+nghost,"pair:duCond");
memoryKK->create_kokkos(k_duMech,duMech,nlocal+nghost,"pair:duMech");
d_duCond = k_duCond.view<DeviceType>();
d_duMech = k_duMech.view<DeviceType>();
h_duCond = k_duCond.h_view;
@ -641,7 +642,7 @@ void PairDPDfdtEnergyKokkos<DeviceType>::allocate()
int nghost = atom->nghost;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_dpd**,Kokkos::LayoutRight,DeviceType>("PairDPDfdtEnergy::params",n+1,n+1);
@ -650,8 +651,8 @@ void PairDPDfdtEnergyKokkos<DeviceType>::allocate()
if (!splitFDT_flag) {
memory->destroy(duCond);
memory->destroy(duMech);
memory->create_kokkos(k_duCond,duCond,nlocal+nghost+1,"pair:duCond");
memory->create_kokkos(k_duMech,duMech,nlocal+nghost+1,"pair:duMech");
memoryKK->create_kokkos(k_duCond,duCond,nlocal+nghost+1,"pair:duCond");
memoryKK->create_kokkos(k_duMech,duMech,nlocal+nghost+1,"pair:duMech");
d_duCond = k_duCond.view<DeviceType>();
d_duMech = k_duMech.view<DeviceType>();
h_duCond = k_duCond.h_view;

14
src/KOKKOS/pair_eam_alloy_kokkos.cpp
View File

@ -28,7 +28,7 @@
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "neigh_request.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -59,8 +59,8 @@ template<class DeviceType>
PairEAMAlloyKokkos<DeviceType>::~PairEAMAlloyKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -80,13 +80,13 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}

17
src/KOKKOS/pair_eam_alloy_kokkos.h
View File

@ -24,6 +24,7 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos<LMPHostType>)
#define LMP_PAIR_EAM_ALLOY_KOKKOS_H
#include <stdio.h>
#include "kokkos_base.h"
#include "pair_kokkos.h"
#include "pair_eam.h"
#include "neigh_list_kokkos.h"
@ -49,7 +50,7 @@ struct TagPairEAMAlloyKernelC{};
// Cannot use virtual inheritance on the GPU
template<class DeviceType>
class PairEAMAlloyKokkos : public PairEAM {
class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
@ -59,7 +60,7 @@ class PairEAMAlloyKokkos : public PairEAM {
PairEAMAlloyKokkos(class LAMMPS *);
virtual ~PairEAMAlloyKokkos();
virtual void compute(int, int);
void compute(int, int);
void init_style();
void *extract(const char *, int &) { return NULL; }
void coeff(int, char **);
@ -107,11 +108,11 @@ class PairEAMAlloyKokkos : public PairEAM {
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const;
virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
virtual void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
virtual int pack_forward_comm(int, int *, double *, int, int *);
virtual void unpack_forward_comm(int, int, double *);
int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
@ -148,7 +149,7 @@ class PairEAMAlloyKokkos : public PairEAM {
t_ffloat_2d_n7_randomread d_rhor_spline;
t_ffloat_2d_n7_randomread d_z2r_spline;
virtual void file2array();
void file2array();
void file2array_alloy();
void array2spline();
void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);

14
src/KOKKOS/pair_eam_fs_kokkos.cpp
View File

@ -28,7 +28,7 @@
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "neigh_request.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -59,8 +59,8 @@ template<class DeviceType>
PairEAMFSKokkos<DeviceType>::~PairEAMFSKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -80,13 +80,13 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}

17
src/KOKKOS/pair_eam_fs_kokkos.h
View File

@ -24,6 +24,7 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos<LMPHostType>)
#define LMP_PAIR_EAM_FS_KOKKOS_H
#include <stdio.h>
#include "kokkos_base.h"
#include "pair_kokkos.h"
#include "pair_eam.h"
#include "neigh_list_kokkos.h"
@ -49,7 +50,7 @@ struct TagPairEAMFSKernelC{};
// Cannot use virtual inheritance on the GPU
template<class DeviceType>
class PairEAMFSKokkos : public PairEAM {
class PairEAMFSKokkos : public PairEAM, public KokkosBase {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
@ -59,7 +60,7 @@ class PairEAMFSKokkos : public PairEAM {
PairEAMFSKokkos(class LAMMPS *);
virtual ~PairEAMFSKokkos();
virtual void compute(int, int);
void compute(int, int);
void init_style();
void *extract(const char *, int &) { return NULL; }
void coeff(int, char **);
@ -107,11 +108,11 @@ class PairEAMFSKokkos : public PairEAM {
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const;
virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
virtual void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
virtual int pack_forward_comm(int, int *, double *, int, int *);
virtual void unpack_forward_comm(int, int, double *);
int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
@ -148,7 +149,7 @@ class PairEAMFSKokkos : public PairEAM {
t_ffloat_2d_n7_randomread d_rhor_spline;
t_ffloat_2d_n7_randomread d_z2r_spline;
virtual void file2array();
void file2array();
void file2array_fs();
void array2spline();
void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);

