diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 3ad1249ace4112f5641b72868db88b6bf47edcc2..ccb94ff5ca4e2bd23ad1f7067520b2ff77a97352 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -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,
diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt
index e14dd8c85e64469642fcc768a962eb5463fe0cd6..ad13879c6dd5b74ab2640135896241d326c04f4b 100644
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@@ -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}
diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt
index 5a878521693c968f09bbbbefbbca130a91832fa6..6af69214d3c4523318945c3bf70ac0547621dd64 100644
--- a/doc/src/create_bonds.txt
+++ b/doc/src/create_bonds.txt
@@ -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
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 30eff08e290c3f3f451c47846c3cd2f93799e314..f271b044b94151d6d9e91c3c4bca02d4326f3e06 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -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
diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a784e2501638ecda41031366b0777346115c94f
--- /dev/null
+++ b/doc/src/pair_extep.txt
@@ -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.
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index 61d6bde6a92ab34ea2a42527f59a3227ab27b163..e7c063ded9f41227210e17970dc9fb7cc59ed757 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -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:]
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index ec21b7a02e429436da14ea8baa3c33ad66b1d8b2..ccd540bf44a6e1f37e374cf4118f7a53655bbbd6 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -32,6 +32,7 @@ Pair Styles :h1
pair_eff
pair_eim
pair_exp6_rx
+ pair_extep
pair_gauss
pair_gayberne
pair_gran
diff --git a/examples/USER/misc/extep/BN.data b/examples/USER/misc/extep/BN.data
new file mode 100644
index 0000000000000000000000000000000000000000..3f51bdff6106035ac7f6c98c694e7c948d91ce56
--- /dev/null
+++ b/examples/USER/misc/extep/BN.data
@@ -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
diff --git a/examples/USER/misc/extep/in.extep-bn b/examples/USER/misc/extep/in.extep-bn
new file mode 100644
index 0000000000000000000000000000000000000000..bb7ed0ea281b1242c5b79f9aa2b36fafb8c6368d
--- /dev/null
+++ b/examples/USER/misc/extep/in.extep-bn
@@ -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
diff --git a/examples/USER/misc/extep/log.23Oct17.extep-bn.g++.1 b/examples/USER/misc/extep/log.23Oct17.extep-bn.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..392e5c4f0e38a061fde9e5cafce9db6463f5af74
--- /dev/null
+++ b/examples/USER/misc/extep/log.23Oct17.extep-bn.g++.1
@@ -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
diff --git a/examples/USER/misc/extep/log.23Oct17.extep-bn.g++.4 b/examples/USER/misc/extep/log.23Oct17.extep-bn.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c5c9236649e84972c774ac9772da0062e4b3059f
--- /dev/null
+++ b/examples/USER/misc/extep/log.23Oct17.extep-bn.g++.4
@@ -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
diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2
index d11ef72fddc80a732684b8eba32a14c3356c4f30..128f05b489885885fdb68c9953572d71e6d44f76 100644
--- a/examples/gcmc/in.gcmc.co2
+++ b/examples/gcmc/in.gcmc.co2
@@ -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
diff --git a/examples/gcmc/in.gcmc.h2o b/examples/gcmc/in.gcmc.h2o
index 7ffaafa9753b22e949efa55ecd482c9ffd2b6fdc..2c03b1ab78cc9dad8626ef76241e2dae1ab37955 100644
--- a/examples/gcmc/in.gcmc.h2o
+++ b/examples/gcmc/in.gcmc.h2o
@@ -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
diff --git a/examples/gcmc/in.gcmc.lj b/examples/gcmc/in.gcmc.lj
index fc9afdb7f837d07984516421ff6e4bb8a5cef9ab..3fe78efb252d2274a03b812f0bd972db2666952c 100644
--- a/examples/gcmc/in.gcmc.lj
+++ b/examples/gcmc/in.gcmc.lj
@@ -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
diff --git a/examples/gcmc/log.6Jul17.gcmc.co2.g++.1 b/examples/gcmc/log.23Oct17.gcmc.co2.g++.1
similarity index 81%
rename from examples/gcmc/log.6Jul17.gcmc.co2.g++.1
rename to examples/gcmc/log.23Oct17.gcmc.co2.g++.1
index f9e494c43fdcd1ccd557a5366c0a6145daf69be1..e7b7c6afda0f28e4bb4b7c7dd5aaa5b86635d39d 100644
--- a/examples/gcmc/log.6Jul17.gcmc.co2.g++.1
+++ b/examples/gcmc/log.23Oct17.gcmc.co2.g++.1
@@ -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
-
-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
+ 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: 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
diff --git a/examples/gcmc/log.6Jul17.gcmc.co2.g++.4 b/examples/gcmc/log.23Oct17.gcmc.co2.g++.4
similarity index 81%
rename from examples/gcmc/log.6Jul17.gcmc.co2.g++.4
rename to examples/gcmc/log.23Oct17.gcmc.co2.g++.4
index 0df25430d26c07b98085c31a2ac162c90f5bd763..b344c7b0685eb0e19deb26e363e9cc43cd292f24 100644
--- a/examples/gcmc/log.6Jul17.gcmc.co2.g++.4
+++ b/examples/gcmc/log.23Oct17.gcmc.co2.g++.4
@@ -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
-
-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
+ 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: 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
diff --git a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 b/examples/gcmc/log.23Oct17.gcmc.h2o.g++.1
similarity index 77%
rename from examples/gcmc/log.6Jul17.gcmc.h2o.g++.1
rename to examples/gcmc/log.23Oct17.gcmc.h2o.g++.1
index 3b1606e65d6979747e5f22a920e516f691e052c2..bc7c3af4541e58dea45b6d917d2645a2fb64683c 100644
--- a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1
+++ b/examples/gcmc/log.23Oct17.gcmc.h2o.g++.1
@@ -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
-
-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
+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: 7.831 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
diff --git a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 b/examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
similarity index 78%
rename from examples/gcmc/log.6Jul17.gcmc.h2o.g++.4
rename to examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
index c04b25f45eaf88e4a82ca9edd8b79a0ec9ac934c..4eeab969ddc8c578baf028394c39064f2b57aace 100644
--- a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4
+++ b/examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
@@ -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
-
-Performance: 18.405 ns/day, 1.304 hours/ns, 213.024 timesteps/s
+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: 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
diff --git a/examples/gcmc/log.6Jul17.gcmc.lj.g++.1 b/examples/gcmc/log.23Oct17.gcmc.lj.g++.1
similarity index 76%
rename from examples/gcmc/log.6Jul17.gcmc.lj.g++.1
rename to examples/gcmc/log.23Oct17.gcmc.lj.g++.1
index 69fc2ede1cd28681f7b139e8bb2b1a4976d6df89..a38dfeee77897b740bfecfaedd046676a6ad56b3 100644
--- a/examples/gcmc/log.6Jul17.gcmc.lj.g++.1
+++ b/examples/gcmc/log.23Oct17.gcmc.lj.g++.1
@@ -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
-
-Performance: 208804.611 tau/day, 483.344 timesteps/s
-99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+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: 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
diff --git a/examples/gcmc/log.6Jul17.gcmc.lj.g++.4 b/examples/gcmc/log.23Oct17.gcmc.lj.g++.4
similarity index 76%
rename from examples/gcmc/log.6Jul17.gcmc.lj.g++.4
rename to examples/gcmc/log.23Oct17.gcmc.lj.g++.4
index 6bd3b3189cfeda01ff29feefff5d861c8d32b888..ea7dc8116febce3c356ca8782599656cf6250986 100644
--- a/examples/gcmc/log.6Jul17.gcmc.lj.g++.4
+++ b/examples/gcmc/log.23Oct17.gcmc.lj.g++.4
@@ -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
-
-Performance: 172857.936 tau/day, 400.134 timesteps/s
-98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+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: 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
diff --git a/lib/atc/Matrix.h b/lib/atc/Matrix.h
index e467128fbc7733af1c7aa551e6a718059194bc59..e806ebd0168c1bbc924a42a8d3ee8d229d4d90a9 100644
--- a/lib/atc/Matrix.h
+++ b/lib/atc/Matrix.h
@@ -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;
}
diff --git a/potentials/BN.extep b/potentials/BN.extep
new file mode 100644
index 0000000000000000000000000000000000000000..8732ada84bf95dc6814d0ef839b18b686a4e914d
--- /dev/null
+++ b/potentials/BN.extep
@@ -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
diff --git a/python/lammps.py b/python/lammps.py
index a53bc431be3c4c841f596ccdf4dc0f1998425d54..0492876476ea7d2ce50a709eb498ec819beac0ae 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -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:
diff --git a/src/.gitignore b/src/.gitignore
index 694a43adb2980be485b4e4771797aaca817bf56d..1f95e50fde4cee633d0781fd83e8e521d381089b 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -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
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index ab0f499a98e6813a875753d63302cfe34bd8fa67..9b42b0a14fab56b44652942973fd122a7fe113da 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -28,6 +28,7 @@
#include "error.h"
#include "neigh_request.h"
#include "gpu_extra.h"
+#include "domain.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index a2b339db9ac6ce197b19ad7705edfb24ea132599..c29b49631ce210121df7479b3fc60867bca31438 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -28,6 +28,7 @@
#include "error.h"
#include "neigh_request.h"
#include "gpu_extra.h"
+#include "domain.h"
using namespace LAMMPS_NS;
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index eeec94fdf729a76694188a715119781adfaaefe5..033c35dbacc0e96bb910cd1c3e6b2fa261eb815a 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -30,6 +30,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
+#include "neighbor.h"
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp
index a09b9dfa421b971df17992722ccc55c1308b1454..d1c5d4c9c771f8a73bd0d95165ee362976f50509 100644
--- a/src/GRANULAR/fix_wall_gran_region.cpp
+++ b/src/GRANULAR/fix_wall_gran_region.cpp
@@ -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;
diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
index df5fc3e5f1a9d146a94f37435842d6076f4edff2..295e46bcaec54282a9511adb4ff5af91a9b75fff 100644
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@@ -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
diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp
index 401a00c856ffcc86543f22024bbb0cec1d9dc2e3..59a20c25df36184d4a23a9bf9f6071c625f5eb38 100644
--- a/src/KOKKOS/angle_charmm_kokkos.cpp
+++ b/src/KOKKOS/angle_charmm_kokkos.cpp
@@ -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>();
//}
}
diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp
index e851e9d500b10246571210a6c38daae5d472528a..108b4f48f225827228fe1a5667edbd7a7c8ad6aa 100644
--- a/src/KOKKOS/angle_class2_kokkos.cpp
+++ b/src/KOKKOS/angle_class2_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp
index 9fd237ddb3e90404aa9e9a979be2ccaba3953e6d..dd5a1e26c7c55d135a5e37a0619dace64b49dbb1 100644
--- a/src/KOKKOS/angle_harmonic_kokkos.cpp
+++ b/src/KOKKOS/angle_harmonic_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp
index 31b33dbdc9a2c406e40e6e36f8898d88d1c50d5b..4ecead5b1d052be975c40069d169a7fad43cbf63 100644
--- a/src/KOKKOS/atom_kokkos.cpp
+++ b/src/KOKKOS/atom_kokkos.cpp
@@ -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);
-
- memory->destroy_kokkos(k_x, x);
- memory->destroy_kokkos(k_v, v);
- memory->destroy_kokkos(k_f, f);
-
- memory->destroy_kokkos(k_mass, mass);
- memory->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);
-
- 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_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);
+
+ memoryKK->destroy_kokkos(k_x, x);
+ memoryKK->destroy_kokkos(k_v, v);
+ memoryKK->destroy_kokkos(k_f, f);
+
+ memoryKK->destroy_kokkos(k_mass, mass);
+ memoryKK->destroy_kokkos(k_q, q);
+
+ 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);
+
+ 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);
-
- memory->destroy_kokkos(k_dvector,dvector);
+ 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);
+
+ 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);
-
- 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_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_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_bond_type, bond_type);
+ memoryKK->destroy_kokkos(k_bond_atom, bond_atom);
+
+ 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_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_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);
}
/* ----------------------------------------------------------------------
diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp
index 05414cf2e45cdc92f9750c552cb390d915e151cb..a9e55f530a2c1ab3e93eb606f7375bf674c678aa 100644
--- a/src/KOKKOS/atom_vec_angle_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp
@@ -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();
diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
index 6c610c8c111409d8c18201d9be23e44a4fe9195c..f021c45db6feb9c1407115dd1cbeadebf9ddf1d6 100644
--- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp
index 076144420c1442c5db69008905263313b4757be2..bf682c507fd5c3210db20a1e50b35dc09d16a1c7 100644
--- a/src/KOKKOS/atom_vec_bond_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp
@@ -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");
-
- 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");
-
- 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_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");
+
+ 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");
+
+ 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);
diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp
index 7b8b74b4051b63411f673b537ca4c1b9ce731198..a9ae5cc2d1e999d8dc94964e43a3f0d8be4a2a84 100644
--- a/src/KOKKOS/atom_vec_charge_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
index c4e493bd8536dd036931e61c0e0f080fc9d925ad..9c54ffccc50213111d7e47bd39751f474c475438 100644
--- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
@@ -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++)
diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp
index 8e9abe40675f7816ca969a23c0ab55855f71c5d1..9369d7e84437f184051aed76f129cbb3fe028efb 100644
--- a/src/KOKKOS/atom_vec_full_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_full_kokkos.cpp
@@ -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();
diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
index e5e361e70ab21645b67608f6d4f68ab07fb19900..b5aadb18d612cfbd30a6c3666fd85a3dfe489d82 100644
--- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
@@ -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"
diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
index dbf6a857b2521874ba7dca32a4cf374030c546e1..6f232a319b06238c95ff903706ad759228045c82 100644
--- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
@@ -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();
diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp
index b3c11c9a06c468be08f9ce2b2a29919c949ff475..df2f2c1e9be24a6d807ecf12e67c239735dde7f6 100644
--- a/src/KOKKOS/bond_class2_kokkos.cpp
+++ b/src/KOKKOS/bond_class2_kokkos.cpp
@@ -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>();
//}
}
diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp
index 8a716a98ef534bfdcc3daf31696d01e1af22b071..20c20542083b35c289d8efdab2f3dce5adc95077 100644
--- a/src/KOKKOS/bond_fene_kokkos.cpp
+++ b/src/KOKKOS/bond_fene_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp
index da45c70d6c7739f08ad0fb559e6d9d7f768437c4..c4e0c3a81763e765ee593ba13b84c4b0fcec3616 100644
--- a/src/KOKKOS/bond_harmonic_kokkos.cpp
+++ b/src/KOKKOS/bond_harmonic_kokkos.cpp
@@ -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>();
//}
}
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index 5534341342d5017378169609dce1a0c5964d8338..e506fa1ad42c849d0b31b0e564a45842d6aa1cfe 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -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;
diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp
index adcc634aa1d766858c62e85a9ec6f7557d37da6c..33cd8eaa6e9eabc518a163d1ffbe68bbe0cffc30 100644
--- a/src/KOKKOS/comm_tiled_kokkos.cpp
+++ b/src/KOKKOS/comm_tiled_kokkos.cpp
@@ -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"
diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp
index 7f2117c97f545021ca35172c62f9299adb9e8275..71635ec76c48d5642e7eccccef8d360c2077fc60 100644
--- a/src/KOKKOS/dihedral_charmm_kokkos.cpp
+++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index 89e42c6f836a1f3fa9e502875332bffb8bb4cd08..d32ea4a4611089808f31faf7756967f6572e0f94 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp
index 0ee00ca8db438c2c47eba7443e93039295ab2f93..4349aff48df93848f097bd1130c758ec6be91951 100644
--- a/src/KOKKOS/dihedral_opls_kokkos.cpp
+++ b/src/KOKKOS/dihedral_opls_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
index 552141ced24f50d68108d372405c5cb82da03360..5c106c19f3432edcc5a432d96031b12270bb39bb 100644
--- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
+++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
@@ -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++) {
diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp
index fb0f329a91bb398bad243493e9d834ac3ab1aa8d..108c3b692ad7f4fcb176a407a558c5dca3685ca8 100644
--- a/src/KOKKOS/fix_langevin_kokkos.cpp
+++ b/src/KOKKOS/fix_langevin_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp
