Update msmeam example and clean up code
This commit is contained in:
rohskopf
130
examples/meam/dump.xyz
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130
examples/meam/dump.xyz
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@ -0,0 +1,130 @@
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128
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Atoms. Timestep: 0
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2 -2.93785 -4.45926 -4.81092
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2 5.62221 -2.7335 -1.71576
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2 -2.66146 -5.54311 1.63537
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2 -5.43268 -4.61746 5.94523
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2 5.86792 -0.112054 -3.58394
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2 -3.71746 -0.662331 -0.371479
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2 -5.07247 -2.56716 4.41035
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2 -3.39514 0.934113 4.93107
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2 -5.43476 1.95238 -5.61809
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2 -4.58847 2.29045 -1.05977
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2 -5.90587 0.621241 2.01276
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2 -4.76807 0.196574 4.32678
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2 -5.42289 5.25697 -4.51629
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2 -5.2684 -5.91937 -2.86487
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2 -2.86109 1.04847 2.02991
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2 -4.07111 5.3133 3.80095
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2 -0.194715 -4.16777 -5.69509
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2 -2.98927 -3.16474 -1.61739
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2 -0.912931 -4.38191 -0.160186
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2 -2.45137 -5.24665 4.88829
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2 -2.888 -0.163345 -3.34011
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1 -4.67388 -1.38073 -2.29468
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2 -0.697395 -1.48853 0.600516
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1 -2.73922 -2.47748 0.238719
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2 -2.65513 -2.723 2.63503
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1 -3.46443 -4.60281 3.38178
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2 0.722761 -2.07094 2.92147
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1 -2.10006 -3.21313 5.72734
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2 -3.10576 2.32048 -2.27256
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1 -2.22988 0.716839 -1.31072
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2 -1.86983 1.40068 0.726511
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1 -4.11034 -0.709334 1.93418
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2 -0.350558 3.27072 -0.288066
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1 -3.40454 -1.4384 4.39035
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2 -3.09405 1.41325 -5.36355
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1 -4.45607 1.20729 -3.73102
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2 -2.6061 4.63735 -4.69039
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1 -3.34774 4.67681 -2.62847
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2 0.81217 4.86024 -4.67109
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1 -2.57569 3.37407 -0.213635
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2 -0.386798 5.87456 -2.11199
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1 -1.67662 1.33743 3.87415
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2 -0.877061 3.37359 4.3847
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1 -1.86093 3.31582 -5.97866
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1 -5.27323 -4.60733 -0.958175
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1 -2.78887 -5.69102 -0.792202
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1 -2.47172 4.58019 2.50832
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1 -3.88199 5.84566 -5.75634
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2 2.23148 -2.77292 -5.23569
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2 0.298198 -3.13853 -3.16082
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2 2.88108 -3.46587 -0.58232
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2 0.250962 -5.75952 2.73898
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2 -0.293412 -0.802943 -3.36985
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1 -1.00757 -2.04819 -1.94193
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2 2.07291 1.49224 -2.38981
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1 1.11109 -3.20042 0.949108
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2 1.67743 -0.790186 2.51588
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1 -0.83423 -4.33425 2.09715
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2 3.27474 -1.31079 4.78847
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1 1.71262 -3.36915 4.5581
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2 0.47706 1.7769 -5.33399
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1 0.294439 0.589278 -2.20301
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2 2.20393 3.15576 -2.02768
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1 -0.0404494 0.476782 1.03964
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2 1.13959 2.37634 2.3481
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1 -0.973837 -1.63252 3.75386
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2 -0.3292 0.299699 5.27708
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1 -1.61856 -0.396427 -5.17712
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2 2.59999 -5.19777 5.82307
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1 -1.62707 2.32109 -3.62999
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2 3.65327 4.92826 -5.43193
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1 0.0788934 4.0241 -2.50115
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2 2.85565 2.61687 2.11255
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1 0.973899 2.62554 4.34121
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2 3.74529 3.45214 4.59464
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1 2.08052 4.7039 5.32803
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1 -1.03242 -5.8155 -4.32658
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1 0.762244 -4.36316 -1.31566
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1 0.326368 3.99374 1.61723
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1 -0.435011 -5.79971 4.59591
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2 3.91611 -4.60528 -3.31917
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2 1.92407 5.73451 -1.97543
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2 -5.97945 -4.23694 1.86465
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2 4.334 -4.48452 5.37374
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2 2.27555 -0.632774 -5.79318
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1 1.87282 -1.55049 -3.456
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2 3.45581 -1.10541 -1.83331
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1 4.37882 -1.94665 -0.328464
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2 2.59992 -3.7549 2.57406
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1 3.99839 -4.48566 1.19687
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2 -5.72956 -2.14757 -5.99636
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1 4.26641 -2.6989 -5.80055
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2 4.52547 2.29068 -3.47658
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1 2.36031 1.34164 -4.41738
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2 4.77671 1.40612 -0.752462
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1 1.80727 -0.783597 -0.458199
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2 4.4745 0.373622 2.10683
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1 3.60812 -1.73157 2.40191
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2 4.62814 -0.286541 4.47565
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1 1.79752 0.289353 4.23308
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2 5.83415 4.49865 -5.96645
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1 3.24013 4.16552 -3.507
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2 4.87203 4.871 -2.33644
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1 3.55265 1.22628 0.692683
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2 -5.81733 4.54205 1.55789
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1 3.96832 1.54411 3.82844
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2 -5.53493 1.9067 3.75041
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1 4.47286 2.64156 -5.59528
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1 1.70009 -4.81154 -4.19539
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1 1.72215 4.18784 -0.371268
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1 3.92182 4.59356 1.32634
