From 56475229060040c22a53a60c5e042dc5d55cd355 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 28 Nov 2017 12:34:23 -0500
Subject: [PATCH] various small cosmetic adjustments to increase conformance
with LAMMPS programming conventions
---
.../USER/misc/extep/{input => in.extep-bn} | 2 +-
.../misc/extep/log.23Oct17.extep-bn.g++.1 | 180 ++++++++++++++++++
.../misc/extep/log.23Oct17.extep-bn.g++.4 | 180 ++++++++++++++++++
potentials/BN.extep | 7 +-
src/.gitignore | 6 +
src/USER-MISC/README | 1 +
src/USER-MISC/pair_extep.cpp | 139 ++++++++------
src/USER-MISC/pair_extep.h | 0
8 files changed, 449 insertions(+), 66 deletions(-)
rename examples/USER/misc/extep/{input => in.extep-bn} (98%)
create mode 100644 examples/USER/misc/extep/log.23Oct17.extep-bn.g++.1
create mode 100644 examples/USER/misc/extep/log.23Oct17.extep-bn.g++.4
mode change 100755 => 100644 src/USER-MISC/pair_extep.cpp
mode change 100755 => 100644 src/USER-MISC/pair_extep.h
diff --git a/examples/USER/misc/extep/input b/examples/USER/misc/extep/in.extep-bn
similarity index 98%
rename from examples/USER/misc/extep/input
rename to examples/USER/misc/extep/in.extep-bn
index d5e81eb82b..bb7ed0ea28 100644
--- a/examples/USER/misc/extep/input
+++ b/examples/USER/misc/extep/in.extep-bn
@@ -19,7 +19,7 @@ pair_coeff * * ../../../../potentials/BN.extep B N
# Output
thermo 10
-thermo_style custom step time etotal pe temp lx ly lz pxx pyy pzz spcpu
+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
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 0000000000..392e5c4f0e
--- /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 0000000000..c5c9236649
--- /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/potentials/BN.extep b/potentials/BN.extep
index fd5e653fb5..1b9f46c768 100644
--- a/potentials/BN.extep
+++ b/potentials/BN.extep
@@ -1,7 +1,8 @@
-# B and N mixture, parameterized for Tersoff potential
-# values are from Los et al. PhysRevB.96.184108 (2017)
+# DATE: 2017-11-28 CONTRIBUTOR: J.H. Los, J.M.H. Kroes CITATION: Los et al. Phys. Rev. B 96, 184108 (2017)
-# Tersoff parameters for various elements and mixtures
+# 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
diff --git a/src/.gitignore b/src/.gitignore
index 8d99776096..13fb446225 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1083,10 +1083,16 @@
/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/USER-MISC/README b/src/USER-MISC/README
index 5af5b22eb7..a8c33fa380 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
old mode 100755
new mode 100644
index 13ca404de3..cf859a28f8
--- a/src/USER-MISC/pair_extep.cpp
+++ b/src/USER-MISC/pair_extep.cpp
@@ -15,10 +15,10 @@
Contributing author: Jan Los
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_extep.h"
#include "atom.h"
#include "neighbor.h"
@@ -100,7 +100,7 @@ PairExTeP::~PairExTeP()
void PairExTeP::SR_neigh()
{
int i,j,ii,jj,n,allnum,jnum,itype,jtype,iparam_ij;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq,dS;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int *neighptr;
@@ -140,7 +140,7 @@ void PairExTeP::SR_neigh()
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
-
+
Nt[i] = 0.0;
Nd[i] = 0.0;
@@ -162,7 +162,7 @@ void PairExTeP::SR_neigh()
neighptr[n++] = j;
double tmp_fc = ters_fc(sqrt(rsq),¶ms[iparam_ij]);
Nt[i] += tmp_fc;
- if(itype!=jtype) {
+ if (itype!=jtype) {
Nd[i] += tmp_fc;
}
}
@@ -184,7 +184,7 @@ void PairExTeP::compute(int eflag, int vflag)
int itype,jtype,ktype,iparam_ij,iparam_ijk;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
- double rsq,rsq1,rsq2,r,r2;
+ 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;
@@ -281,10 +281,10 @@ void PairExTeP::compute(int eflag, int vflag)
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)
+ // 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];