index 7136c776a1de7e39d670fa53c69945f8f1d15b3f..345259e35519b24a6b6b669c175fc9e5bdeaf746 100644
--- a/src/KOKKOS/fix_nh_kokkos.cpp
+++ b/src/KOKKOS/fix_nh_kokkos.cpp
@@ -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"
diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp
index cb52988c318fcbd147a534ac16d2ea5494f5f63d..fe2f101e561f1dca37852084d6be56a6896f8b2d 100644
--- a/src/KOKKOS/fix_property_atom_kokkos.cpp
+++ b/src/KOKKOS/fix_property_atom_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 5d2f6a0438a400302785c70975beee07d4d4f32b..91a22361fc91b4371eb7c7638e4fdb1b9c229d46 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -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"
diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
index 0d74a49ed304498a5f11d55133898a4565e56002..586daadd55e64c3922f52ee16faa454f7b723da5 100644
--- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
+++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
@@ -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);
}
/* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp
index f2719f9f0e7048a6db47bf49dfd09979a6f5074b..a676c7ef27ae81cf7ec39e8467e7ecdceb816e06 100644
--- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp
+++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp
@@ -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"
diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp
index b1cfd20be23f57a25981e151a5098c0b43b13ae6..61290ece33dfb72c50dc787542e4cea50fe5a077 100644
--- a/src/KOKKOS/fix_rx_kokkos.cpp
+++ b/src/KOKKOS/fix_rx_kokkos.cpp
@@ -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;
}
diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp
index 2ef04ad6ee3285534ab1f36a26842641fcf5802c..e99160989497381ef63985fad512ec3e2d3af664 100644
--- a/src/KOKKOS/fix_setforce_kokkos.cpp
+++ b/src/KOKKOS/fix_setforce_kokkos.cpp
@@ -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;
diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp
index 98bbb02714ca454b01e4ac3b65351b3d029ac06e..cc1bd6bede9fabe94f270464cd1ead9558ecad8e 100644
--- a/src/KOKKOS/fix_shardlow_kokkos.cpp
+++ b/src/KOKKOS/fix_shardlow_kokkos.cpp
@@ -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"
diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp
index 6871ef67aee6464b442e67e21dc0776e486d5a43..fdfaf296ef335f30654c1aea300db1102dfca772 100644
--- a/src/KOKKOS/gridcomm_kokkos.cpp
+++ b/src/KOKKOS/gridcomm_kokkos.cpp
@@ -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);
}
}
diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp
index c2cb7dfe2bf55df1f64988abe60a152d42984654..d2d465a250f1ff97bfd4668fe26eec489f62f850 100644
--- a/src/KOKKOS/improper_class2_kokkos.cpp
+++ b/src/KOKKOS/improper_class2_kokkos.cpp
@@ -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>();
//}
}
diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp
index 73e105864f630b0516ac90ba41058cf101878bea..49dd36ed194da6ea94df99144f75602ed11af5ea 100644
--- a/src/KOKKOS/improper_harmonic_kokkos.cpp
+++ b/src/KOKKOS/improper_harmonic_kokkos.cpp
@@ -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>();
//}
}
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index 2b02624dcef30f29947183cb4f2a5acb68916779..5a742233534403a48b99ca12eae8f8873583401f 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -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;
diff --git a/src/KOKKOS/kokkos_base.h b/src/KOKKOS/kokkos_base.h
new file mode 100644
index 0000000000000000000000000000000000000000..3279cb2947272022704036cbd51ddcb10ff788ef
--- /dev/null
+++ b/src/KOKKOS/kokkos_base.h
@@ -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:
+
+*/
diff --git a/src/KOKKOS/memory_kokkos.h b/src/KOKKOS/memory_kokkos.h
index 8ade198c4056727f78b620300b72783f15375431..9f930faae2e4f973a0849064a585888e29a8483f 100644
--- a/src/KOKKOS/memory_kokkos.h
+++ b/src/KOKKOS/memory_kokkos.h
@@ -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
+
diff --git a/src/KOKKOS/nbin_ssa_kokkos.cpp b/src/KOKKOS/nbin_ssa_kokkos.cpp
index ab97cb584805b6328df67cfe954d02ba44fc3907..1a881658567524b181bbeb52af3b97a17246fc12 100644
--- a/src/KOKKOS/nbin_ssa_kokkos.cpp
+++ b/src/KOKKOS/nbin_ssa_kokkos.cpp
@@ -26,7 +26,7 @@
#include "error.h"
#include "atom_masks.h"
-// #include "memory.h"
+// #include "memory_kokkos.h"
using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp
index a674e7cec48a0e16ff9aa91f36ec85c53b23c0a5..3ecc8b5e516c8243a36a668fcdceb7b434e7145c 100644
--- a/src/KOKKOS/neigh_bond_kokkos.cpp
+++ b/src/KOKKOS/neigh_bond_kokkos.cpp
@@ -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());
diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp
index 04454e53cb302e2ad696809c034e1925a8aaa83d..98294a802aaa88e16a2c1ca8269cf235d149ff3a 100644
--- a/src/KOKKOS/neigh_list_kokkos.cpp
+++ b/src/KOKKOS/neigh_list_kokkos.cpp
@@ -13,7 +13,7 @@
#include "neigh_list_kokkos.h"
#include "atom.h"
-#include "memory.h"
+#include "memory_kokkos.h"
using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp
index f34b149864d1c24179fdf2f41be36143ed5f9807..8d36add10bd6a10d8d861cd0cff5a27cef5fd1f3 100644
--- a/src/KOKKOS/neighbor_kokkos.cpp
+++ b/src/KOKKOS/neighbor_kokkos.cpp
@@ -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);
-
- 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_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);
+
+ 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>();
}
diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
index 0da8a0a3d6a9267bc6e45a74aa4b52f2f2471c47..ba3eda64ddee4e389b771f5e47168c98c5a6fa08 100644
--- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
index 3a5cbd868f725c54a95c6c6cb0fc9a2335137ea5..19af349a63588a464f4e1785be291510fd91acfa 100644
--- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp
index e7640471d501bc8be6778c4acb32395e18cf950a..fcf14533dc991d469ad1c0e65951ca80d515b0b2 100644
--- a/src/KOKKOS/pair_buck_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp
index 8edf093e2e118a4315b899aa6c304a9e78f670f9..e20e243c09aefb7313cbe13ce50a498356ea405d 100644
--- a/src/KOKKOS/pair_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp
index c331ab8da8f5881441985a0bfdf69d7f9da8bc8d..4cac18cacfcaf2ba3274a3feeb6e6f3d3a65c4bf 100644
--- a/src/KOKKOS/pair_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
index e6f5407f2d16990085495915562a4c564861aa81..f77e63bbf0551b0412b21e0b7631c098ff082f78 100644
--- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp
index 721e140e3374794dad4016fce79888cb60a07145..f2ade3f367c0e01b8118d454a3d0259618cffddf 100644
--- a/src/KOKKOS/pair_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_long_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
index 75177e2d81e7a3a9a70ccc754db14651a8d29e56..0f3e9b94290918dd78cb8940cc762d5e82494977 100644
--- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
index c559ab412f355c1dc10a51adb4308fbf031003d4..7d71719e0a115d99cf25a3a89a91487f9042edc2 100644
--- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
+++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
@@ -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;
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index aa68d0a05438ad2db1256e62cbb979861be47c47..f263cbb6d90be1cd34d5f0f9abab2b4e04174794 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index fb07eec32b1253c61d309f60f1010fb31d4441a6..a962f559085d767f10c1b347a83b9d006c68a548 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -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);
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index a982f94ec4d607ae2e83d1773ed38a98a082ad09..05ec1a644b829cc587ca30a4f99148d78dbeeb11 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index d71ec2b8870f103ae1f839d5a90ff791c367afaf..ec87e44ece248f93f0193684311f3587be8ec5d3 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -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);
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 8ac92a1766c62eedbaf37663d5ba1092bbab4599..0aa43b26b2112f6970bae5562b506b4cabe6718d 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -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>();
}
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 856cc51f7709f24cec67df5d0e8de930f4796c69..34a4795ec54e97986b9cd39e0e79e7932d5d6bd4 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -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;
diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
index 8d65be23af00e7c37e4ce2ad0f1f781a822fc6c4..a09a1d27e34c544c15c79de45ff28ee6a2650e54 100644
--- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
@@ -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;
diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp
index 337b56c6cee7e11e3a03dcd810bd62e161bb6813..db757f6ce1847806d266de13037d99b6489732a3 100644
--- a/src/KOKKOS/pair_hybrid_kokkos.cpp
+++ b/src/KOKKOS/pair_hybrid_kokkos.cpp
@@ -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;
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index f0e357270c1d5b8340c570f4a1d5be4f26d36a27..4c215ed16287d54ed3237aa678612c74c5faabf0 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -20,6 +20,7 @@
#include "Kokkos_Macros.hpp"
#include "pair.h"
+#include "neighbor_kokkos.h"
#include "neigh_list_kokkos.h"
#include "Kokkos_Vectorization.hpp"
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
index e7cf7ba42ad80ba7166322a2dd1999c3e3c19f3c..7d395cb3b464746f7efeb9e52232f122dcfb8b4d 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
index a456d6e27600c36911da43be21f8151a91943148..2663d71a1febe0aced1bacec03b1c80ff6136715 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
index dffbbb638ff0d1f25819d99b504e58d2d9eae300..81271c7d8ab7b7341601d1141e51c3f5edb5351b 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
index 0081aca4f15ddf196ceb6d104ce75798fa55c736..3f355b1b160bf34df464b833cf1c938e76f5a17e 100644
--- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
index b5dc358feb3fed379c7236e164a0f15d0104e60b..47976ec610aecdef5d6c41bd9d612533e6bc16aa 100644
--- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp
index 34cc15279b4d7a2708fc5c537d14ea44fe4e0dca..5beb520c00feb1971f5248e4ab31a7442133faa7 100644
--- a/src/KOKKOS/pair_lj_class2_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
index c3fda01ce63244bfa591deb80c23e4327288c68a..86e37bea77a6ffadf9ab082a36005ebca6da8aba 100644
--- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
index b7a71cb99ac3d7f22ace36d5537a1dcb920dd60b..76e488c68667e4ac7b19150ba70e876ebc81fe7e 100644
--- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
index 9df59636769a25dc3d512f36d4912486cb43be66..0da5e7f5f511432e5b8e81036caed9ec779dc992 100644
--- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
index 9bd79c7341a7116d74eb789ace8f5a984564278c..77a604534e2ae907a16db82ed013c26af2ec1042 100644
--- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp
index c90d5ad11c5295083eaaa4516c6f108665280def..2a228fb168be97184fda12d80b012745b286fa80 100644
--- a/src/KOKKOS/pair_lj_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp
index 95ec252ad5fdebf3d4829abc524927d17ffa6eef..aca7202b78be66a04ce7443e7eb4f34c34a6a6e0 100644
--- a/src/KOKKOS/pair_lj_expand_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp
@@ -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>();
diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
index 4b21b08eb352ad95c8806bff4ae3175204eaf767..bf269288e076b3c69edf2cbff706426740a5e9f6 100644
--- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
@@ -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);
diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
index 73a17d7b22f577fc31e4d6f3271ff4bab1b7694a..f24ff718c1042992bf47e18a6ce12e54ec7c169f 100644
--- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
@@ -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>
PairLJGromacsKokkos<DeviceType>::~PairLJGromacsKokkos()
{
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_inner_sq = DAT::tdual_ffloat_2d();
memory->sfree(cutsq);
@@ -106,13 +106,13 @@ void PairLJGromacsKokkos<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>();
}
@@ -240,15 +240,15 @@ void PairLJGromacsKokkos<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_inner);
- memory->create_kokkos(k_cut_inner,cut_inner,n+1,n+1,"pair:cut_inner");
+ memoryKK->create_kokkos(k_cut_inner,cut_inner,n+1,n+1,"pair:cut_inner");
d_cut_inner = k_cut_inner.template view<DeviceType>();
memory->destroy(cut_inner_sq);
- memory->create_kokkos(k_cut_inner_sq,cut_inner_sq,n+1,n+1,"pair:cut_inner_sq");
+ memoryKK->create_kokkos(k_cut_inner_sq,cut_inner_sq,n+1,n+1,"pair:cut_inner_sq");
d_cut_inner_sq = k_cut_inner_sq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>("PairLJGromacs::params",n+1,n+1);
diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
index 2063f62b203546f4dfa18fd505b8e64ed7148968..aa579d5dc12995475731589da686ee4271867db9 100644
--- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
@@ -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"
@@ -94,13 +94,13 @@ void PairLJSDKKokkos<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>();
}
@@ -231,7 +231,7 @@ void PairLJSDKKokkos<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>("PairLJSDK::params",n+1,n+1);
params = k_params.template view<DeviceType>();
diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp
index 08a9b82640b4ea439c67457210d6baf31cb34027..5768d7e42cedba7cbdfb16bec74a765af657b837 100644
--- a/src/KOKKOS/pair_morse_kokkos.cpp
+++ b/src/KOKKOS/pair_morse_kokkos.cpp
@@ -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>
PairMorseKokkos<DeviceType>::~PairMorseKokkos()
{
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;
@@ -99,13 +99,13 @@ void PairMorseKokkos<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>();
}
@@ -209,7 +209,7 @@ void PairMorseKokkos<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_morse**,Kokkos::LayoutRight,DeviceType>("PairMorse::params",n+1,n+1);
params = k_params.template view<DeviceType>();
diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
index d9a4f1ab83643ebd27f692c6290e436079c91522..0961cf44eb09ea1211ab7898c9c6532cbd518a14 100644
--- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
@@ -31,13 +31,14 @@
#include "force.h"
#include "comm.h"
#include "neigh_list.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "error.h"
#include "citeme.h"
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "neigh_request.h"
+#include "kokkos.h"
using namespace LAMMPS_NS;
@@ -80,10 +81,10 @@ PairMultiLucyRXKokkos<DeviceType>::~PairMultiLucyRXKokkos()
{
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);
delete h_table;
delete d_table;
@@ -153,13 +154,13 @@ void PairMultiLucyRXKokkos<DeviceType>::compute_style(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>();
}
@@ -864,20 +865,20 @@ void PairMultiLucyRXKokkos<DeviceType>::create_kokkos_tables()
{
const int tlm1 = tablength-1;
- memory->create_kokkos(d_table->innersq,h_table->innersq,ntables,"Table::innersq");
- memory->create_kokkos(d_table->invdelta,h_table->invdelta,ntables,"Table::invdelta");
+ memoryKK->create_kokkos(d_table->innersq,h_table->innersq,ntables,"Table::innersq");
+ memoryKK->create_kokkos(d_table->invdelta,h_table->invdelta,ntables,"Table::invdelta");
if(tabstyle == LOOKUP) {
- memory->create_kokkos(d_table->e,h_table->e,ntables,tlm1,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,tlm1,"Table::f");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tlm1,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,tlm1,"Table::f");
}
if(tabstyle == LINEAR) {
- memory->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
- memory->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
- memory->create_kokkos(d_table->de,h_table->de,ntables,tlm1,"Table::de");
- memory->create_kokkos(d_table->df,h_table->df,ntables,tlm1,"Table::df");
+ memoryKK->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
+ memoryKK->create_kokkos(d_table->de,h_table->de,ntables,tlm1,"Table::de");
+ memoryKK->create_kokkos(d_table->df,h_table->df,ntables,tlm1,"Table::df");
}
for(int i=0; i < ntables; i++) {
@@ -931,11 +932,11 @@ void PairMultiLucyRXKokkos<DeviceType>::allocate()
memory->create(setflag,nt,nt,"pair:setflag");
- memory->create_kokkos(k_cutsq,cutsq,nt,nt,"pair:cutsq");
+ memoryKK->create_kokkos(k_cutsq,cutsq,nt,nt,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
k_cutsq.template modify<LMPHostType>();
- memory->create_kokkos(d_table->tabindex,h_table->tabindex,tabindex,nt,nt,"pair:tabindex");
+ memoryKK->create_kokkos(d_table->tabindex,h_table->tabindex,tabindex,nt,nt,"pair:tabindex");
d_table_const.tabindex = d_table->tabindex;
memset(&setflag[0][0],0,nt*nt*sizeof(int));
diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.h b/src/KOKKOS/pair_multi_lucy_rx_kokkos.h
index b8ced4c847f6088efe98c09f50ea706626531883..aee1763b06e25c019a996c8b1c0c2b5df399188a 100644
--- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.h
+++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.h
@@ -25,6 +25,7 @@ PairStyle(multi/lucy/rx/kk/host,PairMultiLucyRXKokkos<LMPHostType>)
#include "pair_multi_lucy_rx.h"
#include "pair_kokkos.h"
+#include "kokkos_base.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
@@ -43,7 +44,7 @@ template<int NEIGHFLAG, int NEWTON_PAIR, bool ONE_TYPE>
struct TagPairMultiLucyRXComputeLocalDensity{};
template<class DeviceType>
-class PairMultiLucyRXKokkos : public PairMultiLucyRX {
+class PairMultiLucyRXKokkos : public PairMultiLucyRX, public KokkosBase {
public:
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index d5f83f45373d9e4d32d6032f0fe343489077e885..1f596377679fcac252660addc37109675da0260e 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -32,12 +32,13 @@