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1 3.13102 -5.89225 3.60012
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1 4.75587 -2.28778 -3.47421
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1 -5.50503 -2.70274 0.874887
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1 5.84186 -4.60644 3.87141
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1 -4.75169 -3.1692 -4.40998
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1 3.9405 0.71887 -2.28988
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1 -5.68697 0.204238 -0.191674
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1 5.89496 -1.24226 3.12013
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1 5.96758 -0.0712572 5.8964
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1 -5.62085 3.36 -2.94935
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1 5.20653 3.45179 -0.380089
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1 -4.69945 2.54896 1.82974
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1 -4.07584 3.07262 5.0648
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1 4.15876 -5.08968 -1.14435
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1 -4.69638 -5.74298 1.13578
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1 5.59942 4.6887 3.59483
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1 5.09884 -5.37744 -4.90513
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@ -14,9 +14,10 @@ neighbor 0.3 bin
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neigh_modify delay 10
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fix 1 all nve
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thermo 10
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thermo 1
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timestep 0.001
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dump 1 all xyz 100 dump.xyz
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#dump 1 all atom 50 dump.meam
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#dump 2 all image 10 image.*.jpg element element &
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@ -27,4 +28,4 @@ timestep 0.001
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3 element Si C
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run 100
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run 10
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@ -7,9 +7,9 @@ ITEM: BOX BOUNDS pp pp pp
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-4.0000000000000000e+00 4.0000000000000000e+00
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-4.0000000000000000e+00 4.0000000000000000e+00
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ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
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1 0 0 0 -132.308 -88.6953 0 22.6425 -2.1528e+08 -1.63302e+08 -0 -2.06499e+07 -0 -0
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2 2.2 0 0 121.138 -0.446613 0 14.8521 -2.12596e+08 -0 -0 386632 -0 -0
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3 0.3 2.3 0 11.1693 89.1419 0 8.67443 -2.68428e+06 -1.63302e+08 -0 -2.10365e+07 -0 -0
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1 0 0 0 -131.977 -88.3322 0 22.9236 -2.14786e+08 -1.62719e+08 -0 -2.05378e+07 -0 -0
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2 2.2 0 0 120.857 -0.482171 0 14.7745 -2.12113e+08 -0 -0 403352 -0 -0
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3 0.3 2.3 0 11.1201 88.8144 0 8.61773 -2.67245e+06 -1.62719e+08 -0 -2.09411e+07 -0 -0
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ITEM: TIMESTEP
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1
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ITEM: NUMBER OF ATOMS
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@ -19,6 +19,6 @@ ITEM: BOX BOUNDS pp pp pp
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-4.0000000000000000e+00 4.0000000000000000e+00
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-4.0000000000000000e+00 4.0000000000000000e+00
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ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
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1 0 0 0 -132.308 -88.6953 0 22.6425 -2.1528e+08 -1.63302e+08 -0 -2.06499e+07 -0 -0
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2 2.2 0 0 121.138 -0.446613 0 14.8521 -2.12596e+08 -0 -0 386632 -0 -0
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3 0.3 2.3 0 11.1693 89.1419 0 8.67443 -2.68428e+06 -1.63302e+08 -0 -2.10365e+07 -0 -0
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1 0 0 0 -131.977 -88.3322 0 22.9236 -2.14786e+08 -1.62719e+08 -0 -2.05378e+07 -0 -0
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2 2.2 0 0 120.857 -0.482171 0 14.7745 -2.12113e+08 -0 -0 403352 -0 -0
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3 0.3 2.3 0 11.1201 88.8144 0 8.61773 -2.67245e+06 -1.62719e+08 -0 -2.09411e+07 -0 -0
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@ -83,24 +83,24 @@ Neighbor list info ...
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pair build: halffull/newton
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 10.69 | 10.69 | 10.69 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 10.71 | 10.71 | 10.71 Mbytes
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Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms
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0 0 15.389692 492946.21 840939 637899.63 0 80663.676 0 0 8 8 8 512 15.389692
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1 0 15.389692 492946.21 840939 637899.63 0 80663.676 0 0 8 8 8 512 15.389692
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Loop time of 7.9076e-05 on 1 procs for 1 steps with 3 atoms
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0 0 15.438614 491542.52 839006.02 635621.55 0 80225.587 0 0 8 8 8 512 15.438614
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1 0 15.438614 491542.52 839006.02 635621.55 0 80225.587 0 0 8 8 8 512 15.438614
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Loop time of 6.7095e-05 on 1 procs for 1 steps with 3 atoms
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Performance: 1092.620 ns/day, 0.022 hours/ns, 12646.062 timesteps/s
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67.0% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 1287.726 ns/day, 0.019 hours/ns, 14904.240 timesteps/s
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77.5% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.4076e-05 | 2.4076e-05 | 2.4076e-05 | 0.0 | 30.45
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Pair | 2.7954e-05 | 2.7954e-05 | 2.7954e-05 | 0.0 | 41.66
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 3.204e-06 | 3.204e-06 | 3.204e-06 | 0.0 | 4.05
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Output | 4.726e-05 | 4.726e-05 | 4.726e-05 | 0.0 | 59.77
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Modify | 5.97e-07 | 5.97e-07 | 5.97e-07 | 0.0 | 0.75
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Other | | 3.939e-06 | | | 4.98
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Comm | 3.164e-06 | 3.164e-06 | 3.164e-06 | 0.0 | 4.72
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Output | 3.1658e-05 | 3.1658e-05 | 3.1658e-05 | 0.0 | 47.18
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Modify | 1.712e-06 | 1.712e-06 | 1.712e-06 | 0.0 | 2.55
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Other | | 2.607e-06 | | | 3.89
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Nlocal: 3 ave 3 max 3 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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294
examples/meam/msmeam/test.out
Normal file
294
examples/meam/msmeam/test.out
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@ -0,0 +1,294 @@
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LAMMPS (23 Jun 2022)
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log test.log
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# Test of MEAM potential for HGa
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# ------------------------ INITIALIZATION ----------------------------
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units metal
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dimension 3
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boundary p p p
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atom_style atomic
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variable latparam equal 4.646
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variable ncell equal 3
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# ----------------------- ATOM DEFINITION ----------------------------
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region box block -4 4 -4 4 -4 4
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create_box 2 box
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Created orthogonal box = (-4 -4 -4) to (4 4 4)
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1 by 1 by 1 MPI processor grid
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#
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include potential.mod
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# NOTE: This script can be modified for different pair styles
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# See in.elastic for more info.