14
src/KOKKOS/pair_eam_kokkos.cpp
View File

@ -28,7 +28,7 @@
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "neigh_request.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -54,8 +54,8 @@ template<class DeviceType>
PairEAMKokkos<DeviceType>::~PairEAMKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
}
@ -75,13 +75,13 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}

17
src/KOKKOS/pair_eam_kokkos.h
View File

@ -24,6 +24,7 @@ PairStyle(eam/kk/host,PairEAMKokkos<LMPHostType>)
#define LMP_PAIR_EAM_KOKKOS_H
#include <stdio.h>
#include "kokkos_base.h"
#include "pair_kokkos.h"
#include "pair_eam.h"
#include "neigh_list_kokkos.h"
@ -47,7 +48,7 @@ template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
struct TagPairEAMKernelC{};
template<class DeviceType>
class PairEAMKokkos : public PairEAM {
class PairEAMKokkos : public PairEAM, public KokkosBase {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
@ -57,7 +58,7 @@ class PairEAMKokkos : public PairEAM {
PairEAMKokkos(class LAMMPS *);
virtual ~PairEAMKokkos();
virtual void compute(int, int);
void compute(int, int);
void init_style();
void *extract(const char *, int &) { return NULL; }
@ -104,11 +105,11 @@ class PairEAMKokkos : public PairEAM {
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const;
virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
virtual void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
virtual int pack_forward_comm(int, int *, double *, int, int *);
virtual void unpack_forward_comm(int, int, double *);
int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
@ -146,7 +147,7 @@ class PairEAMKokkos : public PairEAM {
t_ffloat_2d_n7_randomread d_z2r_spline;
void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);
virtual void file2array();
void file2array();
void array2spline();
typename AT::t_neighbors_2d d_neighbors;

32
src/KOKKOS/pair_exp6_rx_kokkos.cpp
View File

@ -26,13 +26,15 @@
#include "neigh_list.h"
#include "math_const.h"
#include "math_special_kokkos.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "modify.h"
#include "fix.h"
#include <float.h>
#include "atom_masks.h"
#include "neigh_request.h"
#include "atom_kokkos.h"
#include "kokkos.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -89,18 +91,18 @@ PairExp6rxKokkos<DeviceType>::~PairExp6rxKokkos()
{
if (copymode) return;
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
memory->destroy_kokkos(k_cutsq,cutsq);
memoryKK->destroy_kokkos(k_cutsq,cutsq);
for (int i=0; i < nparams; ++i) {
delete[] params[i].name;
delete[] params[i].potential;
}
memory->destroy_kokkos(k_params,params);
memoryKK->destroy_kokkos(k_params,params);
memory->destroy_kokkos(k_mol2param,mol2param);
memoryKK->destroy_kokkos(k_mol2param,mol2param);
}
/* ---------------------------------------------------------------------- */
@ -151,13 +153,13 @@ void PairExp6rxKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.template view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}
@ -1660,7 +1662,7 @@ void PairExp6rxKokkos<DeviceType>::allocate()
for (int j = i; j <= ntypes; j++)
setflag[i][j] = 0;
memory->create_kokkos(k_cutsq,cutsq,ntypes+1,ntypes+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,ntypes+1,ntypes+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_cutsq.template modify<LMPHostType>();
@ -1697,7 +1699,7 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
int params_per_line = 5;
char **words = new char*[params_per_line+1];
memory->destroy_kokkos(k_params,params);
memoryKK->destroy_kokkos(k_params,params);
params = NULL;
nparams = maxparam = 0;
@ -1777,7 +1779,7 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
if (nparams == maxparam) {
k_params.template modify<LMPHostType>();
maxparam += DELTA;
memory->grow_kokkos(k_params,params,maxparam,
memoryKK->grow_kokkos(k_params,params,maxparam,
"pair:params");
}
@ -1816,8 +1818,8 @@ void PairExp6rxKokkos<DeviceType>::setup()
// set mol2param for all combinations
// must be a single exact match to lines read from file
memory->destroy_kokkos(k_mol2param,mol2param);
memory->create_kokkos(k_mol2param,mol2param,nspecies,"pair:mol2param");
memoryKK->destroy_kokkos(k_mol2param,mol2param);
memoryKK->create_kokkos(k_mol2param,mol2param,nspecies,"pair:mol2param");
for (i = 0; i < nspecies; i++) {
n = -1;