#include "respa.h"
#include "math_const.h"
#include "math_special.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "reaxc_defs.h"
#include "reaxc_lookup.h"
#include "reaxc_tool_box.h"
+#include "modify.h"
#define TEAMSIZE 128
@@ -81,12 +82,12 @@ PairReaxCKokkos<DeviceType>::~PairReaxCKokkos()
{
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_tmpid,tmpid);
+ memoryKK->destroy_kokkos(k_tmpid,tmpid);
tmpid = NULL;
- memory->destroy_kokkos(k_tmpbo,tmpbo);
+ memoryKK->destroy_kokkos(k_tmpbo,tmpbo);
tmpbo = NULL;
}
@@ -1339,10 +1340,10 @@ void PairReaxCKokkos<DeviceType>::allocate_array()
// FixReaxCSpecies
if (fixspecies_flag) {
- memory->destroy_kokkos(k_tmpid,tmpid);
- memory->destroy_kokkos(k_tmpbo,tmpbo);
- memory->create_kokkos(k_tmpid,tmpid,nmax,MAXSPECBOND,"pair:tmpid");
- memory->create_kokkos(k_tmpbo,tmpbo,nmax,MAXSPECBOND,"pair:tmpbo");
+ memoryKK->destroy_kokkos(k_tmpid,tmpid);
+ memoryKK->destroy_kokkos(k_tmpbo,tmpbo);
+ memoryKK->create_kokkos(k_tmpid,tmpid,nmax,MAXSPECBOND,"pair:tmpid");
+ memoryKK->create_kokkos(k_tmpbo,tmpbo,nmax,MAXSPECBOND,"pair:tmpbo");
}
// FixReaxCBonds
@@ -1448,6 +1449,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsFull, const int &
}
}
+ if (rsq > cut_bosq) continue;
+
// bond_list
const F_FLOAT rij = sqrt(rsq);
const F_FLOAT p_bo1 = paramstwbp(itype,jtype).p_bo1;
@@ -1635,6 +1638,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf<NEIGHFLAG>,
}
}
+ if (rsq > cut_bosq) continue;
+
// bond_list
const F_FLOAT rij = sqrt(rsq);
const F_FLOAT p_bo1 = paramstwbp(itype,jtype).p_bo1;
@@ -1856,6 +1861,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf_LessAtomics<
}
}
+ if (rsq > cut_bosq) continue;
+
// bond_list
const F_FLOAT rij = sqrt(rsq);
const F_FLOAT p_bo1 = paramstwbp(itype,jtype).p_bo1;
@@ -3905,14 +3912,14 @@ void PairReaxCKokkos<DeviceType>::ev_setup(int eflag, int vflag)
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
- 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");
v_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
- 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");
v_vatom = k_vatom.view<DeviceType>();
}
diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp
index 3440f7c63923da0467c61b702c1184ab3cb1856c..63b4c19ae1d7c40d4e3234562b6b7eb8c54e9470 100644
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
@@ -27,10 +27,10 @@
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "neighbor.h"
#include "neigh_list_kokkos.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "math_const.h"
@@ -63,8 +63,8 @@ template<class DeviceType>
PairSWKokkos<DeviceType>::~PairSWKokkos()
{
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);
eatom = NULL;
vatom = NULL;
}
@@ -86,13 +86,13 @@ void PairSWKokkos<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>();
}
diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp
index 7f763baae6fe7b40eb4830d243c0b714a6bcf2b1..b3e80d1f664e012555a826834df2d6b78ec7bba4 100644
--- a/src/KOKKOS/pair_table_kokkos.cpp
+++ b/src/KOKKOS/pair_table_kokkos.cpp
@@ -27,7 +27,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
@@ -92,13 +92,13 @@ void PairTableKokkos<DeviceType>::compute_style(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>();
}
@@ -265,41 +265,41 @@ void PairTableKokkos<DeviceType>::create_kokkos_tables()
{
const int tlm1 = tablength-1;
- memory->create_kokkos(d_table->nshiftbits,h_table->nshiftbits,ntables,"Table::nshiftbits");
- memory->create_kokkos(d_table->nmask,h_table->nmask,ntables,"Table::nmask");
- memory->create_kokkos(d_table->innersq,h_table->innersq,ntables,"Table::innersq");
- memory->create_kokkos(d_table->invdelta,h_table->invdelta,ntables,"Table::invdelta");
- memory->create_kokkos(d_table->deltasq6,h_table->deltasq6,ntables,"Table::deltasq6");
+ memoryKK->create_kokkos(d_table->nshiftbits,h_table->nshiftbits,ntables,"Table::nshiftbits");
+ memoryKK->create_kokkos(d_table->nmask,h_table->nmask,ntables,"Table::nmask");
+ memoryKK->create_kokkos(d_table->innersq,h_table->innersq,ntables,"Table::innersq");
+ memoryKK->create_kokkos(d_table->invdelta,h_table->invdelta,ntables,"Table::invdelta");
+ memoryKK->create_kokkos(d_table->deltasq6,h_table->deltasq6,ntables,"Table::deltasq6");
if(tabstyle == LOOKUP) {
- memory->create_kokkos(d_table->e,h_table->e,ntables,tlm1,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,tlm1,"Table::f");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tlm1,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,tlm1,"Table::f");
}
if(tabstyle == LINEAR) {
- memory->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
- memory->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
- memory->create_kokkos(d_table->de,h_table->de,ntables,tlm1,"Table::de");
- memory->create_kokkos(d_table->df,h_table->df,ntables,tlm1,"Table::df");
+ memoryKK->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
+ memoryKK->create_kokkos(d_table->de,h_table->de,ntables,tlm1,"Table::de");
+ memoryKK->create_kokkos(d_table->df,h_table->df,ntables,tlm1,"Table::df");
}
if(tabstyle == SPLINE) {
- memory->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
- memory->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
- memory->create_kokkos(d_table->e2,h_table->e2,ntables,tablength,"Table::e2");
- memory->create_kokkos(d_table->f2,h_table->f2,ntables,tablength,"Table::f2");
+ memoryKK->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
+ memoryKK->create_kokkos(d_table->e2,h_table->e2,ntables,tablength,"Table::e2");
+ memoryKK->create_kokkos(d_table->f2,h_table->f2,ntables,tablength,"Table::f2");
}
if(tabstyle == BITMAP) {
int ntable = 1 << tablength;
- memory->create_kokkos(d_table->rsq,h_table->rsq,ntables,ntable,"Table::rsq");
- memory->create_kokkos(d_table->e,h_table->e,ntables,ntable,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,ntable,"Table::f");
- memory->create_kokkos(d_table->de,h_table->de,ntables,ntable,"Table::de");
- memory->create_kokkos(d_table->df,h_table->df,ntables,ntable,"Table::df");
- memory->create_kokkos(d_table->drsq,h_table->drsq,ntables,ntable,"Table::drsq");
+ memoryKK->create_kokkos(d_table->rsq,h_table->rsq,ntables,ntable,"Table::rsq");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,ntable,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,ntable,"Table::f");
+ memoryKK->create_kokkos(d_table->de,h_table->de,ntables,ntable,"Table::de");
+ memoryKK->create_kokkos(d_table->df,h_table->df,ntables,ntable,"Table::df");
+ memoryKK->create_kokkos(d_table->drsq,h_table->drsq,ntables,ntable,"Table::drsq");
}
@@ -410,8 +410,8 @@ void PairTableKokkos<DeviceType>::allocate()
const int nt = atom->ntypes + 1;
memory->create(setflag,nt,nt,"pair:setflag");
- memory->create_kokkos(d_table->cutsq,h_table->cutsq,cutsq,nt,nt,"pair:cutsq");
- memory->create_kokkos(d_table->tabindex,h_table->tabindex,tabindex,nt,nt,"pair:tabindex");
+ memoryKK->create_kokkos(d_table->cutsq,h_table->cutsq,cutsq,nt,nt,"pair:cutsq");
+ memoryKK->create_kokkos(d_table->tabindex,h_table->tabindex,tabindex,nt,nt,"pair:tabindex");
d_table_const.cutsq = d_table->cutsq;
d_table_const.tabindex = d_table->tabindex;
diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp
index 2f5a670537ce05f528d1c789c3070292cacd8c80..7bc5198d8cef6e8bbfcf40ba24e4d0bb575b9cec 100644
--- a/src/KOKKOS/pair_table_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_table_rx_kokkos.cpp
@@ -27,11 +27,13 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "fix.h"
#include "kokkos_few.h"
+#include "kokkos.h"
+#include "modify.h"
#include <cassert>
using namespace LAMMPS_NS;
@@ -162,12 +164,12 @@ PairTableRXKokkos<DeviceType>::~PairTableRXKokkos()
delete [] site1;
delete [] site2;
- 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(d_table->cutsq, cutsq);
- memory->destroy_kokkos(d_table->tabindex, tabindex);
+ memoryKK->destroy_kokkos(d_table->cutsq, cutsq);
+ memoryKK->destroy_kokkos(d_table->tabindex, tabindex);
}
delete h_table;
@@ -621,13 +623,13 @@ void PairTableRXKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
else evflag = vflag_fdotr = 0;
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>();
}
@@ -798,41 +800,41 @@ void PairTableRXKokkos<DeviceType>::create_kokkos_tables()
{
const int tlm1 = tablength-1;
- memory->create_kokkos(d_table->nshiftbits,h_table->nshiftbits,ntables,"Table::nshiftbits");
- memory->create_kokkos(d_table->nmask,h_table->nmask,ntables,"Table::nmask");
- memory->create_kokkos(d_table->innersq,h_table->innersq,ntables,"Table::innersq");
- memory->create_kokkos(d_table->invdelta,h_table->invdelta,ntables,"Table::invdelta");
- memory->create_kokkos(d_table->deltasq6,h_table->deltasq6,ntables,"Table::deltasq6");
+ memoryKK->create_kokkos(d_table->nshiftbits,h_table->nshiftbits,ntables,"Table::nshiftbits");
+ memoryKK->create_kokkos(d_table->nmask,h_table->nmask,ntables,"Table::nmask");
+ memoryKK->create_kokkos(d_table->innersq,h_table->innersq,ntables,"Table::innersq");
+ memoryKK->create_kokkos(d_table->invdelta,h_table->invdelta,ntables,"Table::invdelta");
+ memoryKK->create_kokkos(d_table->deltasq6,h_table->deltasq6,ntables,"Table::deltasq6");
if(tabstyle == LOOKUP) {
- memory->create_kokkos(d_table->e,h_table->e,ntables,tlm1,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,tlm1,"Table::f");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tlm1,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,tlm1,"Table::f");
}
if(tabstyle == LINEAR) {
- memory->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
- memory->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
- memory->create_kokkos(d_table->de,h_table->de,ntables,tlm1,"Table::de");
- memory->create_kokkos(d_table->df,h_table->df,ntables,tlm1,"Table::df");
+ memoryKK->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
+ memoryKK->create_kokkos(d_table->de,h_table->de,ntables,tlm1,"Table::de");
+ memoryKK->create_kokkos(d_table->df,h_table->df,ntables,tlm1,"Table::df");
}
if(tabstyle == SPLINE) {
- memory->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
- memory->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
- memory->create_kokkos(d_table->e2,h_table->e2,ntables,tablength,"Table::e2");
- memory->create_kokkos(d_table->f2,h_table->f2,ntables,tablength,"Table::f2");
+ memoryKK->create_kokkos(d_table->rsq,h_table->rsq,ntables,tablength,"Table::rsq");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,tablength,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,tablength,"Table::f");
+ memoryKK->create_kokkos(d_table->e2,h_table->e2,ntables,tablength,"Table::e2");
+ memoryKK->create_kokkos(d_table->f2,h_table->f2,ntables,tablength,"Table::f2");
}
if(tabstyle == BITMAP) {
int ntable = 1 << tablength;
- memory->create_kokkos(d_table->rsq,h_table->rsq,ntables,ntable,"Table::rsq");
- memory->create_kokkos(d_table->e,h_table->e,ntables,ntable,"Table::e");
- memory->create_kokkos(d_table->f,h_table->f,ntables,ntable,"Table::f");
- memory->create_kokkos(d_table->de,h_table->de,ntables,ntable,"Table::de");
- memory->create_kokkos(d_table->df,h_table->df,ntables,ntable,"Table::df");
- memory->create_kokkos(d_table->drsq,h_table->drsq,ntables,ntable,"Table::drsq");
+ memoryKK->create_kokkos(d_table->rsq,h_table->rsq,ntables,ntable,"Table::rsq");
+ memoryKK->create_kokkos(d_table->e,h_table->e,ntables,ntable,"Table::e");
+ memoryKK->create_kokkos(d_table->f,h_table->f,ntables,ntable,"Table::f");
+ memoryKK->create_kokkos(d_table->de,h_table->de,ntables,ntable,"Table::de");
+ memoryKK->create_kokkos(d_table->df,h_table->df,ntables,ntable,"Table::df");
+ memoryKK->create_kokkos(d_table->drsq,h_table->drsq,ntables,ntable,"Table::drsq");
}
@@ -943,8 +945,8 @@ void PairTableRXKokkos<DeviceType>::allocate()
const int nt = atom->ntypes + 1;
memory->create(setflag,nt,nt,"pair:setflag");
- memory->create_kokkos(d_table->cutsq,h_table->cutsq,cutsq,nt,nt,"pair:cutsq");
- memory->create_kokkos(d_table->tabindex,h_table->tabindex,tabindex,nt,nt,"pair:tabindex");
+ memoryKK->create_kokkos(d_table->cutsq,h_table->cutsq,cutsq,nt,nt,"pair:cutsq");
+ memoryKK->create_kokkos(d_table->tabindex,h_table->tabindex,tabindex,nt,nt,"pair:tabindex");
d_table_const.cutsq = d_table->cutsq;
d_table_const.tabindex = d_table->tabindex;
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index 3a5c2227efe1b9f71e9b1277096882e86027336e..c585da60297b4a852b50ab19d00a060edaaf6f83 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -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>
PairTersoffKokkos<DeviceType>::~PairTersoffKokkos()
{
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);
}
}
@@ -170,13 +170,13 @@ void PairTersoffKokkos<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>();
}
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index 9a59979f4c9d4d0279f5b830d0e66bcb1af39148..8e718fbf6f16df5017468b116c1b140a82eb0b4c 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -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>
PairTersoffMODKokkos<DeviceType>::~PairTersoffMODKokkos()
{
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);
}
}
@@ -170,13 +170,13 @@ void PairTersoffMODKokkos<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>();
}
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index 8468bb01f5fc545d177ad637de70ae8514087693..11a5ff100753ec02dafa657dd481222bfaf7875c 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -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"
@@ -71,8 +71,8 @@ template<class DeviceType>
PairTersoffZBLKokkos<DeviceType>::~PairTersoffZBLKokkos()
{
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);
}
}
@@ -184,13 +184,13 @@ void PairTersoffZBLKokkos<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>();
}
diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp
index fe2394ae84a9fea6847c5f22eef598c25719b95a..e7dd01bfe4b48e903149db04ab8bb3b7af6cd3b6 100644
--- a/src/KOKKOS/pair_vashishta_kokkos.cpp
+++ b/src/KOKKOS/pair_vashishta_kokkos.cpp
@@ -27,10 +27,10 @@
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "neighbor.h"
#include "neigh_list_kokkos.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "math_const.h"
@@ -62,8 +62,8 @@ template<class DeviceType>
PairVashishtaKokkos<DeviceType>::~PairVashishtaKokkos()
{
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);
eatom = NULL;
vatom = NULL;
}
@@ -85,13 +85,13 @@ void PairVashishtaKokkos<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>();
}
diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..6560ec9684b3f88abb0143aeb39ca791de02affb
--- /dev/null
+++ b/src/KOKKOS/pair_yukawa_kokkos.cpp
@@ -0,0 +1,301 @@
+/* ----------------------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors: Stefan Paquay (Brandeis University)
+------------------------------------------------------------------------- */
+#include <math.h>
+#include <stdlib.h>
+#include "pair_yukawa_kokkos.h"
+#include "kokkos.h"
+#include "atom_kokkos.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "math_const.h"
+#include "memory_kokkos.h"
+#include "error.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define KOKKOS_CUDA_MAX_THREADS 256
+#define KOKKOS_CUDA_MIN_BLOCKS 8
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairYukawaKokkos<DeviceType>::PairYukawaKokkos(LAMMPS *lmp) : PairYukawa(lmp)
+{
+ respa_enable = 0;
+
+ atomKK = (AtomKokkos *) atom;
+ execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+ datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK;
+ datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
+ cutsq = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairYukawaKokkos<DeviceType>::~PairYukawaKokkos()
+{
+ if (allocated) {
+ memoryKK->destroy_kokkos(k_eatom,eatom);
+ memoryKK->destroy_kokkos(k_vatom,vatom);
+ k_cutsq = DAT::tdual_ffloat_2d();
+ memory->sfree(cutsq);
+ eatom = NULL;
+ vatom = NULL;
+ cutsq = NULL;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairYukawaKokkos<DeviceType>::cleanup_copy() {
+ // WHY needed: this prevents parent copy from deallocating any arrays
+ allocated = 0;
+ cutsq = NULL;
+ eatom = NULL;
+ vatom = NULL;
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairYukawaKokkos<DeviceType>::allocate()
+{
+ PairYukawa::allocate();
+
+ int n = atom->ntypes;
+ memory->destroy(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_yukawa**,
+ Kokkos::LayoutRight,DeviceType>(
+ "PairYukawa::params",n+1,n+1);
+
+ params = k_params.template view<DeviceType>();
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairYukawaKokkos<DeviceType>::init_style()
+{
+ PairYukawa::init_style();
+
+ // error if rRESPA with inner levels
+
+ if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
+ int respa = 0;
+ if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+ if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+ if (respa)
+ error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
+ }
+
+ // irequest = neigh request made by parent class
+
+ neighflag = lmp->kokkos->neighflag;
+ int irequest = neighbor->nrequest - 1;
+
+ neighbor->requests[irequest]->
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ !Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+ neighbor->requests[irequest]->
+ kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+
+ if (neighflag == FULL) {
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->half = 0;
+ } else if (neighflag == HALF || neighflag == HALFTHREAD) {
+ neighbor->requests[irequest]->full = 0;
+ neighbor->requests[irequest]->half = 1;
+ } else {
+ error->all(FLERR,"Cannot use chosen neighbor list style with yukawa/kk");
+ }
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+// Rewrite this.