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variable Pu string H
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print "potential chosen ${Pu}"
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potential chosen H
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# Choose potential
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pair_style meam ms # the `ms` flag turns on MS-MEAM
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print "we just executed"
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we just executed
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pair_coeff * * library.MSmeam ${Pu} Ga4 HGaMS.meam ${Pu} Ga4
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pair_coeff * * library.MSmeam H Ga4 HGaMS.meam ${Pu} Ga4
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pair_coeff * * library.MSmeam H Ga4 HGaMS.meam H Ga4
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Reading MEAM library file library.MSmeam with DATE: 2018-09-22
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Tokenizer::next_double() current = 1.0
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Tokenizer::next_int() current = 1
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Tokenizer::next_double() current = 1.0079
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Tokenizer::next_double() current = 2.960
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Tokenizer::next_double() current = 2.960
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Tokenizer::next_double() current = 3.0
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Tokenizer::next_double() current = 1.0
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Tokenizer::next_double() current = 1.0
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Tokenizer::next_double() current = 1.0
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Tokenizer::next_double() current = 3.0
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Tokenizer::next_double() current = 1.0
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Tokenizer::next_double() current = 0.741
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Tokenizer::next_double() current = 2.235
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Tokenizer::next_double() current = 2.50
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Tokenizer::next_double() current = 1.0
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Tokenizer::next_double() current = 0.44721
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Tokenizer::next_double() current = 0.0
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Tokenizer::next_double() current = 0.00
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Tokenizer::next_double() current = 0.0
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Tokenizer::next_double() current = 0.31623
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Tokenizer::next_double() current = 0
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Tokenizer::next_double() current = 6.70
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Tokenizer::next_int() current = 0
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Tokenizer::next_double() current = 12.0
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Tokenizer::next_int() current = 31
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Tokenizer::next_double() current = 69.723
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Tokenizer::next_double() current = 4.42
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Tokenizer::next_double() current = 4.80
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Tokenizer::next_double() current = 3.10
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Tokenizer::next_double() current = 6.00
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Tokenizer::next_double() current = 0.00
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Tokenizer::next_double() current = 0.0
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||||
Tokenizer::next_double() current = 0.0
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Tokenizer::next_double() current = 0.5
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Tokenizer::next_double() current = 4.247
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Tokenizer::next_double() current = 2.897
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||||
Tokenizer::next_double() current = 0.97
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Tokenizer::next_double() current = 1.0
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||||
Tokenizer::next_double() current = 1.649
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||||
Tokenizer::next_double() current = 1.435
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||||
Tokenizer::next_double() current = 0.00
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||||
Tokenizer::next_double() current = 0.0
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||||
Tokenizer::next_double() current = 0.0
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Tokenizer::next_double() current = 2.0
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Tokenizer::next_double() current = 0.70
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Tokenizer::next_int() current = 0
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^^^^^ Filling tm
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^^^^^ Filling tm
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Tokenizer::next_double() current = 1
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Tokenizer::next_double() current = 1
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||||
Tokenizer::next_double() current = 0
|
||||
Tokenizer::next_double() current = 1
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||||
Tokenizer::next_double() current = 5.9
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Tokenizer::next_int() current = 1
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||||
Tokenizer::next_int() current = 1
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||||
Tokenizer::next_double() current = 0.460
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||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 1
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Tokenizer::next_double() current = 0.460
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Tokenizer::next_int() current = 1
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Tokenizer::next_int() current = 1
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Tokenizer::next_int() current = 1
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Tokenizer::next_double() current = 1.3
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Tokenizer::next_int() current = 1
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Tokenizer::next_int() current = 1
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Tokenizer::next_int() current = 1
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Tokenizer::next_double() current = 2.80
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Tokenizer::next_int() current = 1
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Tokenizer::next_int() current = 1
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||||
Tokenizer::next_double() current = 1
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||||
Tokenizer::next_int() current = 2
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||||
Tokenizer::next_double() current = 0.6
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Tokenizer::next_int() current = 2
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Tokenizer::next_int() current = 2
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||||
Tokenizer::next_double() current = 0.097
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||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 0.097
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_int() current = 2
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||||
Tokenizer::next_double() current = 1
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 0.300
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||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 0.300
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 3.19
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = -0.48
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 6.6
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 2.0
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 2.0
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_double() current = 2.0
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_double() current = 1.4
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 1.4
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 1.4
|
||||
Tokenizer::next_int() current = 1
|
||||
Tokenizer::next_int() current = 2
|
||||
Tokenizer::next_double() current = 1
|
||||
# Setup neighbor style
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Setup minimization style
|
||||
variable dmax equal 1.0e-2
|
||||
min_style cg
|
||||
min_modify dmax ${dmax} line quadratic
|
||||
min_modify dmax 0.01 line quadratic
|
||||
compute eng all pe/atom
|
||||
compute eatoms all reduce sum c_eng
|
||||
|
||||
# Setup output
|
||||
thermo 100
|
||||
thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
|
||||
thermo_modify norm yes
|
||||
create_atoms 1 single 0 0 0 units box
|
||||
Created 1 atoms
|
||||
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 single 2.2 0 0 units box
|
||||
Created 1 atoms
|
||||
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 single 0.3 2.3 0 units box
|
||||
Created 1 atoms
|
||||
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
# ---------- Define Settings ---------------------
|
||||
variable teng equal "c_eatoms"
|
||||
compute pot_energy all pe/atom
|
||||
compute stress all stress/atom NULL
|
||||
dump 1 all custom 1 test.dump id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
|
||||
run 1
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.9
|
||||
ghost atom cutoff = 6.9
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/nsq
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
--- compute derivatives of energy wrt ...
|
||||
phip sij -116.571511 1.000000
|
||||
drhodr -1.327736 -0.011564
|
||||
fp 4.976162 -13.618158
|
||||
dUdrij -123.021058
|
||||
--- compute derivatives of energy wrt ...
|
||||
phip sij -86.757953 1.000000
|
||||
drhodr -0.821855 -0.007170
|
||||
fp 4.976162 -14.961215
|
||||
dUdrij -90.740359
|
||||
--- compute derivatives of energy wrt ...
|
||||
phip sij 0.129370 1.000000
|
||||
drhodr -0.000000 -0.002189
|
||||
fp -13.618158 4.976162
|
||||
dUdrij 0.118475
|
||||
--- compute derivatives of energy wrt ...
|
||||
phip sij 0.140206 1.000000
|
||||
drhodr -0.000000 -0.002956
|
||||
fp -14.961215 4.976162
|
||||
dUdrij 0.125499
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.71 | 10.71 | 10.71 Mbytes
|
||||
Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms
|
||||
0 0 15.438614 491542.52 839006.02 635621.55 0 80225.587 0 0 8 8 8 512 15.438614
|
||||
--- compute derivatives of energy wrt ...
|
||||
phip sij -116.571511 1.000000
|
||||
drhodr -1.327736 -0.011564
|
||||
fp 4.976162 -13.618158
|
||||
dUdrij -123.021058
|
||||
--- compute derivatives of energy wrt ...
|
||||
phip sij -86.757953 1.000000
|
||||
drhodr -0.821855 -0.007170
|
||||
fp 4.976162 -14.961215
|
||||
dUdrij -90.740359
|
||||
--- compute derivatives of energy wrt ...
|
||||
phip sij 0.129370 1.000000
|
||||
drhodr -0.000000 -0.002189
|
||||
fp -13.618158 4.976162
|
||||
dUdrij 0.118475
|
||||
--- compute derivatives of energy wrt ...