3
src/KOKKOS/pair_hybrid_kokkos.cpp
View File

@ -23,10 +23,11 @@
#include "neigh_request.h"
#include "update.h"
#include "comm.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "respa.h"
#include "atom_masks.h"
#include "kokkos.h"
using namespace LAMMPS_NS;

1
src/KOKKOS/pair_kokkos.h
View File

@ -20,6 +20,7 @@
#include "Kokkos_Macros.hpp"
#include "pair.h"
#include "neighbor_kokkos.h"
#include "neigh_list_kokkos.h"
#include "Kokkos_Vectorization.hpp"

20
src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -73,8 +73,8 @@ template<class DeviceType>
PairLJCharmmCoulCharmmImplicitKokkos<DeviceType>::~PairLJCharmmCoulCharmmImplicitKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
k_cut_ljsq = DAT::tdual_ffloat_2d();
k_cut_coulsq = DAT::tdual_ffloat_2d();
@ -118,13 +118,13 @@ void PairLJCharmmCoulCharmmImplicitKokkos<DeviceType>::compute(int eflag_in, int
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -315,14 +315,14 @@ void PairLJCharmmCoulCharmmImplicitKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
//memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCharmmCoulCharmmImplicit::params",n+1,n+1);

20
src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -73,8 +73,8 @@ template<class DeviceType>
PairLJCharmmCoulCharmmKokkos<DeviceType>::~PairLJCharmmCoulCharmmKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
k_cut_ljsq = DAT::tdual_ffloat_2d();
k_cut_coulsq = DAT::tdual_ffloat_2d();
@ -118,13 +118,13 @@ void PairLJCharmmCoulCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_i
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -316,14 +316,14 @@ void PairLJCharmmCoulCharmmKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
//memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCharmmCoulCharmm::params",n+1,n+1);

20
src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -73,8 +73,8 @@ template<class DeviceType>
PairLJCharmmCoulLongKokkos<DeviceType>::~PairLJCharmmCoulLongKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
k_cut_ljsq = DAT::tdual_ffloat_2d();
k_cut_coulsq = DAT::tdual_ffloat_2d();
@ -118,13 +118,13 @@ void PairLJCharmmCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -336,14 +336,14 @@ void PairLJCharmmCoulLongKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
//memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCharmmCoulLong::params",n+1,n+1);

22
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
View File

@ -27,7 +27,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -60,9 +60,9 @@ template<class DeviceType>
PairLJClass2CoulCutKokkos<DeviceType>::~PairLJClass2CoulCutKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_cutsq, cutsq);
memory->destroy_kokkos(k_cut_ljsq, cut_ljsq);
memory->destroy_kokkos(k_cut_coulsq, cut_coulsq);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq);
memoryKK->destroy_kokkos(k_cut_coulsq, cut_coulsq);
}
}
@ -95,13 +95,13 @@ void PairLJClass2CoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -255,13 +255,13 @@ void PairLJClass2CoulCutKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->destroy(cut_coulsq);
memory->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJClass2CoulCut::params",n+1,n+1);
params = k_params.template view<DeviceType>();

20
src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
View File

@ -27,7 +27,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -69,8 +69,8 @@ template<class DeviceType>
PairLJClass2CoulLongKokkos<DeviceType>::~PairLJClass2CoulLongKokkos()
{
if (!copymode){
memory->destroy_kokkos(k_cutsq, cutsq);
memory->destroy_kokkos(k_cut_ljsq, cut_ljsq);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq);
}
}
@ -103,13 +103,13 @@ void PairLJClass2CoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -307,13 +307,13 @@ void PairLJClass2CoulLongKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJClass2CoulLong::params",n+1,n+1);
params = k_params.template view<DeviceType>();

12
src/KOKKOS/pair_lj_class2_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -95,13 +95,13 @@ void PairLJClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -200,7 +200,7 @@ void PairLJClass2Kokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>("PairLJClass2::params",n+1,n+1);
params = k_params.template view<DeviceType>();

22
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
View File

@ -27,7 +27,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -60,9 +60,9 @@ template<class DeviceType>
PairLJCutCoulCutKokkos<DeviceType>::~PairLJCutCoulCutKokkos()
{
if (allocated){
memory->destroy_kokkos(k_cutsq, cutsq);
memory->destroy_kokkos(k_cut_ljsq, cut_ljsq);
memory->destroy_kokkos(k_cut_coulsq, cut_coulsq);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq);
memoryKK->destroy_kokkos(k_cut_coulsq, cut_coulsq);
}
}
@ -95,13 +95,13 @@ void PairLJCutCoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -247,13 +247,13 @@ void PairLJCutCoulCutKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->destroy(cut_coulsq);
memory->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCutCoulCut::params",n+1,n+1);
params = k_params.template view<DeviceType>();