+template<class DeviceType>
+double PairYukawaKokkos<DeviceType>::init_one(int i, int j)
+{
+ double cutone = PairYukawa::init_one(i,j);
+
+ k_params.h_view(i,j).a = a[i][j];
+ k_params.h_view(i,j).offset = offset[i][j];
+ k_params.h_view(i,j).cutsq = cutone*cutone;
+ k_params.h_view(j,i) = k_params.h_view(i,j);
+
+ if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
+ m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
+ m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
+ }
+
+ k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone;
+ k_cutsq.template modify<LMPHostType>();
+ k_params.template modify<LMPHostType>();
+
+ return cutone;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairYukawaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
+{
+ eflag = eflag_in;
+ vflag = vflag_in;
+
+
+ if (neighflag == FULL) no_virial_fdotr_compute = 1;
+
+ if (eflag || vflag) ev_setup(eflag,vflag,0);
+ else evflag = vflag_fdotr = 0;
+
+ // reallocate per-atom arrays if necessary
+
+ if (eflag_atom) {
+ memoryKK->destroy_kokkos(k_eatom,eatom);
+ memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
+ d_eatom = k_eatom.view<DeviceType>();
+ }
+ if (vflag_atom) {
+ memoryKK->destroy_kokkos(k_vatom,vatom);
+ memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
+ d_vatom = k_vatom.view<DeviceType>();
+ }
+
+ atomKK->sync(execution_space,datamask_read);
+ k_cutsq.template sync<DeviceType>();
+ k_params.template sync<DeviceType>();
+ if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
+ else atomKK->modified(execution_space,F_MASK);
+
+ x = atomKK->k_x.view<DeviceType>();
+ c_x = atomKK->k_x.view<DeviceType>();
+ f = atomKK->k_f.view<DeviceType>();
+ type = atomKK->k_type.view<DeviceType>();
+ tag = atomKK->k_tag.view<DeviceType>();
+ nlocal = atom->nlocal;
+ nall = atom->nlocal + atom->nghost;
+ newton_pair = force->newton_pair;
+ special_lj[0] = force->special_lj[0];
+ special_lj[1] = force->special_lj[1];
+ special_lj[2] = force->special_lj[2];
+ special_lj[3] = force->special_lj[3];
+
+ // loop over neighbors of my atoms
+
+ EV_FLOAT ev = pair_compute<PairYukawaKokkos<DeviceType>,void >(
+ this,(NeighListKokkos<DeviceType>*)list);
+
+ if (eflag_global) eng_vdwl += ev.evdwl;
+ if (vflag_global) {
+ virial[0] += ev.v[0];
+ virial[1] += ev.v[1];
+ virial[2] += ev.v[2];
+ virial[3] += ev.v[3];
+ virial[4] += ev.v[4];
+ virial[5] += ev.v[5];
+ }
+
+ if (vflag_fdotr) pair_virial_fdotr_compute(this);
+
+ if (eflag_atom) {
+ k_eatom.template modify<DeviceType>();
+ k_eatom.template sync<LMPHostType>();
+ }
+
+ if (vflag_atom) {
+ k_vatom.template modify<DeviceType>();
+ k_vatom.template sync<LMPHostType>();
+ }
+}
+
+
+
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairYukawaKokkos<DeviceType>::
+compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const {
+ (void) i;
+ (void) j;
+ const F_FLOAT rr = sqrt(rsq);
+ // Fetch the params either off the stack or from some mapped memory?
+ const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].a
+ : params(itype,jtype).a;
+
+ // U = a * exp(-kappa*r) / r
+ // f = (kappa * a * exp(-kappa*r) / r + a*exp(-kappa*r)/r^2)*grad(r)
+ // = (kappa + 1/r) * (a * exp(-kappa*r) / r)
+ // f/r = (kappa + 1/r) * (a * exp(-kappa*r) / r^2)
+ const F_FLOAT rinv = 1.0 / rr;
+ const F_FLOAT rinv2 = rinv*rinv;
+ const F_FLOAT screening = exp(-kappa*rr);
+ const F_FLOAT forceyukawa = aa * screening * (kappa + rinv);
+ const F_FLOAT fpair = forceyukawa * rinv2;
+
+ return fpair;
+}
+
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairYukawaKokkos<DeviceType>::
+compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const {
+ (void) i;
+ (void) j;
+ const F_FLOAT rr = sqrt(rsq);
+ const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].a
+ : params(itype,jtype).a;
+ const F_FLOAT offset = STACKPARAMS ? m_params[itype][jtype].offset
+ : params(itype,jtype).offset;
+
+ // U = a * exp(-kappa*r) / r
+ // f = (kappa * a * exp(-kappa*r) / r + a*exp(-kappa*r)/r^2)*grad(r)
+ // = (kappa + 1/r) * (a * exp(-kappa*r) / r)
+ // f/r = (kappa + 1/r) * (a * exp(-kappa*r) / r^2)
+ const F_FLOAT rinv = 1.0 / rr;
+ const F_FLOAT screening = exp(-kappa*rr);
+
+ return aa * screening * rinv - offset;
+}
+
+
+namespace LAMMPS_NS {
+template class PairYukawaKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class PairYukawaKokkos<LMPHostType>;
+#endif
+}
diff --git a/src/KOKKOS/pair_yukawa_kokkos.h b/src/KOKKOS/pair_yukawa_kokkos.h
new file mode 100644
index 0000000000000000000000000000000000000000..a4c8cf05b781ddbfd7ad65c53eb900aba7e4a9a0
--- /dev/null
+++ b/src/KOKKOS/pair_yukawa_kokkos.h
@@ -0,0 +1,146 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(yukawa/kk,PairYukawaKokkos<LMPDeviceType>)
+PairStyle(yukawa/kk/device,PairYukawaKokkos<LMPDeviceType>)
+PairStyle(yukawa/kk/host,PairYukawaKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_PAIR_YUKAWA_KOKKOS_H
+#define LMP_PAIR_YUKAWA_KOKKOS_H
+
+#include "pair_kokkos.h"
+#include "pair_yukawa.h"
+#include "neigh_list_kokkos.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class PairYukawaKokkos : public PairYukawa {
+ public:
+ enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
+ enum {COUL_FLAG=0};
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ PairYukawaKokkos(class LAMMPS *);
+ virtual ~PairYukawaKokkos();
+
+ void compute(int, int);
+ void init_style();
+ double init_one(int,int);
+
+ struct params_yukawa {
+ KOKKOS_INLINE_FUNCTION
+ params_yukawa(){ cutsq=0, a = 0; offset = 0; }
+ KOKKOS_INLINE_FUNCTION
+ params_yukawa(int i){ cutsq=0, a = 0; offset = 0; }
+ F_FLOAT cutsq, a, offset;
+ };
+
+
+ protected:
+ void cleanup_copy();
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const
+ {
+ return 0;
+ }
+
+
+ Kokkos::DualView<params_yukawa**,Kokkos::LayoutRight,DeviceType> k_params;
+ typename Kokkos::DualView<params_yukawa**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
+ params_yukawa m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ typename AT::t_x_array_randomread x;
+ typename AT::t_x_array c_x;
+ typename AT::t_f_array f;
+ typename AT::t_int_1d_randomread type;
+
+ DAT::tdual_efloat_1d k_eatom;
+ DAT::tdual_virial_array k_vatom;
+ typename AT::t_efloat_1d d_eatom;
+ typename AT::t_virial_array d_vatom;
+ typename AT::t_tagint_1d tag;
+
+ int newton_pair;
+ double special_lj[4];
+
+ typename AT::tdual_ffloat_2d k_cutsq;
+ typename AT::t_ffloat_2d d_cutsq;
+
+
+ int neighflag;
+ int nlocal,nall,eflag,vflag;
+
+ void allocate();
+ friend class PairComputeFunctor<PairYukawaKokkos,FULL,true>;
+ friend class PairComputeFunctor<PairYukawaKokkos,HALF,true>;
+ friend class PairComputeFunctor<PairYukawaKokkos,HALFTHREAD,true>;
+ friend class PairComputeFunctor<PairYukawaKokkos,N2,true>;
+ friend class PairComputeFunctor<PairYukawaKokkos,FULL,false>;
+ friend class PairComputeFunctor<PairYukawaKokkos,HALF,false>;
+ friend class PairComputeFunctor<PairYukawaKokkos,HALFTHREAD,false>;
+ friend class PairComputeFunctor<PairYukawaKokkos,N2,false>;
+ friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,FULL,void>(
+ PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,HALF,void>(
+ PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,HALFTHREAD,void>(
+ PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,N2,void>(
+ PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute<PairYukawaKokkos,void>(
+ PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
+ friend void pair_virial_fdotr_compute<PairYukawaKokkos>(PairYukawaKokkos*);
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: Cannot use chosen neighbor list style with yukawa/kk
+
+That style is not supported by Kokkos.
+
+*/
diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp
index bd3ed3644f53373305a995382144a6d5c27a5432..cf6e2814c0e0bb56f5a19b2a2481ea019259e114 100644
--- a/src/KOKKOS/pppm_kokkos.cpp
+++ b/src/KOKKOS/pppm_kokkos.cpp
@@ -32,9 +32,10 @@
#include "domain.h"
#include "fft3d_wrap.h"
#include "remap_wrap.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
+#include "kokkos.h"
#include "math_const.h"
#include "math_special_kokkos.h"
@@ -162,8 +163,8 @@ PPPMKokkos<DeviceType>::~PPPMKokkos()
//memory->destroy(part2grid);
//memory->destroy(acons);
- 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;
}
@@ -618,13 +619,13 @@ void PPPMKokkos<DeviceType>::compute(int eflag, 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>();
}
@@ -805,12 +806,12 @@ void PPPMKokkos<DeviceType>::allocate()
{
d_density_brick = typename AT::t_FFT_SCALAR_3d("pppm:density_brick",nzhi_out-nzlo_out+1,nyhi_out-nylo_out+1,nxhi_out-nxlo_out+1);
- memory->create_kokkos(k_density_fft,density_fft,nfft_both,"pppm:d_density_fft");
+ memoryKK->create_kokkos(k_density_fft,density_fft,nfft_both,"pppm:d_density_fft");
d_density_fft = k_density_fft.view<DeviceType>();
d_greensfn = typename AT::t_float_1d("pppm:greensfn",nfft_both);
- memory->create_kokkos(k_work1,work1,2*nfft_both,"pppm:work1");
- memory->create_kokkos(k_work2,work2,2*nfft_both,"pppm:work2");
+ memoryKK->create_kokkos(k_work1,work1,2*nfft_both,"pppm:work1");
+ memoryKK->create_kokkos(k_work2,work2,2*nfft_both,"pppm:work2");
d_work1 = k_work1.view<DeviceType>();
d_work2 = k_work2.view<DeviceType>();
d_vg = typename AT::t_virial_array("pppm:vg",nfft_both);
@@ -878,13 +879,13 @@ void PPPMKokkos<DeviceType>::allocate()
template<class DeviceType>
void PPPMKokkos<DeviceType>::deallocate()
{
- memory->destroy_kokkos(d_density_fft,density_fft);
+ memoryKK->destroy_kokkos(d_density_fft,density_fft);
density_fft = NULL;
- memory->destroy_kokkos(d_greensfn,greensfn);
+ memoryKK->destroy_kokkos(d_greensfn,greensfn);
greensfn = NULL;
- memory->destroy_kokkos(d_work1,work1);
+ memoryKK->destroy_kokkos(d_work1,work1);
work1 = NULL;
- memory->destroy_kokkos(d_work2,work2);
+ memoryKK->destroy_kokkos(d_work2,work2);
work2 = NULL;
delete fft1;
@@ -2631,7 +2632,7 @@ void PPPMKokkos<DeviceType>::operator()(TagPPPM_fieldforce_peratom, const int &i
------------------------------------------------------------------------- */
template<class DeviceType>
-void PPPMKokkos<DeviceType>::pack_forward_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
+void PPPMKokkos<DeviceType>::pack_forward_kspace_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
{
typename AT::t_int_2d_um d_list = k_list.view<DeviceType>();
d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL());
@@ -2687,7 +2688,7 @@ void PPPMKokkos<DeviceType>::operator()(TagPPPM_pack_forward2, const int &i) con
------------------------------------------------------------------------- */
template<class DeviceType>
-void PPPMKokkos<DeviceType>::unpack_forward_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
+void PPPMKokkos<DeviceType>::unpack_forward_kspace_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
{
typename AT::t_int_2d_um d_list = k_list.view<DeviceType>();
d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL());
@@ -2744,7 +2745,7 @@ void PPPMKokkos<DeviceType>::operator()(TagPPPM_unpack_forward2, const int &i) c
------------------------------------------------------------------------- */
template<class DeviceType>
-void PPPMKokkos<DeviceType>::pack_reverse_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
+void PPPMKokkos<DeviceType>::pack_reverse_kspace_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
{
typename AT::t_int_2d_um d_list = k_list.view<DeviceType>();
d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL());
@@ -2774,7 +2775,7 @@ void PPPMKokkos<DeviceType>::operator()(TagPPPM_pack_reverse, const int &i) cons
------------------------------------------------------------------------- */
template<class DeviceType>
-void PPPMKokkos<DeviceType>::unpack_reverse_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
+void PPPMKokkos<DeviceType>::unpack_reverse_kspace_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
{
typename AT::t_int_2d_um d_list = k_list.view<DeviceType>();
d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL());
diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h
index 4e6bb1d74c293a74397b94dcc355b2972216186b..c328b488d0260e5e4c45993f6b83ee4846a392e9 100644
--- a/src/KOKKOS/pppm_kokkos.h
+++ b/src/KOKKOS/pppm_kokkos.h
@@ -24,6 +24,7 @@ KSpaceStyle(pppm/kk/host,PPPMKokkos<LMPHostType>)
#include "pppm.h"
#include "gridcomm_kokkos.h"
+#include "kokkos_base.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
@@ -86,7 +87,7 @@ struct TagPPPM_slabcorr4{};
struct TagPPPM_timing_zero{};
template<class DeviceType>
-class PPPMKokkos : public PPPM {
+class PPPMKokkos : public PPPM, public KokkosBase {
public:
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
@@ -379,10 +380,10 @@ class PPPMKokkos : public PPPM {
// grid communication
- virtual void pack_forward_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
- virtual void unpack_forward_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
- virtual void pack_reverse_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
- virtual void unpack_reverse_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
+ void pack_forward_kspace_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
+ void unpack_forward_kspace_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
+ void pack_reverse_kspace_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
+ void unpack_reverse_kspace_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
// triclinic
diff --git a/src/KOKKOS/region_block_kokkos.h b/src/KOKKOS/region_block_kokkos.h
index e14ac4d0c0db75fe98f3e7525f43d8505ab30d7e..532bc588e29746f16a427d44264c39d8f48b0608 100644
--- a/src/KOKKOS/region_block_kokkos.h
+++ b/src/KOKKOS/region_block_kokkos.h
@@ -23,6 +23,7 @@ RegionStyle(block/kk/host,RegBlockKokkos<LMPHostType>)
#define LMP_REGION_BLOCK_KOKKOS_H
#include "region_block.h"
+#include "kokkos_base.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
@@ -30,7 +31,7 @@ namespace LAMMPS_NS {
struct TagRegBlockMatchAll{};
template<class DeviceType>
-class RegBlockKokkos : public RegBlock {
+class RegBlockKokkos : public RegBlock, public KokkosBase {
friend class FixPour;
public:
diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp
index adec5ff1bd9d7520c2c469638d497759375c362a..5fa03a098925430d50f5dd09bc59612398a9d759 100644
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@@ -32,8 +32,9 @@
#include "compute.h"
#include "fix.h"
#include "timer.h"
-#include "memory.h"
+#include "memory_kokkos.h"
#include "error.h"
+#include "kokkos.h"
#include <ctime>
diff --git a/src/Makefile b/src/Makefile
index e0f0db77fe3d5eea0ed95b04541047344919ee45..c3c84b366575930279960c624dec871a42869342 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -17,12 +17,12 @@ SHLINK = liblammps.so