|
||||
phip sij 0.140206 1.000000
|
||||
drhodr -0.000000 -0.002956
|
||||
fp -14.961215 4.976162
|
||||
dUdrij 0.125499
|
||||
1 0 15.438614 491542.52 839006.02 635621.55 0 80225.587 0 0 8 8 8 512 15.438614
|
||||
Loop time of 6.7095e-05 on 1 procs for 1 steps with 3 atoms
|
||||
|
||||
Performance: 1287.726 ns/day, 0.019 hours/ns, 14904.240 timesteps/s
|
||||
77.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.7954e-05 | 2.7954e-05 | 2.7954e-05 | 0.0 | 41.66
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 3.164e-06 | 3.164e-06 | 3.164e-06 | 0.0 | 4.72
|
||||
Output | 3.1658e-05 | 3.1658e-05 | 3.1658e-05 | 0.0 | 47.18
|
||||
Modify | 1.712e-06 | 1.712e-06 | 1.712e-06 | 0.0 | 2.55
|
||||
Other | | 2.607e-06 | | | 3.89
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 78 ave 78 max 78 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7 ave 7 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 14 ave 14 max 14 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14
|
||||
Ave neighs/atom = 4.6666667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
write_data test.data
|
||||
System init for write_data ...
|
||||
|
||||
print "All done!"
|
||||
All done!
|
||||
Total wall time: 0:00:00
|
||||
@ -25,8 +25,8 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
|
||||
double denom, rho_bkgd, Fl;
|
||||
double scaleii;
|
||||
|
||||
printf("meam_dens_final arho3m\n");
|
||||
printf("%f\n", arho3m[0][0]);
|
||||
//printf("meam_dens_final arho3m\n");
|
||||
//printf("%f\n", arho3m[0][0]);
|
||||
|
||||
// Complete the calculation of density
|
||||
|
||||
@ -52,14 +52,14 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
|
||||
for (m = 0; m < 10; m++) {
|
||||
rho3[i] = rho3[i] + this->v3D[m] * (arho3[i][m] * arho3[i][m]
|
||||
- arho3m[i][m] * arho3m[i][m]);
|
||||
printf("arho loop %f %f\n", arho3[i][m], arho3m[i][m]);
|
||||
//printf("arho loop %f %f\n", arho3[i][m], arho3m[i][m]);
|
||||
}
|
||||
|
||||
// Compared to Greg's original, all of the t weightings are already accounted for.
|
||||
// Code block for t_ave removed.
|
||||
printf("gam rho %f %f %f\n", rho1[i], rho2[i], rho3[i]);
|
||||
//printf("gam rho %f %f %f\n", rho1[i], rho2[i], rho3[i]);
|
||||
gamma[i] = rho1[i] + rho2[i] + rho3[i];
|
||||
printf("gam check 0 %f\n", gamma[i]);
|
||||
//printf("gam check 0 %f\n", gamma[i]);
|
||||
|
||||
/*
|
||||
if (rho0[i] > 0.0) {
|
||||
@ -80,11 +80,11 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
|
||||
|
||||
gamma[i] = t_ave[i][0] * rho1[i] + t_ave[i][1] * rho2[i] + t_ave[i][2] * rho3[i];
|
||||
*/
|
||||
printf("rho0 %f\n", rho0[i]);
|
||||
//printf("rho0 %f\n", rho0[i]);
|
||||
if (rho0[i] > 0.0) {
|
||||
gamma[i] = gamma[i] / (rho0[i] * rho0[i]);
|
||||
}
|
||||
printf("gam check1 %f\n", gamma[i]);
|
||||
//printf("gam check1 %f\n", gamma[i]);
|
||||
|
||||
Z = get_Zij(this->lattce_meam[elti][elti]);
|
||||
|
||||
@ -97,7 +97,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
|
||||
if (this->ibar_meam[elti] <= 0) {
|
||||
Gbar = 1.0;
|
||||
dGbar = 0.0;
|
||||
printf("ibar meam <= 0\n");
|
||||
//printf("ibar meam <= 0\n");
|
||||
} else {
|
||||
if (this->mix_ref_t == 1) {
|
||||
gam = (t_ave[i][0] * shp[0] + t_ave[i][1] * shp[1] + t_ave[i][2] * shp[2]) / (Z * Z);
|
||||
@ -106,7 +106,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
|
||||
(Z * Z);
|
||||
}
|
||||
Gbar = G_gam(gam, this->ibar_meam[elti], errorflag);
|
||||
printf("ibar meam > 0\n");
|
||||
//printf("ibar meam > 0\n");
|
||||
}
|
||||
rho[i] = rho0[i] * G;
|
||||
|
||||
@ -130,7 +130,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
|
||||
rhob = rho[i] / rho_bkgd;
|
||||
denom = 1.0 / rho_bkgd;
|
||||
|
||||
printf("dgam rhob denom %f %f\n", rhob, denom);
|
||||
//printf("dgam rhob denom %f %f\n", rhob, denom);
|
||||
|
||||
G = dG_gam(gamma[i], this->ibar_meam[elti], dG);
|
||||
|
||||
|
||||
@ -90,7 +90,7 @@ MEAM::meam_dens_setup(int atom_nmax, int nall, int n_neigh)
|
||||
}
|
||||
|
||||
// zero out local arrays
|
||||
printf("^^^ zero out local arrays in mean_dens_init\n");
|
||||
//printf("^^^ zero out local arrays in mean_dens_init\n");
|
||||
for (i = 0; i < nall; i++) {
|
||||
rho0[i] = 0.0;
|
||||
arho2b[i] = 0.0;
|
||||
@ -119,7 +119,7 @@ MEAM::meam_dens_setup(int atom_nmax, int nall, int n_neigh)
|
||||
tsq_ave[i][0] = tsq_ave[i][1] = tsq_ave[i][2] = 0.0;
|
||||
}
|
||||
|
||||
printf("^^^ arho3m %f\n", arho3m[0][0]);
|
||||
//printf("^^^ arho3m %f\n", arho3m[0][0]);
|
||||
}
|
||||
|
||||
void
|
||||
@ -361,9 +361,11 @@ MEAM::calc_rho1(int i, int /*ntype*/, int* type, int* fmap, double** x, int numn
|
||||
rhoa2i = rhoa2i * this->t2_meam[elti];
|
||||
rhoa3i = rhoa3i * this->t3_meam[elti];
|
||||
}
|
||||
/*
|
||||
printf("rhos1 %d %d %f %f %f %f\n", i, j, rhoa1i, rhoa1j, rhoa1mi, rhoa1mj);
|
||||
printf("rhos2 %d %d %f %f %f %f\n", i, j, rhoa2i, rhoa2j, rhoa2mi, rhoa2mj);
|
||||