22
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -64,9 +64,9 @@ template<class DeviceType>
PairLJCutCoulDebyeKokkos<DeviceType>::~PairLJCutCoulDebyeKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_cutsq, cutsq);
memory->destroy_kokkos(k_cut_ljsq, cut_ljsq);
memory->destroy_kokkos(k_cut_coulsq, cut_coulsq);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq);
memoryKK->destroy_kokkos(k_cut_coulsq, cut_coulsq);
}
}
@ -99,13 +99,13 @@ void PairLJCutCoulDebyeKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -261,13 +261,13 @@ void PairLJCutCoulDebyeKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->destroy(cut_coulsq);
memory->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCutCoulDebye::params",n+1,n+1);
params = k_params.template view<DeviceType>();

22
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -72,9 +72,9 @@ template<class DeviceType>
PairLJCutCoulDSFKokkos<DeviceType>::~PairLJCutCoulDSFKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_cutsq, cutsq);
memory->destroy_kokkos(k_cut_ljsq, cut_ljsq);
//memory->destroy_kokkos(k_cut_coulsq, cut_coulsq);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq);
//memoryKK->destroy_kokkos(k_cut_coulsq, cut_coulsq);
}
}
@ -107,13 +107,13 @@ void PairLJCutCoulDSFKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -279,13 +279,13 @@ void PairLJCutCoulDSFKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
//memory->destroy(cut_coulsq);
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCutCoulDSF::params",n+1,n+1);
params = k_params.template view<DeviceType>();

24
src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
View File

@ -27,7 +27,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -68,13 +68,13 @@ PairLJCutCoulLongKokkos<DeviceType>::PairLJCutCoulLongKokkos(LAMMPS *lmp):PairLJ
template<class DeviceType>
PairLJCutCoulLongKokkos<DeviceType>::~PairLJCutCoulLongKokkos()
{
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
eatom = NULL;
vatom = NULL;
if (allocated){
memory->destroy_kokkos(k_cutsq, cutsq);
memory->destroy_kokkos(k_cut_ljsq, cut_ljsq);
memoryKK->destroy_kokkos(k_cutsq, cutsq);
memoryKK->destroy_kokkos(k_cut_ljsq, cut_ljsq);
}
}
@ -108,13 +108,13 @@ void PairLJCutCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -304,13 +304,13 @@ void PairLJCutCoulLongKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCutCoulLong::params",n+1,n+1);
params = k_params.template view<DeviceType>();

16
src/KOKKOS/pair_lj_cut_kokkos.cpp
View File

@ -27,7 +27,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -57,8 +57,8 @@ template<class DeviceType>
PairLJCutKokkos<DeviceType>::~PairLJCutKokkos()
{
if (allocated) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
memory->sfree(cutsq);
eatom = NULL;
@ -95,13 +95,13 @@ void PairLJCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -195,7 +195,7 @@ void PairLJCutKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>("PairLJCut::params",n+1,n+1);
params = k_params.template view<DeviceType>();

12
src/KOKKOS/pair_lj_expand_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -94,13 +94,13 @@ void PairLJExpandKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -202,7 +202,7 @@ void PairLJExpandKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>("PairLJExpand::params",n+1,n+1);
params = k_params.template view<DeviceType>();

20
src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
View File

@ -31,7 +31,7 @@
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@ -64,8 +64,8 @@ template<class DeviceType>
PairLJGromacsCoulGromacsKokkos<DeviceType>::~PairLJGromacsCoulGromacsKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
k_cut_ljsq = DAT::tdual_ffloat_2d();
k_cut_coulsq = DAT::tdual_ffloat_2d();
@ -109,13 +109,13 @@ void PairLJGromacsCoulGromacsKokkos<DeviceType>::compute(int eflag_in, int vflag
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.view<DeviceType>();
}
@ -299,14 +299,14 @@ void PairLJGromacsCoulGromacsKokkos<DeviceType>::allocate()
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
//memory->destroy(cut_ljsq);
memory->create_kokkos(k_cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memoryKK->create_kokkos(k_cut_ljsq,n+1,n+1,"pair:cut_ljsq");
d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memoryKK->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj_coul_gromacs**,Kokkos::LayoutRight,DeviceType>("PairLJGromacsCoulGromacs::params",n+1,n+1);

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