OBJDIR = Obj_$@
OBJSHDIR = Obj_shared_$@
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
+SRC = $(filter-out library.cpp,$(wildcard *.cpp))
+INC = $(filter-out library.h,$(wildcard *.h))
OBJ = $(SRC:.cpp=.o)
-SRCLIB = $(filter-out main.cpp,$(SRC))
-OBJLIB = $(filter-out main.o,$(OBJ))
+SRCLIB = $(filter-out main.cpp,$(SRC)) library.cpp
+OBJLIB = $(filter-out main.o,$(OBJ)) library.o
# Command-line options for mode: exe (default), shexe, lib, shlib
@@ -176,7 +176,7 @@ help:
then cp Makefile.package.settings.empty Makefile.package.settings; fi
@cp Makefile.package Makefile.package.settings $(objdir)
@cd $(objdir); rm -f .depend; \
- $(MAKE) $(MFLAGS) "SRC = $(SRC)" "INC = $(INC)" depend || :
+ $(MAKE) $(MFLAGS) "SRC = $(SRC) library.cpp" "INC = $(INC) library.h" depend || :
ifeq ($(mode),exe)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" "SHFLAGS =" \
diff --git a/src/Purge.list b/src/Purge.list
index e4a9e46309188b75307d1bfe43fe25a95ef0d5f6..d4a824b36c1317d477ec0813847f92cb4dfa3cff 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -19,6 +19,9 @@ style_neigh_stencil.h
# deleted on 15 December 2017
fix_python.cpp
fix_python.h
+# deleted on 1 December 2017
+npair_half_bin_newtoff_intel.cpp
+npair_half_bin_newtoff_intel.h
# deleted on 11 October 2017
fix_shear_history_omp.cpp
fix_shear_history_omp.h
diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
index 4163a816ac9bcd8662fd25facb1200019071cd76..f78ced3d8bd96caaa35798db21f1bce5f19a05e2 100644
--- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
+++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
@@ -32,6 +32,8 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
+#include "modify.h"
+#include "domain.h"
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp
index abb37b82b766581aafadb5519f76169ca8289491..ace119ce523892b0ad7a8d52c0288f0bc0f725b4 100644
--- a/src/USER-DRUDE/pair_thole.cpp
+++ b/src/USER-DRUDE/pair_thole.cpp
@@ -25,6 +25,8 @@
#include "error.h"
#include "fix.h"
#include "fix_store.h"
+#include "domain.h"
+#include "modify.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp
index 031c9642000c22a6aa7f4156db319de5409fce6e..bcaecb4696fa1d93e277d473e931b268298c5153 100644
--- a/src/USER-INTEL/angle_charmm_intel.cpp
+++ b/src/USER-INTEL/angle_charmm_intel.cpp
@@ -23,6 +23,7 @@
#include "domain.h"
#include "comm.h"
#include "force.h"
+#include "modify.h"
#include "math_const.h"
#include "memory.h"
#include "suffix.h"
diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp
index 84220277d7a736131c30fa37d79fd93364e0c4ca..ffc81c496d77c654f35d6f0e1ad71a39a06844ee 100644
--- a/src/USER-INTEL/angle_harmonic_intel.cpp
+++ b/src/USER-INTEL/angle_harmonic_intel.cpp
@@ -23,6 +23,7 @@
#include "domain.h"
#include "comm.h"
#include "force.h"
+#include "modify.h"
#include "math_const.h"
#include "memory.h"
#include "suffix.h"
diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp
index 93d64ed631f5466baec735c52a2770160b2eb8fb..004a2e5413d6d566cb536b9d4290e80540315e81 100644
--- a/src/USER-INTEL/bond_fene_intel.cpp
+++ b/src/USER-INTEL/bond_fene_intel.cpp
@@ -19,6 +19,7 @@
#include <stdlib.h>
#include "bond_fene_intel.h"
#include "atom.h"
+#include "modify.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp
index 0ac466f11386c99bef29b95a33e086349389239c..0c714edc0959519621b624d19dd6e79b5b081977 100644
--- a/src/USER-INTEL/bond_harmonic_intel.cpp
+++ b/src/USER-INTEL/bond_harmonic_intel.cpp
@@ -19,6 +19,7 @@
#include <stdlib.h>
#include "bond_harmonic_intel.h"
#include "atom.h"
+#include "modify.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/USER-INTEL/dihedral_charmm_intel.cpp
index 0e13e92251594d04348d98f2200c3501a5b29fd5..c8429dc8ff7079930f00459c33ad85674ebaf222 100644
--- a/src/USER-INTEL/dihedral_charmm_intel.cpp
+++ b/src/USER-INTEL/dihedral_charmm_intel.cpp
@@ -21,6 +21,7 @@
#include "atom.h"
#include "comm.h"
#include "memory.h"
+#include "modify.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp
index 805ffc0e256177f294bc8f2b118e778c4cd7054e..772ea5b02fdf4a84838bd7a59a90def0b8a3d107 100644
--- a/src/USER-INTEL/dihedral_fourier_intel.cpp
+++ b/src/USER-INTEL/dihedral_fourier_intel.cpp
@@ -21,6 +21,7 @@
#include "atom.h"
#include "comm.h"
#include "memory.h"
+#include "modify.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp
index 5d16b0da745425abd66617ab50043ef796d78db3..b35ea4e03a9b67a3b619028c0c559b304cbbaf07 100644
--- a/src/USER-INTEL/dihedral_harmonic_intel.cpp
+++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp
@@ -21,6 +21,7 @@
#include "atom.h"
#include "comm.h"
#include "memory.h"
+#include "modify.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp
index e290ab90616b94df0135264dcbbf66fe8546a36a..6b7b2c81ebd75bace530cbde5dd9bee1f0981c57 100644
--- a/src/USER-INTEL/dihedral_opls_intel.cpp
+++ b/src/USER-INTEL/dihedral_opls_intel.cpp
@@ -21,6 +21,7 @@
#include "atom.h"
#include "comm.h"
#include "memory.h"
+#include "modify.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index eac48b8510b4aa67a5e93f689ae1381510e02b57..3e36c8f7a937b0e254389c4099897a62aa9ac236 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -32,6 +32,7 @@
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
+#include <math.h>
#ifdef _LMP_INTEL_OFFLOAD
#ifndef INTEL_OFFLOAD_NOAFFINITY
diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp
index 3a36ead499ebe34a1dfcce5350abbd1f13fb8d6b..9a1dae36ca465b08d8cbbf63407597306b810553 100644
--- a/src/USER-INTEL/nbin_intel.cpp
+++ b/src/USER-INTEL/nbin_intel.cpp
@@ -18,8 +18,9 @@
#include "nbin_intel.h"
#include "atom.h"
#include "group.h"
-#include "domain.h"
#include "comm.h"
+#include "domain.h"
+#include "modify.h"
#include "update.h"
#include "error.h"
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
index e6d45d7b2c6941fa87c24cd089ee46863b4828ee..a814891f2599ad73fcac0d8db7064e56ce173168 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
@@ -21,6 +21,8 @@
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
+#include "comm.h"
+#include "domain.h"
#include "molecule.h"
#include "error.h"
diff --git a/src/USER-INTEL/npair_full_bin_intel.cpp b/src/USER-INTEL/npair_full_bin_intel.cpp
index 06c10c080fd9e506760c0d1e66c93ff76233ee7c..60b912d796146d2c9a7f7a15d116afdc430c20ff 100644
--- a/src/USER-INTEL/npair_full_bin_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_intel.cpp
@@ -20,6 +20,7 @@
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
+#include "domain.h"
#include "group.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_intel.cpp
index c761557097cf96b677dc20a355a94e186ac5d8c5..8c024a46046827985db3f8047446ad06df61eba1 100644
--- a/src/USER-INTEL/npair_half_bin_newton_intel.cpp
+++ b/src/USER-INTEL/npair_half_bin_newton_intel.cpp
@@ -20,6 +20,7 @@
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
+#include "domain.h"
#include "group.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
index d70f1ec5897a0d7b1e8a7b5b9633f9882ce2c54f..653a95139498dbe1d34b5c8d77ca706664e02c56 100644
--- a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
+++ b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
@@ -20,6 +20,7 @@
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
+#include "domain.h"
#include "group.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
index 0068e02635c7d6d7bd145fe45a35bade50f64f0c..234557c941c1ce7d765e745fb918d6a42297c033 100644
--- a/src/USER-INTEL/npair_intel.cpp
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -15,6 +15,10 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
+#include "comm.h"
+#include "domain.h"
+#include "timer.h"
+#include "modify.h"
#include "npair_intel.h"
#include "nstencil.h"
diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp
index b97128bf9ff434fbc71c02d204c25128e9583a20..ea4ee30d52602440b06b81603a3d93897b72cba3 100644
--- a/src/USER-INTEL/pair_eam_intel.cpp
+++ b/src/USER-INTEL/pair_eam_intel.cpp
@@ -23,6 +23,7 @@
#include "atom.h"
#include "force.h"
#include "comm.h"
+#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp
index 1269579ff4f26addaa08d00c19ff433626d5a089..bd41f8b531cc18be1e6cf79376de773a52c9d7c3 100644
--- a/src/USER-INTEL/pppm_disp_intel.cpp
+++ b/src/USER-INTEL/pppm_disp_intel.cpp
@@ -20,7 +20,10 @@
#include <math.h>
#include "pppm_disp_intel.h"
#include "atom.h"
+#include "comm.h"
+#include "domain.h"
#include "error.h"
+#include "modify.h"
#include "fft3d_wrap.h"
#include "gridcomm.h"
#include "math_const.h"
diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp
index db855b75ef8f877303ae6186e12fc59314729397..30f8f4c5c0677890115a5f5668a557f2053bb054 100644
--- a/src/USER-INTEL/pppm_intel.cpp
+++ b/src/USER-INTEL/pppm_intel.cpp
@@ -23,7 +23,10 @@
#include <math.h>
#include "pppm_intel.h"
#include "atom.h"
+#include "comm.h"
+#include "domain.h"
#include "error.h"
+#include "modify.h"
#include "fft3d_wrap.h"
#include "gridcomm.h"
#include "math_const.h"
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 5af5b22eb7889609834a4449bb5a118e75789c86..a8c33fa38056454194ff2346c9bd2d4822019200 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -63,6 +63,7 @@ pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09
+pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..cf859a28f8380fbfb65dd2b72092486f7d5941f3
--- /dev/null
+++ b/src/USER-MISC/pair_extep.cpp
@@ -0,0 +1,1189 @@
+/* ----------------------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Jan Los
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_extep.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "my_page.h"
+#include "force.h"
+#include "comm.h"
+#include "memory.h"
+#include "error.h"
+
+#include "math_const.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define MAXLINE 1024
+#define DELTA 4
+#define PGDELTA 1
+
+/* ---------------------------------------------------------------------- */
+
+PairExTeP::PairExTeP(LAMMPS *lmp) : Pair(lmp)
+{
+ single_enable = 0;
+ restartinfo = 0;
+ one_coeff = 1;
+ manybody_flag = 1;
+ ghostneigh = 1;
+
+ nelements = 0;
+ elements = NULL;
+ nparams = maxparam = 0;
+ params = NULL;
+ elem2param = NULL;
+
+ maxlocal = 0;
+ SR_numneigh = NULL;
+ SR_firstneigh = NULL;
+ ipage = NULL;
+ pgsize = oneatom = 0;
+ map = NULL;
+
+ Nt = NULL;
+ Nd = NULL;
+}
+
+/* ----------------------------------------------------------------------
+ check if allocated, since class can be destructed when incomplete
+------------------------------------------------------------------------- */
+
+PairExTeP::~PairExTeP()
+{
+ if (elements)
+ for (int i = 0; i < nelements; i++) delete [] elements[i];
+ delete [] elements;
+ memory->destroy(params);
+ memory->destroy(elem2param);
+
+ memory->destroy(SR_numneigh);
+ memory->sfree(SR_firstneigh);
+ delete [] ipage;
+ memory->destroy(Nt);
+ memory->destroy(Nd);
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ memory->destroy(cutghost);
+ delete [] map;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ create SR neighbor list from main neighbor list
+ SR neighbor list stores neighbors of ghost atoms
+------------------------------------------------------------------------- */
+
+void PairExTeP::SR_neigh()
+{
+ int i,j,ii,jj,n,allnum,jnum,itype,jtype,iparam_ij;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ int *neighptr;
+
+ double **x = atom->x;
+ int *type = atom->type;
+
+ if (atom->nmax > maxlocal) { // ensure there is enough space
+ maxlocal = atom->nmax; // for atoms and ghosts allocated
+ memory->destroy(SR_numneigh);
+ memory->sfree(SR_firstneigh);
+ memory->destroy(Nt);
+ memory->destroy(Nd);
+ memory->create(SR_numneigh,maxlocal,"ExTeP:numneigh");
+ SR_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),
+ "ExTeP:firstneigh");
+ memory->create(Nt,maxlocal,"ExTeP:Nt");
+ memory->create(Nd,maxlocal,"ExTeP:Nd");
+ }
+
+ allnum = list->inum + list->gnum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // store all SR neighs of owned and ghost atoms
+ // scan full neighbor list of I
+
+ ipage->reset();
+
+ for (ii = 0; ii < allnum; ii++) {
+ i = ilist[ii];
+ itype=map[type[i]];
+
+ n = 0;
+ neighptr = ipage->vget();
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+ Nt[i] = 0.0;
+ Nd[i] = 0.0;
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ jtype=map[type[j]];
+ iparam_ij = elem2param[itype][jtype][jtype];
+
+ if (rsq < params[iparam_ij].cutsq) {
+ neighptr[n++] = j;
+ double tmp_fc = ters_fc(sqrt(rsq),¶ms[iparam_ij]);
+ Nt[i] += tmp_fc;
+ if (itype!=jtype) {
+ Nd[i] += tmp_fc;
+ }
+ }
+ }
+ //printf("SR_neigh : N[%d] = %f\n",i,N[i]);
+
+ ipage->vgot(n);
+ if (ipage->status())
+ error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
+ }
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void PairExTeP::compute(int eflag, int vflag)
+{
+ int i,j,k,ii,jj,kk,inum,jnum;
+ int itype,jtype,ktype,iparam_ij,iparam_ijk;
+ tagint itag,jtag;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+ double rsq,rsq1,rsq2,r2;
+ double delr1[3],delr2[3],fi[3],fj[3],fk[3];
+ double zeta_ij,prefactor;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = vflag_atom = 0;
+
+ SR_neigh();
+
+ double **x = atom->x;
+ double **f = atom->f;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over full neighbor list of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itag = tag[i];
+ itype = map[type[i]];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+ // two-body interactions, skip half of them
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ jtag = tag[j];
+
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < x[i][2]) continue;
+ if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
+ if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+
+ jtype = map[type[j]];
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ iparam_ij = elem2param[itype][jtype][jtype];
+ if (rsq > params[iparam_ij].cutsq) continue;
+
+ repulsive(¶ms[iparam_ij],rsq,fpair,eflag,evdwl);
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,fpair,delx,dely,delz);
+ }
+
+ // three-body interactions -(bij + Fcorrection) * fA
+ // skip immediately if I-J is not within cutoff
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ jtag = tag[j];
+ jtype = map[type[j]];
+ iparam_ij = elem2param[itype][jtype][jtype];
+
+ delr1[0] = x[j][0] - xtmp;
+ delr1[1] = x[j][1] - ytmp;
+ delr1[2] = x[j][2] - ztmp;
+ rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
+ if (rsq1 > params[iparam_ij].cutsq) continue;
+
+ // accumulate bondorder zeta for each i-j interaction via loop over k
+
+ zeta_ij = 0.0;
+
+ /* F_IJ (1) */
+ // compute correction to energy and forces
+ // dE/dr = -Fij(Zi,Zj) dV/dr
+ // - dFij/dZi dZi/dr V
+ // (conjugate term is computed when j is a central atom)
+