printf("rhos3 %d %d %f %f %f %f\n", i, j, rhoa3i, rhoa3j, rhoa3mi, rhoa3mj);
|
||||
*/
|
||||
rho0[i] = rho0[i] + rhoa0j;
|
||||
rho0[j] = rho0[j] + rhoa0i;
|
||||
// For ialloy = 2, use single-element value (not average)
|
||||
@ -405,7 +407,7 @@ MEAM::calc_rho1(int i, int /*ntype*/, int* type, int* fmap, double** x, int numn
|
||||
A2mi = rhoa2mi/rij2;
|
||||
A3mi = rhoa3mi/(rij2*rij);
|
||||
}
|
||||
printf("arho2mb i j %d %d %f %f\n", i, j, arho2mb[i], arho2mb[j]);
|
||||
//printf("arho2mb i j %d %d %f %f\n", i, j, arho2mb[i], arho2mb[j]);
|
||||
for (m = 0; m < 3; m++) {
|
||||
arho1[i][m] = arho1[i][m] + A1j * delij[m];
|
||||
arho1[j][m] = arho1[j][m] - A1i * delij[m];
|
||||
@ -417,8 +419,8 @@ MEAM::calc_rho1(int i, int /*ntype*/, int* type, int* fmap, double** x, int numn
|
||||
arho3mb[i][m] = arho3mb[i][m] + rhoa3mj*delij[m] / rij;
|
||||
arho3mb[j][m] = arho3mb[j][m] - rhoa3mi*delij[m] / rij;
|
||||
}
|
||||
printf("arho1m %f %f\n", arho1m[i][m], arho1m[j][m]);
|
||||
printf("arho3mb %f %f\n", arho3mb[i][m], arho3mb[j][m]);
|
||||
//printf("arho1m %f %f\n", arho1m[i][m], arho1m[j][m]);
|
||||
//printf("arho3mb %f %f\n", arho3mb[i][m], arho3mb[j][m]);
|
||||
for (n = m; n < 3; n++) {
|
||||
arho2[i][nv2] = arho2[i][nv2] + A2j * delij[m] * delij[n];
|
||||
arho2[j][nv2] = arho2[j][nv2] + A2i * delij[m] * delij[n];
|
||||
@ -427,7 +429,7 @@ MEAM::calc_rho1(int i, int /*ntype*/, int* type, int* fmap, double** x, int numn
|
||||
arho2m[j][nv2] = arho2m[j][nv2] + A2mi*delij[m] * delij[n];
|
||||
}
|
||||
//printf("delij %f %f\n", delij[m], delij[n]);
|
||||
printf("arho2m %d %d %f %f\n", nv2, m, arho2m[i][nv2], arho2m[j][nv2]);
|
||||
//printf("arho2m %d %d %f %f\n", nv2, m, arho2m[i][nv2], arho2m[j][nv2]);
|
||||
nv2 = nv2 + 1;
|
||||
for (p = n; p < 3; p++) {
|
||||
arho3[i][nv3] = arho3[i][nv3] + A3j * delij[m] * delij[n] * delij[p];
|
||||
@ -437,7 +439,7 @@ MEAM::calc_rho1(int i, int /*ntype*/, int* type, int* fmap, double** x, int numn
|
||||
arho3m[j][nv3] = arho3m[j][nv3] - A3mi*delij[m]*delij[n]*delij[p];
|
||||
}
|
||||
//arho3m[0][0]=500.0;
|
||||
printf("arho3m %d %f %f\n", p, arho3m[i][nv3], arho3m[j][nv3]);
|
||||
//printf("arho3m %d %f %f\n", p, arho3m[i][nv3], arho3m[j][nv3]);
|
||||
nv3 = nv3 + 1;
|
||||
}
|
||||
}
|
||||
|
||||
@ -75,8 +75,8 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
double drho3mdr1, drho3mdr2, drho3mds1, drho3mds2;
|
||||
double drho3mdrm1[3], drho3mdrm2[3];
|
||||
|
||||
printf("----- begin meam_force -----\n");
|
||||
printf("forces f %d %f\n", i, f[0][0]);
|
||||
//printf("----- begin meam_force -----\n");
|
||||
//printf("forces f %d %f\n", i, f[0][0]);
|
||||
|
||||
third = 1.0 / 3.0;
|
||||
sixth = 1.0 / 6.0;
|
||||
@ -89,7 +89,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
xitmp = x[i][0];
|
||||
yitmp = x[i][1];
|
||||
zitmp = x[i][2];
|
||||
printf("xtmp ytmp ztmp: %f %f %f\n", xitmp, yitmp, zitmp);
|
||||
//printf("xtmp ytmp ztmp: %f %f %f\n", xitmp, yitmp, zitmp);
|
||||
|
||||
// Treat each pair
|
||||
|
||||
@ -98,7 +98,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
eltj = fmap[type[j]];
|
||||
scaleij = scale[type[i]][type[j]];
|
||||
|
||||
printf("in j loop %d %d %d %d %f\n", i, j, eltj, type[j], scrfcn[fnoffset + jn]);
|
||||
//printf("in j loop %d %d %d %d %f\n", i, j, eltj, type[j], scrfcn[fnoffset + jn]);
|
||||
if (!iszero(scrfcn[fnoffset + jn]) && eltj >= 0) {
|
||||
|
||||
sij = scrfcn[fnoffset + jn] * fcpair[fnoffset + jn];
|
||||
@ -110,7 +110,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
if (rij2 < this->cutforcesq) {
|
||||
rij = sqrt(rij2);
|
||||
recip = 1.0 / rij;
|
||||
printf("forces, sij, rij = %f %f for i = %d and j = %d\n", sij, rij, i, j);
|
||||
//printf("forces, sij, rij = %f %f for i = %d and j = %d\n", sij, rij, i, j);
|
||||
// Compute phi and phip
|
||||
ind = this->eltind[elti][eltj];
|
||||
pp = rij * this->rdrar;
|
||||
@ -120,12 +120,14 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
pp = std::min(pp, 1.0);
|
||||
phi = ((this->phirar3[ind][kk] * pp + this->phirar2[ind][kk]) * pp + this->phirar1[ind][kk]) * pp + this->phirar[ind][kk];
|
||||
phip = (this->phirar6[ind][kk] * pp + this->phirar5[ind][kk]) * pp + this->phirar4[ind][kk];
|
||||
/*
|
||||
printf("--- phi and phip i = %d ---\n", i);
|
||||
printf("phi %f %f\n", this->phirar3[ind][kk], this->phirar2[ind][kk]);
|
||||
printf("phi2 %f %f\n", this->phirar1[ind][kk], this->phirar[ind][kk]);
|
||||
printf("phip %f %f\n", this->phirar6[ind][kk], this->phirar5[ind][kk]);
|
||||
printf("phip2 %f\n", this->phirar4[ind][kk]);
|
||||
printf("-----");
|
||||
*/
|
||||
|
||||
if (eflag_either != 0) {
|
||||
double phi_sc = phi * scaleij;
|
||||
@ -212,9 +214,11 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
const double t2mj = this->t2_meam[eltj];
|
||||
const double t3mj = this->t3_meam[eltj];
|
||||
|
||||
// ialloy mod not needed in msmeam according to fortran code