@@ -296,14 +296,14 @@ void PairExTeP::compute(int eflag, int vflag)
Ntij -= fc_ij;
Ntji -= fc_ij;
- if(jtype!=itype) {
+ 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.; }
+ 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
@@ -350,7 +350,7 @@ void PairExTeP::compute(int eflag, int vflag)
/* 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];
+ 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;
@@ -706,7 +706,7 @@ void PairExTeP::read_file(char *file)
error->all(FLERR,"Illegal ExTeP parameter");
nparams++;
- if(nparams >= pow(atom->ntypes,3)) break;
+ if (nparams >= pow(atom->ntypes,3)) break;
}
// deallocate words array
@@ -719,18 +719,18 @@ void PairExTeP::read_file(char *file)
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++)
+ 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);
+ //fputs(line,stdout);
if (ptr == NULL) {
eof = 1;
fclose(fp);
@@ -759,7 +759,8 @@ void PairExTeP::read_file(char *file)
// 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
+ // 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;
@@ -775,8 +776,9 @@ void PairExTeP::read_file(char *file)
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) {
+ 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;
@@ -785,7 +787,7 @@ void PairExTeP::read_file(char *file)
F_corr_data[jelement][ielement][Nj][Ni][1] = spline_dery;
F_corr_data[jelement][ielement][Nj][Ni][2] = spline_derx;
}
- }
+ }
}
delete [] words;
@@ -821,7 +823,6 @@ void PairExTeP::setup()
elem2param[i][j][k] = n;
}
-
// compute parameter values derived from inputs
for (m = 0; m < nparams; m++) {
@@ -993,10 +994,10 @@ double PairExTeP::ters_bij_d(double zeta, Param *param)
/* ---------------------------------------------------------------------- */
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 *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];
@@ -1052,8 +1053,8 @@ void PairExTeP::ters_zetaterm_d(double prefactor,
/* ---------------------------------------------------------------------- */
void PairExTeP::costheta_d(double *rij_hat, double rij,
- double *rik_hat, double rik,
- double *dri, double *drj, double *drk)
+ double *rik_hat, double rik,
+ double *dri, double *drj, double *drk)
{
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
@@ -1074,10 +1075,10 @@ void PairExTeP::costheta_d(double *rij_hat, double rij,
// 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++ ) {
+ 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
@@ -1096,7 +1097,6 @@ void PairExTeP::spline_init() {
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);
-
}
}
}
@@ -1113,7 +1113,7 @@ double PairExTeP::envelop_function(double x, double y, double *func_der) {
if (x <= 3.0) {
fx = 1.0;
dfx = 0.0;
- if(x < 1.0 && y < 1.0) {
+ if (x < 1.0 && y < 1.0) {
double gx=(1.0-x);
double gy=(1.0-y);
double gxsq=gx*gx;
@@ -1122,22 +1122,22 @@ double PairExTeP::envelop_function(double x, double y, double *func_der) {
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;
+ 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;
+ del = 4.0-y;
+ delsq = del*del;
+ fy = (3.0-2.0*del)*delsq;
+ } else {
+ fy = 0.0;
}
double func_val = fxy*fx*fy;
@@ -1147,22 +1147,38 @@ double PairExTeP::envelop_function(double x, double y, double *func_der) {
}
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;
- const TF_corr_param &f = F_corr_param[iel][jel][Ndij_int][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;
+ 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;
@@ -1171,4 +1187,3 @@ double PairExTeP::F_corr(int iel, int jel, double Ndij, double Ndji, double *dFN
return result;
}
/* F_IJ (4) */
-
diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h
old mode 100755
new mode 100644
--
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