+ double FXY, dFXY_dNdij, dFXY_dNdji, fa, fa_d, deng, fpair;
+ double Ntij = Nt[i];
+ double Ndij = Nd[i];
+ double Ntji = Nt[j];
+ double Ndji = Nd[j];
+ double r = sqrt(rsq1);
+ double fc_ij = ters_fc(r,¶ms[iparam_ij]);
+
+ Ntij -= fc_ij;
+ Ntji -= fc_ij;
+ if (jtype!=itype) {
+ Ndij -= fc_ij;
+ Ndji -= fc_ij;
+ }
+ if (Ntij<0) { Ntij=0.; }
+ if (Ndij<0) { Ndij=0.; }
+ if (Ntji<0) { Ntji=0.; }
+ if (Ndji<0) { Ndji=0.; }
+ FXY = F_corr(itype, jtype, Ndij, Ndji, &dFXY_dNdij, &dFXY_dNdji);
+
+ // envelop functions
+ double fenv, dfenv_ij;
+ fenv = envelop_function(Ntij, Ntji, &dfenv_ij);
+ //
+ double Fc = fenv * FXY;
+ double dFc_dNtij = dfenv_ij * FXY;
+ double dFc_dNdij = fenv * dFXY_dNdij;
+
+ fa = ters_fa(r,¶ms[iparam_ij]);
+ fa_d = ters_fa_d(r,¶ms[iparam_ij]);
+ deng = 0.5 * fa * Fc;
+ fpair = 0.5 * fa_d * Fc / r;
+
+ f[i][0] += delr1[0]*fpair;
+ f[i][1] += delr1[1]*fpair;
+ f[i][2] += delr1[2]*fpair;
+ f[j][0] -= delr1[0]*fpair;
+ f[j][1] -= delr1[1]*fpair;
+ f[j][2] -= delr1[2]*fpair;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ deng,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
+ /* END F_IJ (1) */
+
+ for (kk = 0; kk < jnum; kk++) {
+ if (jj == kk) continue;
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
+
+ r2 = sqrt(rsq2);
+
+ zeta_ij += zeta(¶ms[iparam_ijk],r,r2,delr1,delr2);
+
+ /* F_IJ (2) */
+ // compute force components due to spline derivatives
+ // uses only the part with FXY_x (FXY_y is done when i and j are inversed)
+ int iparam_ik = elem2param[itype][ktype][0];
+ double fc_ik_d = ters_fc_d(r2,¶ms[iparam_ik]);
+ double fc_prefac_ik_0 = 1.0 * fc_ik_d * fa / r2;
+ double fc_prefac_ik = dFc_dNtij * fc_prefac_ik_0;
+ f[i][0] += fc_prefac_ik * delr2[0];
+ f[i][1] += fc_prefac_ik * delr2[1];
+ f[i][2] += fc_prefac_ik * delr2[2];
+ f[k][0] -= fc_prefac_ik * delr2[0];
+ f[k][1] -= fc_prefac_ik * delr2[1];
+ f[k][2] -= fc_prefac_ik * delr2[2];
+ if ( itype != ktype ) {
+ fc_prefac_ik = dFc_dNdij * fc_prefac_ik_0;
+ f[i][0] += fc_prefac_ik * delr2[0];
+ f[i][1] += fc_prefac_ik * delr2[1];
+ f[i][2] += fc_prefac_ik * delr2[2];
+ f[k][0] -= fc_prefac_ik * delr2[0];
+ f[k][1] -= fc_prefac_ik * delr2[1];
+ f[k][2] -= fc_prefac_ik * delr2[2];
+ }
+ /* END F_IJ (2) */
+
+ }
+
+ // pairwise force due to zeta
+
+ force_zeta(¶ms[iparam_ij],r,zeta_ij,fpair,prefactor,eflag,evdwl);
+
+ f[i][0] += delr1[0]*fpair;
+ f[i][1] += delr1[1]*fpair;
+ f[i][2] += delr1[2]*fpair;
+ f[j][0] -= delr1[0]*fpair;
+ f[j][1] -= delr1[1]*fpair;
+ f[j][2] -= delr1[2]*fpair;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
+
+ // attractive term via loop over k
+
+ for (kk = 0; kk < jnum; kk++) {
+ if (jj == kk) continue;
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[iparam_ijk].cutsq) continue;
+
+ attractive(¶ms[iparam_ijk],prefactor,
+ rsq1,rsq2,delr1,delr2,fi,fj,fk);
+
+
+ f[i][0] += fi[0];
+ f[i][1] += fi[1];
+ f[i][2] += fi[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ f[k][0] += fk[0];
+ f[k][1] += fk[1];
+ f[k][2] += fk[2];
+
+ if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairExTeP::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+ memory->create(cutghost,n+1,n+1,"pair:cutghost");
+
+ map = new int[n+1];
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairExTeP::settings(int narg, char **arg)
+{
+ if (narg != 0) error->all(FLERR,"Illegal pair_style command");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairExTeP::coeff(int narg, char **arg)
+{
+ int i,j,n;
+
+ if (!allocated) allocate();
+
+ if (narg != 3 + atom->ntypes)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+
+ // insure I,J args are * *
+
+ if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+
+ // read args that map atom types to elements in potential file
+ // map[i] = which element the Ith atom type is, -1 if NULL
+ // nelements = # of unique elements
+ // elements = list of element names
+
+ if (elements) {
+ for (i = 0; i < nelements; i++) delete [] elements[i];
+ delete [] elements;
+ }
+ elements = new char*[atom->ntypes];
+ for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
+
+ nelements = 0;
+ for (i = 3; i < narg; i++) {
+ if (strcmp(arg[i],"NULL") == 0) {
+ map[i-2] = -1;
+ continue;
+ }
+ for (j = 0; j < nelements; j++)
+ if (strcmp(arg[i],elements[j]) == 0) break;
+ map[i-2] = j;
+ if (j == nelements) {
+ n = strlen(arg[i]) + 1;
+ elements[j] = new char[n];
+ strcpy(elements[j],arg[i]);
+ nelements++;
+ }
+ }
+
+ // read potential file and initialize potential parameters
+
+ read_file(arg[2]);
+ spline_init();
+ setup();
+
+ // clear setflag since coeff() called once with I,J = * *
+
+ n = atom->ntypes;
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ // set setflag i,j for type pairs where both are mapped to elements
+
+ int count = 0;
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ if (map[i] >= 0 && map[j] >= 0) {
+ setflag[i][j] = 1;
+ count++;
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairExTeP::init_style()
+{
+ if (atom->tag_enable == 0)
+ error->all(FLERR,"Pair style ExTeP requires atom IDs");
+ if (force->newton_pair == 0)
+ error->all(FLERR,"Pair style ExTeP requires newton pair on");
+
+ // need a full neighbor list
+
+ int irequest = neighbor->request(this);
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+
+ // including neighbors of ghosts
+ neighbor->requests[irequest]->ghost = 1;
+
+ // create pages if first time or if neighbor pgsize/oneatom has changed
+
+ int create = 0;
+ if (ipage == NULL) create = 1;
+ if (pgsize != neighbor->pgsize) create = 1;
+ if (oneatom != neighbor->oneatom) create = 1;
+
+ if (create) {
+ delete [] ipage;
+ pgsize = neighbor->pgsize;
+ oneatom = neighbor->oneatom;
+
+ int nmypage= comm->nthreads;
+ ipage = new MyPage<int>[nmypage];
+ for (int i = 0; i < nmypage; i++)
+ ipage[i].init(oneatom,pgsize,PGDELTA);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairExTeP::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+ cutghost[i][j] = cutmax ;
+ cutghost[j][i] = cutghost[i][j];
+
+ return cutmax;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairExTeP::read_file(char *file)
+{
+ int params_per_line = 17;
+ char **words = new char*[params_per_line+1];
+
+ memory->sfree(params);
+ params = NULL;
+ nparams = maxparam = 0;
+
+ // open file on proc 0
+
+ FILE *fp;
+ if (comm->me == 0) {
+ fp = force->open_potential(file);
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open ExTeP potential file %s",file);
+ error->one(FLERR,str);
+ }
+ }
+
+ // read each line out of file, skipping blank lines or leading '#'
+ // store line of params if all 3 element tags are in element list
+
+ int n,nwords,ielement,jelement,kelement;
+ char line[MAXLINE],*ptr;
+ int eof = 0;
+
+ while (1) {
+ if (comm->me == 0) {
+ ptr = fgets(line,MAXLINE,fp);
+ if (ptr == NULL) {
+ eof = 1;
+ fclose(fp);
+ } else n = strlen(line) + 1;
+ }
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
+ if (eof) break;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+
+ // strip comment, skip line if blank
+
+ if ((ptr = strchr(line,'#'))) *ptr = '\0';
+ nwords = atom->count_words(line);
+ if (nwords == 0) continue;
+
+ // concatenate additional lines until have params_per_line words
+
+ while (nwords < params_per_line) {
+ n = strlen(line);
+ if (comm->me == 0) {
+ ptr = fgets(&line[n],MAXLINE-n,fp);
+ if (ptr == NULL) {
+ eof = 1;
+ fclose(fp);
+ } else n = strlen(line) + 1;
+ }
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
+ if (eof) break;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+ if ((ptr = strchr(line,'#'))) *ptr = '\0';
+ nwords = atom->count_words(line);
+ }
+
+ if (nwords != params_per_line)
+ error->all(FLERR,"Insufficient spline parameters in potential file");
+
+ // words = ptrs to all words in line
+
+ nwords = 0;
+ words[nwords++] = strtok(line," \t\n\r\f");
+ while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
+
+ // ielement,jelement,kelement = 1st args
+ // if all 3 args are in element list, then parse this line
+ // else skip to next line
+
+ for (ielement = 0; ielement < nelements; ielement++)
+ if (strcmp(words[0],elements[ielement]) == 0) break;
+ if (ielement == nelements) continue;
+ for (jelement = 0; jelement < nelements; jelement++)
+ if (strcmp(words[1],elements[jelement]) == 0) break;
+ if (jelement == nelements) continue;
+ for (kelement = 0; kelement < nelements; kelement++)
+ if (strcmp(words[2],elements[kelement]) == 0) break;
+ if (kelement == nelements) continue;
+
+ // load up parameter settings and error check their values
+
+ if (nparams == maxparam) {
+ maxparam += DELTA;
+ params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
+ "pair:params");
+ }
+
+ params[nparams].ielement = ielement;
+ params[nparams].jelement = jelement;
+ params[nparams].kelement = kelement;
+ params[nparams].powerm = atof(words[3]);
+ params[nparams].gamma = atof(words[4]);
+ params[nparams].lam3 = atof(words[5]);
+ params[nparams].c = atof(words[6]);
+ params[nparams].d = atof(words[7]);
+ params[nparams].h = atof(words[8]);
+ params[nparams].powern = atof(words[9]);
+ params[nparams].beta = atof(words[10]);
+ params[nparams].lam2 = atof(words[11]);
+ params[nparams].bigb = atof(words[12]);
+ params[nparams].bigr = atof(words[13]);
+ params[nparams].bigd = atof(words[14]);
+ params[nparams].lam1 = atof(words[15]);
+ params[nparams].biga = atof(words[16]);
+
+ // currently only allow m exponent of 1 or 3
+
+ params[nparams].powermint = int(params[nparams].powerm);
+
+ if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
+ params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
+ params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
+ params[nparams].bigr < 0.0 ||params[nparams].bigd < 0.0 ||
+ params[nparams].bigd > params[nparams].bigr ||
+ params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0 ||
+ params[nparams].powerm - params[nparams].powermint != 0.0 ||
+ (params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
+ params[nparams].gamma < 0.0)
+ error->all(FLERR,"Illegal ExTeP parameter");
+
+ nparams++;
+ if (nparams >= pow(atom->ntypes,3)) break;
+ }
+
+ // deallocate words array
+ delete [] words;
+
+ /* F_IJ (3) */
+ // read the spline coefficients
+ params_per_line = 8;
+ // reallocate with new size
+ words = new char*[params_per_line+1];
+
+ // intialize F_corr_data to all zeros
+ for (int iel=0;iel<atom->ntypes;iel++)
+ for (int jel=0;jel<atom->ntypes;jel++)
+ for (int in=0;in<4;in++)
+ for (int jn=0;jn<4;jn++)
+ for (int ivar=0;ivar<3;ivar++)
+ F_corr_data[iel][jel][in][jn][ivar]=0;
+
+ // loop until EOF
+ while (1) {
+ if (comm->me == 0) {
+ ptr = fgets(line,MAXLINE,fp);
+ //fputs(line,stdout);
+ if (ptr == NULL) {
+ eof = 1;
+ fclose(fp);
+ } else n = strlen(line) + 1;
+ }
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
+ if (eof) break;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+
+ // strip comment, skip line if blank
+
+ if ((ptr = strchr(line,'#'))) *ptr = '\0';
+ nwords = atom->count_words(line);
+ if (nwords == 0) continue;
+
+ if (nwords != params_per_line)
+ error->all(FLERR,"Incorrect format in ExTeP potential file");
+
+ // words = ptrs to all words in line
+
+ nwords = 0;
+ words[nwords++] = strtok(line," \t\n\r\f");
+ while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
+
+ // ielement,jelement = 1st args
+ // if all 3 args are in element list, then parse this line
+ // else skip to next line
+ // these lines set ielement and jelement to the
+ // integers matching the strings from the input
+
+ for (ielement = 0; ielement < nelements; ielement++)
+ if (strcmp(words[0],elements[ielement]) == 0) break;
+ if (ielement == nelements) continue;
+ for (jelement = 0; jelement < nelements; jelement++)
+ if (strcmp(words[1],elements[jelement]) == 0) break;
+ if (jelement == nelements) continue;
+
+ int Ni = atoi(words[2]);
+ int Nj = atoi(words[3]);
+ double spline_val = atof(words[4]);
+ double spline_derx = atof(words[5]);
+ double spline_dery = atof(words[6]);
+
+ // Set value for all pairs of ielement,jelement (any kelement)
+ for (int iparam = 0; iparam < nparams; iparam++) {
+ if ( ielement == params[iparam].ielement
+ && jelement == params[iparam].jelement) {
+ F_corr_data[ielement][jelement][Ni][Nj][0] = spline_val;
+ F_corr_data[ielement][jelement][Ni][Nj][1] = spline_derx;
+ F_corr_data[ielement][jelement][Ni][Nj][2] = spline_dery;
+
+ F_corr_data[jelement][ielement][Nj][Ni][0] = spline_val;
+ F_corr_data[jelement][ielement][Nj][Ni][1] = spline_dery;
+ F_corr_data[jelement][ielement][Nj][Ni][2] = spline_derx;
+ }
+ }
+ }
+
+ delete [] words;
+ /* END F_IJ (3) */
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairExTeP::setup()
+{
+ int i,j,k,m,n;
+
+ // set elem2param for all element triplet combinations
+ // must be a single exact match to lines read from file
+ // do not allow for ACB in place of ABC
+
+ memory->destroy(elem2param);
+ memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
+
+ for (i = 0; i < nelements; i++)
+ for (j = 0; j < nelements; j++)
+ for (k = 0; k < nelements; k++) {
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ if (i == params[m].ielement && j == params[m].jelement &&
+ k == params[m].kelement) {
+ if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+ n = m;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
+ }
+
+ // compute parameter values derived from inputs
+
+ for (m = 0; m < nparams; m++) {
+ params[m].cut = params[m].bigr + params[m].bigd;
+ params[m].cutsq = params[m].cut*params[m].cut;
+
+ params[m].c1 = pow(2.0*params[m].powern*1.0e-16,-1.0/params[m].powern);
+ params[m].c2 = pow(2.0*params[m].powern*1.0e-8,-1.0/params[m].powern);
+ params[m].c3 = 1.0/params[m].c2;
+ params[m].c4 = 1.0/params[m].c1;
+ }
+
+ // set cutmax to max of all params
+
+ cutmax = 0.0;
+ for (m = 0; m < nparams; m++)
+ if (params[m].cut > cutmax) cutmax = params[m].cut;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairExTeP::repulsive(Param *param, double rsq, double &fforce,
+ int eflag, double &eng)
+{
+ double r,tmp_fc,tmp_fc_d,tmp_exp;
+
+ r = sqrt(rsq);
+ tmp_fc = ters_fc(r,param);
+ tmp_fc_d = ters_fc_d(r,param);
+ tmp_exp = exp(-param->lam1 * r);
+ fforce = -param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1) / r;
+ if (eflag) eng = tmp_fc * param->biga * tmp_exp;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairExTeP::zeta(Param *param, double rij, double rik,
+ double *delrij, double *delrik)
+{
+ double costheta,arg,ex_delr;
+
+ costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
+ delrij[2]*delrik[2]) / (rij*rik);
+
+ if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
+ else arg = param->lam3 * (rij-rik);
+