|
||||
// if we remove this, need to multiply rhoali and rhoalj above by t vars
|
||||
if (this->ialloy == 1) {
|
||||
// ialloy mod not needed in msmeam, but similarity here is that we need to multiply rhos by t
|
||||
// msmeam fortran code accomplishes this by multiplying rho's with t's above, like we did
|
||||
// with rhoa1mj, rhoa2mj, etc
|
||||
|
||||
if (this->ialloy == 1 || this->msmeamflag) {
|
||||
rhoa1j *= t1mj;
|
||||
rhoa2j *= t2mj;
|
||||
rhoa3j *= t3mj;
|
||||
@ -229,10 +233,12 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
drhoa3i *= t3mi;
|
||||
}
|
||||
|
||||
/*
|
||||
printf("forces, rhoali %f %f %f %f\n", rhoa0i, rhoa1i, rhoa2i, rhoa3i);
|
||||
printf("forces, rhoalmi %f %f %f\n", rhoa1mi, rhoa2mi, rhoa3mi);
|
||||
printf("forces, rhoalj %f %f %f %f\n", rhoa0j, rhoa1j, rhoa2j, rhoa3j);
|
||||
printf("forces, rhoalmj %f %f %f\n", rhoa1mj, rhoa2mj, rhoa3mj);
|
||||
*/
|
||||
|
||||
nv2 = 0;
|
||||
nv3 = 0;
|
||||
@ -288,7 +294,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
arg = delij[n] * delij[p] * this->v2D[nv2];
|
||||
arg1i2m = arg1i2m + arho2m[i][nv2] * arg;
|
||||
arg1j2m = arg1j2m + arho2m[j][nv2] * arg;
|
||||
printf(" arho2m[j][nv2] %d %d %f\n", j, nv2, arho2m[j][nv2]);
|
||||
//printf(" arho2m[j][nv2] %d %d %f\n", j, nv2, arho2m[j][nv2]);
|
||||
nv2 = nv2 + 1;
|
||||
}
|
||||
arg1i1m = arg1i1m - arho1m[i][n] * delij[n];
|
||||
@ -298,10 +304,12 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
printf("rho1 terms arg1i %d %d %f %f\n", i, j, arg1i1, arg1i1m);
|
||||
printf("rho1 terms arg1j %d %d %f %f\n", i, j, arg1j1, arg1j1m);
|
||||
printf("rho1 terms rhoa1j %d %d %f %f\n", i, j, rhoa1j, rhoa1mj);
|
||||
printf("rho1 terms drhoa1j %d %d %f %f\n", i,j, drhoa1j, drhoa1mj);
|
||||
*/
|
||||
|
||||
// rho0 terms
|
||||
drho0dr1 = drhoa0j * sij;
|
||||
@ -374,8 +382,8 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
a2 = 2 * sij / rij2;
|
||||
drho2mdr1 = a2 * (drhoa2mj - 2 * rhoa2mj / rij) * arg1i2m - 2.0 / 3.0 * arho2mb[i] * drhoa2mj * sij;
|
||||
drho2mdr2 = a2 * (drhoa2mi - 2 * rhoa2mi / rij) * arg1j2m - 2.0 / 3.0 * arho2mb[j] * drhoa2mi * sij;
|
||||
printf(" drho2mdr arho %d %d %f %f\n", i, j, arho2mb[i], arho2mb[j]);
|
||||
printf(" drhoa rhoa arg1 %f %f %f\n", drhoa2mi, rhoa2mi, arg1j2m);
|
||||
//printf(" drho2mdr arho %d %d %f %f\n", i, j, arho2mb[i], arho2mb[j]);
|
||||
//printf(" drhoa rhoa arg1 %f %f %f\n", drhoa2mi, rhoa2mi, arg1j2m);
|
||||
a2 = 4 * sij / rij2;
|
||||
for (m = 0; m < 3; m++) {
|
||||
drho2mdrm1[m] = 0.0;
|
||||
@ -388,13 +396,13 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
drho2mdrm2[m] = -a2 * rhoa2mi * drho2mdrm2[m];
|
||||
}
|
||||
|
||||
printf("forces drho2 %f %f %f %f\n", drho2drm1[0], drho2mdrm1[0], drho2drm2[0], drho2mdrm2[0]);
|
||||
//printf("forces drho2 %f %f %f %f\n", drho2drm1[0], drho2mdrm1[0], drho2drm2[0], drho2mdrm2[0]);
|
||||
|
||||
// rho3m terms
|
||||
rij3 = rij * rij2;
|
||||
a3 = 2 * sij / rij3;
|
||||
a3a = 6.0 / 5.0 * sij / rij;
|
||||
printf("args %f %f %f %f\n", arg1i3m, arg3i3m, arg1j3m, arg3j3m);
|
||||
//printf("args %f %f %f %f\n", arg1i3m, arg3i3m, arg1j3m, arg3j3m);
|
||||
drho3mdr1 = a3 * (drhoa3mj - 3 * rhoa3mj / rij) * arg1i3m - a3a * (drhoa3mj - rhoa3mj / rij) * arg3i3m;
|
||||
drho3mdr2 = a3 * (drhoa3mi - 3 * rhoa3mi / rij) * arg1j3m - a3a * (drhoa3mi - rhoa3mi / rij) * arg3j3m;
|
||||
drho3mdr1 *= -1.0;
|
||||
@ -402,7 +410,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
|
||||
a3 = 6 * sij / rij3;
|
||||
a3a = 6 * sij / (5 * rij);
|
||||
printf("forces drho3mdr %f %f\n", drho3mdr1, drho3mdr2);
|
||||
//printf("forces drho3mdr %f %f\n", drho3mdr1, drho3mdr2);
|
||||
for (m = 0; m < 3; m++) {
|
||||
drho3mdrm1[m] = 0.0;
|
||||
drho3mdrm2[m] = 0.0;
|
||||
@ -426,11 +434,12 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
drho3mdrm1[m] = 0.0;
|
||||
drho3mdrm2[m] = 0.0;
|
||||
}
|
||||
|
||||
/*
|
||||
printf("rho2 terms drho2dr1 %f %f\n", drho2dr1, drho2mdr1);
|
||||
printf("rho2 terms drho2dr2 %f %f\n", drho2dr2, drho2mdr2);
|
||||
printf("rho2 terms %f %f\n", drho2drm1[0], drho2mdrm1[0]);
|
||||
printf("rho2 terms %f %f\n", drho2drm2[0], drho2mdrm2[0]);
|
||||
*/
|
||||
|
||||
|
||||
// compute derivatives of weighting functions t wrt rij
|
||||
@ -509,6 +518,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
get_shpfcn(this->lattce_meam[eltj][eltj], this->stheta_meam[elti][elti], this->ctheta_meam[elti][elti], shpj);
|
||||
|
||||
if (this->msmeamflag){
|
||||
/*
|
||||
printf("test rhodg %f %f %f\n", dgamma1[i], dgamma2[i], dgamma3[i]);
|
||||
printf("test rhod dtdr %f %f %f\n", dt1dr1, dt2dr1, dt3dr1);
|
||||
printf("test rhod rho %f %f %f\n", rho1[i], rho2[i], rho3[i]);
|
||||
@ -520,6 +530,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
printf(" %f %f %f\n", dgamma1[i], dgamma2[i], dgamma3[i]);
|
||||
printf(" %f %f %f\n", drho1dr2, drho2dr2, drho3dr2);
|
||||
printf(" %f %f %f\n", drho1mdr2, drho2mdr2, drho3mdr2);
|
||||
*/
|
||||
drhodr1 = dgamma1[i] * drho0dr1 +
|
||||
dgamma2[i] * (dt1dr1 * rho1[i] + t1i * (drho1dr1 - drho1mdr1) +
|
||||
dt2dr1 * rho2[i] + t2i * (drho2dr1 - drho2mdr1) +
|
||||
@ -530,7 +541,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
dt2dr2 * rho2[j] + t2j * (drho2dr2 - drho2mdr2) +
|
||||
dt3dr2 * rho3[j] + t3j * (drho3dr2 - drho3mdr2)) -
|
||||
dgamma3[j] * (shpj[0] * dt1dr2 + shpj[1] * dt2dr2 + shpj[2] * dt3dr2);
|
||||
printf(" drhodr1&2 %f %f\n", drhodr1, drhodr2);
|
||||
//printf(" drhodr1&2 %f %f\n", drhodr1, drhodr2);
|
||||
for (m = 0; m < 3; m++) {
|
||||
drhodrm1[m] = 0.0;
|
||||
drhodrm2[m] = 0.0;
|
||||
@ -559,12 +570,12 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
}
|
||||
}
|
||||
|
||||
printf("rhod terms drhodr1 %f %f\n", drhodr1, drhodr2);
|
||||
printf("rhod terms drhodr1 %f %f\n", drhodrm1[0], drhodrm2[0]);
|
||||
//printf("rhod terms drhodr1 %f %f\n", drhodr1, drhodr2);
|
||||
//printf("rhod terms drhodr1 %f %f\n", drhodrm1[0], drhodrm2[0]);
|
||||
|
||||
// Compute derivatives wrt sij, but only if necessary
|
||||
if (!iszero(dscrfcn[fnoffset + jn])) {
|
||||
printf("computing derivatives wrt sij\n");
|
||||
//printf("computing derivatives wrt sij\n");
|
||||
drho0ds1 = rhoa0j;
|
||||
drho0ds2 = rhoa0i;
|
||||
a1 = 2.0 / rij;
|
||||
@ -598,6 +609,7 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
}
|
||||
|
||||
if (this->ialloy == 1) {
|
||||
|
||||
a1i = fdiv_zero(rhoa0j, tsq_ave[i][0]);
|
||||
a1j = fdiv_zero(rhoa0i, tsq_ave[j][0]);
|
||||
a2i = fdiv_zero(rhoa0j, tsq_ave[i][1]);
|
||||
@ -667,11 +679,13 @@ MEAM::meam_force(int i, int eflag_global, int eflag_atom, int vflag_global, int
|
||||
|
||||
dUdrij = phip * sij + frhop[i] * drhodr1 + frhop[j] * drhodr2;
|
||||
dUdsij = 0.0;
|
||||
|
||||
printf("--- compute derivatives of energy wrt ...\n");
|
||||
printf("phip sij %f %f\n", phip,sij);
|
||||
printf("drhodr %f %f\n", drhodr1, drhodr2);
|
||||
printf("fp %f %f\n", frhop[i], frhop[j]);
|
||||
printf("dUdrij %f\n", dUdrij);
|
||||
|
||||
if (!iszero(dscrfcn[fnoffset + jn])) {
|
||||
dUdsij = phi + frhop[i] * drhods1 + frhop[j] * drhods2;
|
||||
}
|
||||
|
||||
@ -377,7 +377,7 @@ double MEAM::phi_meam(double r, int a, int b)
|
||||
|
||||
// calculate average weighting factors for the reference structure
|
||||
if (this->lattce_meam[a][b] == C11) {
|
||||
// note ialloy and t_ave not used in MS-MEAM
|
||||
// note ialloy and t_ave not used in msmeam
|
||||
if (this->ialloy == 2) {
|
||||
t11av = this->t1_meam[a];
|
||||
t12av = this->t1_meam[b];
|
||||
@ -399,7 +399,7 @@ double MEAM::phi_meam(double r, int a, int b)
|
||||
get_tavref(&t11av, &t21av, &t31av, &t12av, &t22av, &t32av, this->t1_meam[a], this->t2_meam[a],
|
||||
this->t3_meam[a], this->t1_meam[b], this->t2_meam[b], this->t3_meam[b], r, a, b,
|
||||
this->lattce_meam[a][b]);
|
||||
// msmeam - call twice with different sets of variables
|
||||
// with msmeam call twice with different sets of variables
|
||||
if (this->msmeamflag){
|
||||
get_tavref(&t1m1av, &t2m1av, &t3m1av, &t1m2av, &t2m2av, &t3m2av, this->t1m_meam[a], this->t2m_meam[a],
|
||||
this->t3m_meam[a], this->t1m_meam[b], this->t2m_meam[b], this->t3m_meam[b], r, a, b,
|
||||
@ -731,6 +731,7 @@ void MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, dou
|
||||
rhoa22 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta2_meam[b] * a2);
|
||||
rhoa32 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta3_meam[b] * a2);
|
||||
*/
|
||||
/*
|
||||
rhoa11 = this->rho0_meam[a] * this->t1_meam[a] * MathSpecial::fm_exp(-this->beta1_meam[a] * a1);
|
||||
rhoa21 = this->rho0_meam[a] * this->t2_meam[a] * MathSpecial::fm_exp(-this->beta2_meam[a] * a1);
|
||||
rhoa31 = this->rho0_meam[a] * this->t3_meam[a] * MathSpecial::fm_exp(-this->beta3_meam[a] * a1);
|
||||
@ -738,7 +739,17 @@ void MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, dou
|
||||
rhoa12 = this->rho0_meam[b] * this->t1_meam[b] * MathSpecial::fm_exp(-this->beta1_meam[b] * a2);
|
||||
rhoa22 = this->rho0_meam[b] * this->t2_meam[b] * MathSpecial::fm_exp(-this->beta2_meam[b] * a2);
|
||||
rhoa32 = this->rho0_meam[b] * this->t3_meam[b] * MathSpecial::fm_exp(-this->beta3_meam[b] * a2);
|
||||
*/
|
||||
if (this->msmeamflag){
|
||||
// in msmeam, the rho variables are multiplied by t here since we don't use ialloy
|
||||
rhoa11 = this->rho0_meam[a] * this->t1_meam[a] * MathSpecial::fm_exp(-this->beta1_meam[a] * a1);
|
||||
rhoa21 = this->rho0_meam[a] * this->t2_meam[a] * MathSpecial::fm_exp(-this->beta2_meam[a] * a1);
|
||||
rhoa31 = this->rho0_meam[a] * this->t3_meam[a] * MathSpecial::fm_exp(-this->beta3_meam[a] * a1);
|
||||
rhoa02 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
|
||||
rhoa12 = this->rho0_meam[b] * this->t1_meam[b] * MathSpecial::fm_exp(-this->beta1_meam[b] * a2);
|