+ if (arg > 69.0776) ex_delr = 1.e30;
+ else if (arg < -69.0776) ex_delr = 0.0;
+ else ex_delr = exp(arg);
+
+ return ters_fc(rik,param) * ters_gijk(costheta,param) * ex_delr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairExTeP::force_zeta(Param *param, double r, double zeta_ij,
+ double &fforce, double &prefactor,
+ int eflag, double &eng)
+{
+ double fa,fa_d,bij;
+
+ fa = ters_fa(r,param);
+ fa_d = ters_fa_d(r,param);
+ bij = ters_bij(zeta_ij,param);
+ fforce = 0.5*bij*fa_d / r;
+ prefactor = -0.5*fa * ( ters_bij_d(zeta_ij,param) );
+ if (eflag) eng = 0.5*bij*fa;
+}
+
+/* ----------------------------------------------------------------------
+ attractive term
+ use param_ij cutoff for rij test
+ use param_ijk cutoff for rik test
+------------------------------------------------------------------------- */
+
+void PairExTeP::attractive(Param *param, double prefactor,
+ double rsqij, double rsqik,
+ double *delrij, double *delrik,
+ double *fi, double *fj, double *fk)
+{
+ double rij_hat[3],rik_hat[3];
+ double rij,rijinv,rik,rikinv;
+
+ rij = sqrt(rsqij);
+ rijinv = 1.0/rij;
+ vec3_scale(rijinv,delrij,rij_hat);
+
+ rik = sqrt(rsqik);
+ rikinv = 1.0/rik;
+ vec3_scale(rikinv,delrik,rik_hat);
+
+ ters_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,fi,fj,fk,param);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairExTeP::ters_fc(double r, Param *param)
+{
+ double ters_R = param->bigr;
+ double ters_D = param->bigd;
+
+ if (r < ters_R-ters_D) return 1.0;
+ if (r > ters_R+ters_D) return 0.0;
+ return 0.5*(1.0 - sin(MY_PI2*(r - ters_R)/ters_D));
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairExTeP::ters_fc_d(double r, Param *param)
+{
+ double ters_R = param->bigr;
+ double ters_D = param->bigd;
+
+ if (r < ters_R-ters_D) return 0.0;
+ if (r > ters_R+ters_D) return 0.0;
+ return -(MY_PI4/ters_D) * cos(MY_PI2*(r - ters_R)/ters_D);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairExTeP::ters_fa(double r, Param *param)
+{
+ if (r > param->bigr + param->bigd) return 0.0;
+ return -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairExTeP::ters_fa_d(double r, Param *param)
+{
+ if (r > param->bigr + param->bigd) return 0.0;
+ return param->bigb * exp(-param->lam2 * r) *
+ (param->lam2 * ters_fc(r,param) - ters_fc_d(r,param));
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairExTeP::ters_bij(double zeta, Param *param)
+{
+ double tmp = param->beta * zeta;
+ if (tmp > param->c1) return 1.0/sqrt(tmp);
+ if (tmp > param->c2)
+ return (1.0 - pow(tmp,-param->powern) / (2.0*param->powern))/sqrt(tmp);
+ if (tmp < param->c4) return 1.0;
+ if (tmp < param->c3)
+ return 1.0 - pow(tmp,param->powern)/(2.0*param->powern);
+ return pow(1.0 + pow(tmp,param->powern), -1.0/(2.0*param->powern));
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairExTeP::ters_bij_d(double zeta, Param *param)
+{
+ double tmp = param->beta * zeta;
+ if (tmp > param->c1) return param->beta * -0.5*pow(tmp,-1.5);
+ if (tmp > param->c2)
+ return param->beta * (-0.5*pow(tmp,-1.5) *
+ (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
+ pow(tmp,-param->powern)));
+ if (tmp < param->c4) return 0.0;
+ if (tmp < param->c3)
+ return -0.5*param->beta * pow(tmp,param->powern-1.0);
+
+ double tmp_n = pow(tmp,param->powern);
+ return -0.5 * pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern)))*tmp_n / zeta;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairExTeP::ters_zetaterm_d(double prefactor,
+ double *rij_hat, double rij,
+ double *rik_hat, double rik,
+ double *dri, double *drj, double *drk,
+ Param *param)
+{
+ double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
+ double dcosdri[3],dcosdrj[3],dcosdrk[3];
+
+ fc = ters_fc(rik,param);
+ dfc = ters_fc_d(rik,param);
+ if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
+ else tmp = param->lam3 * (rij-rik);
+
+ if (tmp > 69.0776) ex_delr = 1.e30;
+ else if (tmp < -69.0776) ex_delr = 0.0;
+ else ex_delr = exp(tmp);
+
+ if (param->powermint == 3)
+ ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
+ else ex_delr_d = param->lam3 * ex_delr;
+
+ cos_theta = vec3_dot(rij_hat,rik_hat);
+ gijk = ters_gijk(cos_theta,param);
+ gijk_d = ters_gijk_d(cos_theta,param);
+ costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
+
+ // compute the derivative wrt Ri
+ // dri = -dfc*gijk*ex_delr*rik_hat;
+ // dri += fc*gijk_d*ex_delr*dcosdri;
+ // dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
+
+ vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
+ vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
+ vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
+ vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
+ vec3_scale(prefactor,dri,dri);
+
+ // compute the derivative wrt Rj
+ // drj = fc*gijk_d*ex_delr*dcosdrj;
+ // drj += fc*gijk*ex_delr_d*rij_hat;
+
+ vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
+ vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
+ vec3_scale(prefactor,drj,drj);
+
+ // compute the derivative wrt Rk
+ // drk = dfc*gijk*ex_delr*rik_hat;
+ // drk += fc*gijk_d*ex_delr*dcosdrk;
+ // drk += -fc*gijk*ex_delr_d*rik_hat;
+
+ vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
+ vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
+ vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
+ vec3_scale(prefactor,drk,drk);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairExTeP::costheta_d(double *rij_hat, double rij,
+ double *rik_hat, double rik,
+ double *dri, double *drj, double *drk)
+{
+ // first element is devative wrt Ri, second wrt Rj, third wrt Rk
+
+ double cos_theta = vec3_dot(rij_hat,rik_hat);
+
+ vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
+ vec3_scale(1.0/rij,drj,drj);
+ vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
+ vec3_scale(1.0/rik,drk,drk);
+ vec3_add(drj,drk,dri);
+ vec3_scale(-1.0,dri,dri);
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+/* F_IJ (4) */
+// initialize spline for F_corr (based on PairLCBOP::F_conj)
+
+void PairExTeP::spline_init() {
+ for ( size_t iel=0; iel<atom->ntypes; iel++) {
+ for ( size_t jel=0; jel<atom->ntypes; jel++) {
+ for ( size_t N_ij=0; N_ij<4; N_ij++ ) {
+ for ( size_t N_ji=0; N_ji<4; N_ji++ ) {
+ TF_corr_param &f = F_corr_param[iel][jel][N_ij][N_ji];
+
+ // corner points for each spline function
+ f.f_00 = F_corr_data[iel][jel][N_ij ][N_ji ][0];
+ f.f_01 = F_corr_data[iel][jel][N_ij ][N_ji+1][0];
+ f.f_10 = F_corr_data[iel][jel][N_ij+1][N_ji ][0];
+ f.f_11 = F_corr_data[iel][jel][N_ij+1][N_ji+1][0];
+
+ // compute f tilde according to [Los & Fasolino, PRB 68, 024107 2003]
+ f.f_x_00 = F_corr_data[iel][jel][N_ij ][N_ji ][1] - f.f_10 + f.f_00;
+ f.f_x_01 = F_corr_data[iel][jel][N_ij ][N_ji+1][1] - f.f_11 + f.f_01;
+ f.f_x_10 = -(F_corr_data[iel][jel][N_ij+1][N_ji ][1] - f.f_10 + f.f_00);
+ f.f_x_11 = -(F_corr_data[iel][jel][N_ij+1][N_ji+1][1] - f.f_11 + f.f_01);
+
+ f.f_y_00 = F_corr_data[iel][jel][N_ij ][N_ji ][2] - f.f_01 + f.f_00;
+ f.f_y_01 = -(F_corr_data[iel][jel][N_ij ][N_ji+1][2] - f.f_01 + f.f_00);
+ f.f_y_10 = F_corr_data[iel][jel][N_ij+1][N_ji ][2] - f.f_11 + f.f_10;
+ f.f_y_11 = -(F_corr_data[iel][jel][N_ij+1][N_ji+1][2] - f.f_11 + f.f_10);
+ }
+ }
+ }
+ }
+}
+
+double PairExTeP::envelop_function(double x, double y, double *func_der) {
+ double fx,fy,fxy,dfx,dfxydx;
+ double del, delsq;
+
+ fxy = 1.0;
+ dfxydx = 0.0;
+
+ if (x <= 3.0) {
+ fx = 1.0;
+ dfx = 0.0;
+ if (x < 1.0 && y < 1.0) {
+ double gx=(1.0-x);
+ double gy=(1.0-y);
+ double gxsq=gx*gx;
+ double gysq=gy*gy;
+ fxy = 1.0 - gxsq*gysq;
+ dfxydx = 2.0*gx*gysq;
+ }
+ } else if (x < 4.0) {
+ del = 4.0-x;
+ delsq = del*del;
+ fx = (3.0-2.0*del)*delsq;
+ dfx = - 6.0*del*(1.0-del);
+ } else {
+ fx = 0.0;
+ dfx = 0.0;
+ }
+ if (y <= 3.0) {
+ fy = 1.0;
+ } else if (y < 4.0) {
+ del = 4.0-y;
+ delsq = del*del;
+ fy = (3.0-2.0*del)*delsq;
+ } else {
+ fy = 0.0;
+ }
+
+ double func_val = fxy*fx*fy;
+ *func_der = dfxydx*fx*fy+fxy*dfx*fy;
+
+ return func_val;
+}
+
+double PairExTeP::F_corr(int iel, int jel, double Ndij, double Ndji, double *dFN_x, double *dFN_y ) {
+
+ // compute F_XY
+
+ size_t Ndij_int = static_cast<size_t>( floor( Ndij ) );
+ size_t Ndji_int = static_cast<size_t>( floor( Ndji ) );
+ double x = Ndij - Ndij_int;
+ double y = Ndji - Ndji_int;
+ TF_corr_param &f = F_corr_param[iel][jel][Ndij_int][Ndji_int];
+ double F = 0;
+ double dF_dx = 0, dF_dy = 0;
+ double l, r;
+ if (Ndij_int < 4 && Ndji_int < 4) {
+ l = (1-y)* (1-x);
+ r = ( f.f_00 + x*x* f.f_x_10 + y*y* f.f_y_01 );
+ F += l*r;
+ dF_dx += -(1-y)*r +l*2*x* f.f_x_10;
+ dF_dy += -(1-x)*r +l*2*y* f.f_y_01;
+ l = (1-y)*x;
+ r = ( f.f_10 + (1-x)*(1-x)*f.f_x_00 + y* y* f.f_y_11 );
+ F += l*r;
+ dF_dx += (1-y)*r -l*2*(1-x)*f.f_x_00;
+ dF_dy += -x*r +l*2*y* f.f_y_11;
+ l = y* (1-x);
+ r = ( f.f_01 + x*x* f.f_x_11 + (1-y)*(1-y)*f.f_y_00 );
+ F += l*r;
+ dF_dx += -y*r +l*2*x* f.f_x_11;
+ dF_dy += (1-x)*r -l*2*(1-y)*f.f_y_00;
+ l = y* x;
+ r = ( f.f_11 + (1-x)*(1-x)*f.f_x_01 + (1-y)*(1-y)*f.f_y_10 );
+ F += l*r;
+ dF_dx += y*r -l*2*(1-x)*f.f_x_01;
+ dF_dy += x*r -l*2*(1-y)*f.f_y_10;
+ }
+ double result = F;
+ *dFN_x = dF_dx;
+ *dFN_y = dF_dy;
+
+ return result;
+}
+/* F_IJ (4) */
diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h
new file mode 100644
index 0000000000000000000000000000000000000000..bad433455ed58e75c71fb92ff1c3bdbc1b5cc0fb
--- /dev/null
+++ b/src/USER-MISC/pair_extep.h
@@ -0,0 +1,225 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(extep,PairExTeP)
+
+#else
+
+#ifndef LMP_PAIR_EXTEP_H
+#define LMP_PAIR_EXTEP_H
+
+#include "pair.h"
+#include "my_page.h"
+
+#define MAXTYPES 8
+#define NSPLINE 5
+
+namespace LAMMPS_NS {
+
+class PairExTeP : public Pair {
+ public:
+ PairExTeP(class LAMMPS *);
+ virtual ~PairExTeP();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_style();
+ double init_one(int, int);
+
+ protected:
+ struct Param {
+ double lam1,lam2,lam3;
+ double c,d,h;
+ double gamma,powerm;
+ double powern,beta;
+ double biga,bigb,bigd,bigr;
+ double cut,cutsq;
+ double c1,c2,c3,c4;
+ int ielement,jelement,kelement;
+ int powermint;
+ double Z_i,Z_j; // added for ExTePZBL
+ double ZBLcut,ZBLexpscale;
+ double c5,ca1,ca4; // added for ExTePMOD
+ double powern_del;
+ };
+
+ Param *params; // parameter set for an I-J-K interaction
+ char **elements; // names of unique elements
+ int ***elem2param; // mapping from element triplets to parameters
+ int *map; // mapping from atom types to elements
+ double cutmax; // max cutoff for all elements
+ int nelements; // # of unique elements
+ int nparams; // # of stored parameter sets
+ int maxparam; // max # of parameter sets
+
+ int maxlocal; // size of numneigh, firstneigh arrays
+ int maxpage; // # of pages currently allocated
+ int pgsize; // size of neighbor page
+ int oneatom; // max # of neighbors for one atom
+ MyPage<int> *ipage; // neighbor list pages
+ int *SR_numneigh; // # of pair neighbors for each atom
+ int **SR_firstneigh; // ptr to 1st neighbor of each atom
+
+ double *Nt, *Nd; // sum of cutoff fns ( f_C ) with SR neighs
+
+ void allocate();
+ void spline_init();
+ virtual void read_file(char *);
+ virtual void setup();
+ virtual void repulsive(Param *, double, double &, int, double &);
+ virtual double zeta(Param *, double, double, double *, double *);
+ virtual void force_zeta(Param *, double, double, double &,
+ double &, int, double &);
+ void attractive(Param *, double, double, double, double *, double *,
+ double *, double *, double *);
+
+ virtual double ters_fc(double, Param *);
+ virtual double ters_fc_d(double, Param *);
+ virtual double ters_fa(double, Param *);
+ virtual double ters_fa_d(double, Param *);
+ virtual double ters_bij(double, Param *);
+ virtual double ters_bij_d(double, Param *);
+
+ virtual void ters_zetaterm_d(double, double *, double, double *, double,
+ double *, double *, double *, Param *);
+ void costheta_d(double *, double, double *, double,
+ double *, double *, double *);
+
+ // inlined functions for efficiency
+
+ inline double ters_gijk(const double costheta,
+ const Param * const param) const {
+ const double ters_c = param->c * param->c;
+ const double ters_d = param->d * param->d;
+ const double hcth = param->h - costheta;
+
+ return param->gamma*(1.0 + ters_c/ters_d - ters_c / (ters_d + hcth*hcth));
+ }
+
+ inline double ters_gijk_d(const double costheta,
+ const Param * const param) const {
+ const double ters_c = param->c * param->c;
+ const double ters_d = param->d * param->d;
+ const double hcth = param->h - costheta;
+ const double numerator = -2.0 * ters_c * hcth;
+ const double denominator = 1.0/(ters_d + hcth*hcth);
+ return param->gamma*numerator*denominator*denominator;
+ }
+
+ inline double vec3_dot(const double x[3], const double y[3]) const {
+ return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
+ }
+
+ inline void vec3_add(const double x[3], const double y[3],
+ double * const z) const {
+ z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
+ }
+
+ inline void vec3_scale(const double k, const double x[3],
+ double y[3]) const {
+ y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
+ }
+
+ inline void vec3_scaleadd(const double k, const double x[3],
+ const double y[3], double * const z) const {
+ z[0] = k*x[0]+y[0];
+ z[1] = k*x[1]+y[1];
+ z[2] = k*x[2]+y[2];
+ }
+
+ // splines parameters
+ // F[Ni=0-1, 1-2, 2-3,
+ // Nj=...,
+ struct TF_corr_param {
+ double
+ f_00,
+ f_01,
+ f_10,
+ f_11,
+ f_x_00,
+ f_x_01,
+ f_x_10,
+ f_x_11,
+ f_y_00,
+ f_y_01,
+ f_y_10,
+ f_y_11;
+ } F_corr_param[MAXTYPES][MAXTYPES][NSPLINE][NSPLINE];
+
+ double F_corr_data[MAXTYPES][MAXTYPES][NSPLINE][NSPLINE][3];
+
+ double F_corr( int, int, double, double, double*, double* );
+ void SR_neigh();
+
+ double envelop_function(double, double, double*);
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: Pair style ExTeP requires atom IDs
+
+This is a requirement to use the ExTeP potential.
+
+E: Pair style ExTeP requires newton pair on
+
+See the newton command. This is a restriction to use the ExTeP
+potential.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+E: Cannot open ExTeP potential file %s
+
+The specified potential file cannot be opened. Check that the path
+and name are correct.
+
+E: Incorrect format in ExTeP potential file
+
+Incorrect number of words per line in the potential file.
+
+E: Illegal ExTeP parameter
+
+One or more of the coefficients defined in the potential file is
+invalid.
+
+E: Potential file has duplicate entry
+
+The potential file for a SW or ExTeP potential has more than
+one entry for the same 3 ordered elements.
+
+E: Potential file is missing an entry
+
+The potential file for a SW or ExTeP potential does not have a
+needed entry.