||||
rhoa22 = this->rho0_meam[b] * this->t2_meam[b] * MathSpecial::fm_exp(-this->beta2_meam[b] * a2);
|
||||
rhoa32 = this->rho0_meam[b] * this->t3_meam[b] * MathSpecial::fm_exp(-this->beta3_meam[b] * a2);
|
||||
// msmeam specific rho vars
|
||||
rhoa1m1 = this->rho0_meam[a] * this->t1m_meam[a] * MathSpecial::fm_exp(-this->beta1m_meam[a] * a1);
|
||||
rhoa2m1 = this->rho0_meam[a] * this->t2m_meam[a] * MathSpecial::fm_exp(-this->beta2m_meam[a] * a1);
|
||||
rhoa3m1 = this->rho0_meam[a] * this->t3m_meam[a] * MathSpecial::fm_exp(-this->beta3m_meam[a] * a1);
|
||||
@ -746,6 +757,15 @@ void MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, dou
|
||||
rhoa2m2 = this->rho0_meam[b] * this->t2m_meam[b] * MathSpecial::fm_exp(-this->beta2m_meam[b] * a2);
|
||||
rhoa3m2 = this->rho0_meam[b] * this->t3m_meam[b] * MathSpecial::fm_exp(-this->beta3m_meam[b] * a2);
|
||||
}
|
||||
else{
|
||||
rhoa11 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta1_meam[a] * a1);
|
||||
rhoa21 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta2_meam[a] * a1);
|
||||
rhoa31 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta3_meam[a] * a1);
|
||||
rhoa02 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
|
||||
rhoa12 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta1_meam[b] * a2);
|
||||
rhoa22 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta2_meam[b] * a2);
|
||||
rhoa32 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta3_meam[b] * a2);
|
||||
}
|
||||
//printf("rhoa0 %f %f\n", rhoa01, rhoa02);
|
||||
//printf("rhoai1 %f %f %f\n", rhoa11, rhoa21, rhoa31);
|
||||
//printf("rhoai2 %f %f %f\n", rhoa12, rhoa22, rhoa32);
|
||||
@ -842,9 +862,11 @@ void MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, dou
|
||||
case L12:
|
||||
*rho01 = 8 * rhoa01 + 4 * rhoa02;
|
||||
*rho02 = 12 * rhoa01;
|
||||
// not modified by choice with msmeam; use of t's inconsistent with above
|
||||
// don't use with msmeam; use of t's inconsistent with above
|
||||
// also we should not use ialloy with msmeam
|
||||
// possibly make ialloy not an option when using msmeam
|
||||
if (this->ialloy == 1 && !this->msmeamflag) {
|
||||
printf("^^^ ialloy=1 in getdensref\n");
|
||||
//printf("^^^ ialloy=1 in getdensref\n");
|
||||
*rho21 = 8. / 3. * MathSpecial::square(rhoa21 * this->t2_meam[a] - rhoa22 * this->t2_meam[b]);
|
||||
denom = 8 * rhoa01 * MathSpecial::square(this->t2_meam[a]) + 4 * rhoa02 * MathSpecial::square(this->t2_meam[b]);
|
||||
if (denom > 0.)
|
||||
|
||||
@ -40,11 +40,6 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* /*atwt*
|
||||
double *t3m)
|
||||
{
|
||||
|
||||
printf("^^^^^ meam setup global msmeamflag: %d\n", this->msmeamflag);
|
||||
if (this->msmeamflag){
|
||||
printf("b1m[0]: %f\n", b1m[0]);
|
||||
}
|
||||
|
||||
int i;
|
||||
double tmplat[maxelt];
|
||||
|
||||
@ -60,7 +55,7 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* /*atwt*
|
||||
this->beta2_meam[i] = b2[i];
|
||||
this->beta3_meam[i] = b3[i];
|
||||
if (this->msmeamflag){
|
||||
printf("^^^^^ Filling betam\n");
|
||||
//printf("^^^^^ Filling betam\n");
|
||||
this->beta1m_meam[i] = b1m[i];
|
||||
this->beta2m_meam[i] = b2m[i];
|
||||
this->beta3m_meam[i] = b3m[i];
|
||||
|
||||
@ -134,7 +134,7 @@ void PairMEAM::compute(int eflag, int vflag)
|
||||
int offset = 0;
|
||||
errorflag = 0;
|
||||
|
||||
printf("before meam_dens_init %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
//printf("before meam_dens_init %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
|
||||
for (ii = 0; ii < inum_half; ii++) {
|
||||
i = ilist_half[ii];
|
||||
@ -144,18 +144,18 @@ void PairMEAM::compute(int eflag, int vflag)
|
||||
offset);
|
||||
offset += numneigh_half[i];
|
||||
}
|
||||
printf("after meam_dens_init %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
printf("before revcomm %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
//printf("after meam_dens_init %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
//printf("before revcomm %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
comm->reverse_comm(this);
|
||||
printf("after revcomm %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
//printf("after revcomm %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
meam_inst->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom,
|
||||
&eng_vdwl,eatom,ntype,type,map,scale,errorflag);
|
||||
if (errorflag)
|
||||
error->one(FLERR,"MEAM library error {}",errorflag);
|
||||
|
||||
printf("before forcomm %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
//printf("before forcomm %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
comm->forward_comm(this);
|
||||
printf("after forcomm %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
//printf("after forcomm %f %f\n", meam_inst->arho2m[0][0], meam_inst->arho3m[0][0]);
|
||||
|
||||
offset = 0;
|
||||
|
||||
|
||||
Reference in New Issue
Block a user