+
+*/
diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp
index ecc3147ed5d0515dfb13d743531ed28599e11b40..1b212732de66a2928cc9c5dbf2d28bb71e12485b 100644
--- a/src/USER-OMP/fix_neigh_history_omp.cpp
+++ b/src/USER-OMP/fix_neigh_history_omp.cpp
@@ -356,7 +356,7 @@ void FixNeighHistoryOMP::pre_exchange_newton()
#endif
{
maxpartner = MAX(m,maxpartner);
- comm->maxexchange_fix = MAX(comm->maxexchange_fix,4*maxpartner+1);
+ comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
}
}
diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
index 85c7e44f8c8654d4eb9e7128c93f8a5e964c309c..110b8917cf07366b02aa0eeda1b99daeaffbe99a 100644
--- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
@@ -29,6 +29,7 @@
#include "math_const.h"
#include "error.h"
#include "suffix.h"
+#include "domain.h"
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp
index 6fec7a7e4d614a1c50306d528bce63af8255df13..321d104b00921e9af51f691191fad4402aea0213 100644
--- a/src/USER-OMP/reaxc_forces_omp.cpp
+++ b/src/USER-OMP/reaxc_forces_omp.cpp
@@ -601,44 +601,17 @@ void Compute_ForcesOMP( reax_system *system, control_params *control,
MPI_Comm comm = mpi_data->world;
// Init Forces
-#if defined(LOG_PERFORMANCE)
- double t_start = 0;
- if( system->my_rank == MASTER_NODE )
- t_start = Get_Time( );
-#endif
-
Init_Forces_noQEq_OMP( system, control, data, workspace,
- lists, out_control, comm );
-
-#if defined(LOG_PERFORMANCE)
- //MPI_Barrier( comm );
- if( system->my_rank == MASTER_NODE )
- Update_Timing_Info( &t_start, &(data->timing.init_forces) );
-#endif
+ lists, out_control, comm );
// Bonded Interactions
Compute_Bonded_ForcesOMP( system, control, data, workspace,
lists, out_control, mpi_data->world );
-#if defined(LOG_PERFORMANCE)
- if( system->my_rank == MASTER_NODE )
- Update_Timing_Info( &t_start, &(data->timing.bonded) );
-#endif
-
// Nonbonded Interactions
Compute_NonBonded_ForcesOMP( system, control, data, workspace,
lists, out_control, mpi_data->world );
-#if defined(LOG_PERFORMANCE)
- if( system->my_rank == MASTER_NODE )
- Update_Timing_Info( &t_start, &(data->timing.nonb) );
-#endif
-
// Total Force
Compute_Total_ForceOMP( system, control, data, workspace, lists, mpi_data );
-
-#if defined(LOG_PERFORMANCE)
- if( system->my_rank == MASTER_NODE )
- Update_Timing_Info( &t_start, &(data->timing.bonded) );
-#endif
}
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 0f4bd49cc855c7e78cc4cd69b3c66b69964b572f..7c135463add0c68cc3a7fb2a036a601bf75c7928 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -697,7 +697,7 @@ int PairReaxC::write_reax_lists()
int itr_i, itr_j, i, j;
int num_nbrs;
int *ilist, *jlist, *numneigh, **firstneigh;
- double d_sqr;
+ double d_sqr, cutoff_sqr;
rvec dvec;
double *dist, **x;
reax_list *far_nbrs;
@@ -712,6 +712,7 @@ int PairReaxC::write_reax_lists()
far_list = far_nbrs->select.far_nbr_list;
num_nbrs = 0;
+ int inum = list->inum;
dist = (double*) calloc( system->N, sizeof(double) );
int numall = list->inum + list->gnum;
@@ -721,12 +722,17 @@ int PairReaxC::write_reax_lists()
jlist = firstneigh[i];
Set_Start_Index( i, num_nbrs, far_nbrs );
+ if (i < inum)
+ cutoff_sqr = control->nonb_cut*control->nonb_cut;
+ else
+ cutoff_sqr = control->bond_cut*control->bond_cut;
+
for( itr_j = 0; itr_j < numneigh[i]; ++itr_j ){
j = jlist[itr_j];
j &= NEIGHMASK;
get_distance( x[j], x[i], &d_sqr, &dvec );
- if( d_sqr <= (control->nonb_cut*control->nonb_cut) ){
+ if( d_sqr <= (cutoff_sqr) ){
dist[j] = sqrt( d_sqr );
set_far_nbr( &far_list[num_nbrs], j, dist[j], dvec );
++num_nbrs;
diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp
index 5f29aea5b22cd3b892596ec4f3356e9184a85602..3ec6c188fc385026ce3fd93383fa87e38559b15f 100644
--- a/src/USER-TALLY/compute_force_tally.cpp
+++ b/src/USER-TALLY/compute_force_tally.cpp
@@ -12,6 +12,7 @@
------------------------------------------------------------------------- */
#include <string.h>
+#include <math.h>
#include "compute_force_tally.h"
#include "atom.h"
#include "group.h"
@@ -20,6 +21,7 @@
#include "memory.h"
#include "error.h"
#include "force.h"
+#include "comm.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp
index c090050b1540925d3ca76cb3e4f23fcaf7471c4e..43b663b27a580495943b5d4835650ae01811b0cd 100644
--- a/src/USER-TALLY/compute_heat_flux_tally.cpp
+++ b/src/USER-TALLY/compute_heat_flux_tally.cpp
@@ -20,6 +20,7 @@
#include "memory.h"
#include "error.h"
#include "force.h"
+#include "comm.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp
index 25a172b7f81eb6cd68a75fcb520c401bb89ec1de..0328740e0395bc6ca7914ee8d7b7b88e212e0000 100644
--- a/src/USER-TALLY/compute_pe_mol_tally.cpp
+++ b/src/USER-TALLY/compute_pe_mol_tally.cpp
@@ -20,6 +20,7 @@
#include "memory.h"
#include "error.h"
#include "force.h"
+#include "comm.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp
index 5b4644d4e16833f8177a0d22aa29de9802877bc1..caa4cf134a89dd10d73169eae5ba02510a8bf2dd 100644
--- a/src/USER-TALLY/compute_pe_tally.cpp
+++ b/src/USER-TALLY/compute_pe_tally.cpp
@@ -20,6 +20,7 @@
#include "memory.h"
#include "error.h"
#include "force.h"
+#include "comm.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp
index 32253d2cad78857a31c52753f85b856e7b84cec2..e44313d695c46959b87ddb89bbf50ec99078bd7c 100644
--- a/src/USER-TALLY/compute_stress_tally.cpp
+++ b/src/USER-TALLY/compute_stress_tally.cpp
@@ -20,6 +20,8 @@
#include "memory.h"
#include "error.h"
#include "force.h"
+#include "comm.h"
+#include "domain.h"
using namespace LAMMPS_NS;
diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h
index 8ea5b9d4d2dd93dd4f85147035bfc5be1633024a..708592a25eb000cf3bdc5bb38add4b413809a94b 100644
--- a/src/accelerator_kokkos.h
+++ b/src/accelerator_kokkos.h
@@ -25,6 +25,7 @@
#include "comm_tiled_kokkos.h"
#include "domain_kokkos.h"
#include "neighbor_kokkos.h"
+#include "memory_kokkos.h"
#include "modify_kokkos.h"
#else
@@ -37,6 +38,7 @@
#include "comm_tiled.h"
#include "domain.h"
#include "neighbor.h"
+#include "memory.h"
#include "modify.h"
namespace LAMMPS_NS {
@@ -89,6 +91,13 @@ class NeighborKokkos : public Neighbor {
~NeighborKokkos() {}
};
+class MemoryKokkos : public Memory {
+ public:
+ MemoryKokkos(class LAMMPS *lmp) : Memory(lmp) {}
+ ~MemoryKokkos() {}
+ void grow_kokkos(tagint **, tagint **, int, int, const char*) {}
+};
+
class ModifyKokkos : public Modify {
public:
ModifyKokkos(class LAMMPS *lmp) : Modify(lmp) {}
diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp
index 1155ac437adfb439cda2813ea0b8d4f4a850afed..1e91327e54639be94bf89810058c7d9e1df5e2a9 100644
--- a/src/compute_aggregate_atom.cpp
+++ b/src/compute_aggregate_atom.cpp
@@ -16,6 +16,7 @@
------------------------------------------------------------------------- */
#include <string.h>
+#include <math.h>
#include "compute_aggregate_atom.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp
index bc5a374fadb8c53f713c1d176f1998a0ebe93437..69cd87f96b6b62d800eb0a7e54587525bc779cfd 100644
--- a/src/compute_msd_chunk.cpp
+++ b/src/compute_msd_chunk.cpp
@@ -126,7 +126,7 @@ void ComputeMSDChunk::setup()
if (fix->nrow == nchunk && fix->ncol == 3) return;
fix->reset_global(nchunk,3);
-
+
double **cominit = fix->astore;
for (int i = 0; i < nchunk; i++) {
cominit[i][0] = comall[i][0];
diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp
index 90e2830e39e55881884bb6cb57f137ec387f62bf..b443d56bf82b3fd7a8d4f50b58181ecb49e922e4 100644
--- a/src/compute_orientorder_atom.cpp
+++ b/src/compute_orientorder_atom.cpp
@@ -18,6 +18,7 @@
#include <string.h>
#include <stdlib.h>
+#include <math.h>
#include "compute_orientorder_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp
index 167de4576dfcbe7c24d8db5c1049c84806c29ecb..bcb620f3b36c59dd842669dd626baebcda760f31 100644
--- a/src/compute_rdf.cpp
+++ b/src/compute_rdf.cpp
@@ -32,6 +32,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
+#include "comm.h"
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index 825426b2b6759734da67a39fea0342c0305ab70b..489c5bf5d5f4ce5837d42ee64d8fcd04be3103f3 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -28,6 +28,7 @@
#include "random_mars.h"
#include "memory.h"
#include "error.h"
+#include "modify.h"
#include <map>
diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp
index 5c677a43385a071a99d1e89489b6cb2a6ace6e8c..6b1e89227985acb0dc12336520962ff7599ffee3 100644
--- a/src/fix_addforce.cpp
+++ b/src/fix_addforce.cpp
@@ -16,7 +16,6 @@
#include "fix_addforce.h"
#include "atom.h"
#include "atom_masks.h"
-#include "accelerator_kokkos.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 1060acd7bb8c6ac289e6ef7606de8de515cbdd35..73df50c66cfa08c10ab2e6e93cf94fa4fabf0322 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -63,6 +63,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
strcpy(idchunk,arg[6]);
global_freq = nfreq;
+ peratom_freq = nfreq;
no_change_box = 1;
// expand args if any have wildcard character "*"
diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp
index 322c8d55619abd0ef17b0a7788523f978261e53b..623fbff756e5be8f4cb215767533e6d9bc88979e 100644
--- a/src/fix_neigh_history.cpp
+++ b/src/fix_neigh_history.cpp
@@ -35,7 +35,7 @@ enum{DEFAULT,NPARTNER,PERPARTNER}; // also set in fix neigh/history/omp
FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- npartner(NULL), partner(NULL), valuepartner(NULL), pair(NULL),
+ npartner(NULL), partner(NULL), valuepartner(NULL), pair(NULL),
ipage_atom(NULL), dpage_atom(NULL), ipage_neigh(NULL), dpage_neigh(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal fix NEIGH_HISTORY command");
@@ -295,7 +295,7 @@ void FixNeighHistory::pre_exchange_onesided()
// set maxpartner = max # of partners of any owned atom
// bump up comm->maxexchange_fix if necessary
-
+
maxpartner = 0;
for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
@@ -318,7 +318,7 @@ void FixNeighHistory::pre_exchange_newton()
int *allflags;
double *allvalues,*onevalues,*jvalues;
- // NOTE: all operations until very end are with
+ // NOTE: all operations until very end are with
// nlocal_neigh <= current nlocal and nall_neigh
// b/c previous neigh list was built with nlocal_neigh & nghost_neigh
// nlocal can be larger if other fixes added atoms at this pre_exchange()
@@ -424,7 +424,7 @@ void FixNeighHistory::pre_exchange_newton()
maxpartner = 0;
for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
- comm->maxexchange_fix = MAX(comm->maxexchange_fix,4*maxpartner+1);
+ comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
// zero npartner values from previous nlocal_neigh to current nlocal
@@ -526,7 +526,7 @@ void FixNeighHistory::pre_exchange_no_newton()
// set maxpartner = max # of partners of any owned atom
// bump up comm->maxexchange_fix if necessary
-
+
maxpartner = 0;
for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
@@ -571,9 +571,9 @@ void FixNeighHistory::post_neighbor()
memory->sfree(firstflag);
memory->sfree(firstvalue);
maxatom = nall;
- firstflag = (int **)
+ firstflag = (int **)
memory->smalloc(maxatom*sizeof(int *),"neighbor_history:firstflag");
- firstvalue = (double **)
+ firstvalue = (double **)
memory->smalloc(maxatom*sizeof(double *),"neighbor_history:firstvalue");
}
@@ -720,7 +720,7 @@ int FixNeighHistory::pack_reverse_comm_size(int n, int first)
last = first + n;
for (i = first; i < last; i++)
- m += 1 + 4*npartner[i];
+ m += 1 + (dnum+1)*npartner[i];
return m;
}
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index c856bb2db29e6de5b21a9adaa70e0fc03eb64927..84e94fc2b7807c3fc3c1a8938e8d6ce370885d30 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -155,8 +155,7 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
else memory->create(astore,nrow,ncol,"fix/store:astore");
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
-
- printf("AAA HOW GET HERE\n");
+ // printf("AAA HOW GET HERE\n");
}
/* ----------------------------------------------------------------------
diff --git a/src/input.cpp b/src/input.cpp
index d18be498fd50d062866cf5ec2f50f14cb1341a9c..06403276824a471aaafdc3453706ca951624c657 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -27,7 +27,6 @@
#include "comm.h"
#include "comm_brick.h"
#include "comm_tiled.h"
-#include "accelerator_kokkos.h"
#include "group.h"
#include "domain.h"
#include "output.h"
diff --git a/src/kspace.h b/src/kspace.h
index ad29c214728f56eb0eec5739aeac18b076c752b9..5a2e5b78840456b2b4b555ef9f7f8eb47d70b66c 100644
--- a/src/kspace.h
+++ b/src/kspace.h
@@ -15,7 +15,6 @@
#define LMP_KSPACE_H
#include "pointers.h"
-#include "accelerator_kokkos.h"
#ifdef FFT_SINGLE
typedef float FFT_SCALAR;
@@ -124,11 +123,6 @@ class KSpace : protected Pointers {
virtual void pack_reverse(int, FFT_SCALAR *, int, int *) {};
virtual void unpack_reverse(int, FFT_SCALAR *, int, int *) {};
- virtual void pack_forward_kokkos(int, DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {};
- virtual void unpack_forward_kokkos(int, DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {};
- virtual void pack_reverse_kokkos(int, DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {};
- virtual void unpack_reverse_kokkos(int, DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int) {};
-
virtual int timing(int, double &, double &) {return 0;}
virtual int timing_1d(int, double &) {return 0;}
virtual int timing_3d(int, double &) {return 0;}
diff --git a/src/lammps.h b/src/lammps.h
index c432784a0b14c92f571dc032040f22e35ec30f96..e3b815e6237a7ad660b90b97ee7c65b64db858db 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -53,6 +53,7 @@ class LAMMPS {
class KokkosLMP *kokkos; // KOKKOS accelerator class
class AtomKokkos *atomKK; // KOKKOS version of Atom class
+ class MemoryKokkos *memoryKK; // KOKKOS version of Memory class
class Python * python; // Python interface
diff --git a/src/memory.h b/src/memory.h
index b83482e4c2b69c9d11259e7c5d1ea73ba7ba077b..f2faecf6e177587e4aaf9dfc14991c6ef4f94f58 100644
--- a/src/memory.h
+++ b/src/memory.h
@@ -16,9 +16,6 @@
#include "lmptype.h"
#include "pointers.h"
-#ifdef LMP_KOKKOS
-#include "kokkos_type.h"
-#endif
namespace LAMMPS_NS {
@@ -31,16 +28,6 @@ class Memory : protected Pointers {
void sfree(void *);
void fail(const char *);
- // Kokkos memory allocation functions
- // provide a dummy prototpye for any Kokkos memory function
- // called in main LAMMPS even when not built with KOKKOS package
-
-#ifdef LMP_KOKKOS
-#include "memory_kokkos.h"
-#else
- void grow_kokkos(tagint **, tagint **, int, int, const char*) {}
-#endif
-
/* ----------------------------------------------------------------------
create/grow/destroy vecs and multidim arrays with contiguous memory blocks
only use with primitive data types, e.g. 1d vec of ints, 2d array of doubles
diff --git a/src/pair.h b/src/pair.h
index eb71e8822474aed87e024988e27b669196385cd9..cfb6576653c3aca4d21dfa99a0a6feda78a4977a 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -15,7 +15,6 @@
#define LMP_PAIR_H
#include "pointers.h"
-#include "accelerator_kokkos.h"
namespace LAMMPS_NS {
@@ -165,10 +164,6 @@ class Pair : protected Pointers {
virtual int pack_forward_comm(int, int *, double *, int, int *) {return 0;}
virtual void unpack_forward_comm(int, int, double *) {}
- 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 &) {}
virtual int pack_reverse_comm(int, int, double *) {return 0;}
virtual void unpack_reverse_comm(int, int *, double *) {}
virtual double memory_usage();
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index 2ba6633d9e21719f8c06beccf263c88ac438110e..9be9237734343588dda84aceb4d650c067c8f525 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -139,7 +139,6 @@ void PairYukawa::allocate()
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
-
memory->create(rad,n+1,"pair:rad");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(a,n+1,n+1,"pair:a");
diff --git a/src/pair_yukawa.h b/src/pair_yukawa.h
index 3859d163af5dd7a6843c7b5a178a53722691abf6..3222019a0ae94d4b4a9ccb4ca95fdcf3519ef59b 100644
--- a/src/pair_yukawa.h
+++ b/src/pair_yukawa.h
@@ -46,7 +46,7 @@ class PairYukawa : public Pair {
double *rad;
double **cut,**a,**offset;
- void allocate();
+ virtual void allocate();
};
}
diff --git a/src/pointers.h b/src/pointers.h
index 82b49c1dad05e6988ec02bd1b5646ee2078b6442..44967f51359a28067fee329362a65c8b3a8920dd 100644
--- a/src/pointers.h
+++ b/src/pointers.h
@@ -57,6 +57,7 @@ class Pointers {
screen(ptr->screen),
logfile(ptr->logfile),
atomKK(ptr->atomKK),
+ memoryKK(ptr->memoryKK),
python(ptr->python) {}
virtual ~Pointers() {}
@@ -84,6 +85,7 @@ class Pointers {
FILE *&logfile;
class AtomKokkos *&atomKK;
+ class MemoryKokkos *&memoryKK;
class Python *&python;
};
diff --git a/src/region.cpp b/src/region.cpp
index d2ef481cb79595ec51d22380cff51b95f12c4d77..da814746ad24ef686a7224e9df7ecad8570a0bd0 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -142,15 +142,6 @@ int Region::match(double x, double y, double z)
return !(inside(x,y,z) ^ interior);
}
-/* ----------------------------------------------------------------------
- generate error if Kokkos function defaults to base class
-------------------------------------------------------------------------- */
-
-void Region::match_all_kokkos(int, DAT::tdual_int_1d)
-{
- error->all(FLERR,"Can only use Kokkos supported regions with Kokkos package");
-}
-
/* ----------------------------------------------------------------------
generate list of contact points for interior or exterior regions
if region has variable shape, invoke shape_update() once per timestep
diff --git a/src/region.h b/src/region.h
index 5b4238acb4b071e10de309f04c6d3af2083a4e0e..7e8c45cb2ea91360ceffdf3dfe0b735a61b0684c 100644
--- a/src/region.h
+++ b/src/region.h
@@ -15,7 +15,6 @@
#define LMP_REGION_H
#include "pointers.h"
-#include "accelerator_kokkos.h"
namespace LAMMPS_NS {
@@ -97,10 +96,6 @@ class Region : protected Pointers {
virtual void set_velocity_shape() {}
virtual void velocity_contact_shape(double*, double*) {}
- // Kokkos function, implemented by each Kokkos region
-
- virtual void match_all_kokkos(int, DAT::tdual_int_1d);
-
protected:
void add_contact(int, double *, double, double, double);
void options(int, char **);
diff --git a/src/set.cpp b/src/set.cpp
index 2b1c0edee2da90faaf506c9ce6976ab3f49a325f..11b91df4c4b8f76000b8d59ed5267dd0b2242610 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -36,6 +36,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
+#include "modify.h"
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/special.cpp b/src/special.cpp
index 381a763dd29ad9cec5254e8556763f0967d826ac..56529e748b8d52e070696543627bfba255b87e0a 100644
--- a/src/special.cpp
+++ b/src/special.cpp
@@ -591,7 +591,8 @@ void Special::combine()
AtomKokkos* atomKK = (AtomKokkos*) atom;
atomKK->modified(Host,SPECIAL_MASK);
atomKK->sync(Device,SPECIAL_MASK);
- memory->grow_kokkos(atomKK->k_special,atom->special,
+ MemoryKokkos* memoryKK = (MemoryKokkos*) memory;
+ memoryKK->grow_kokkos(atomKK->k_special,atom->special,
atom->nmax,atom->maxspecial,"atom:special");
atomKK->modified(Device,SPECIAL_MASK);
atomKK->sync(Host,SPECIAL_MASK);
diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp
index d4d4f99bf388c597f9ef5b674b06ec07a933871d..0556d647cf36d1046f4864002f2e6fa5e5d656f5 100644
--- a/src/write_coeff.cpp
+++ b/src/write_coeff.cpp
@@ -23,6 +23,7 @@
#include "force.h"
#include "universe.h"
#include "error.h"
+#include "domain.h"
using namespace LAMMPS_NS;