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Modified the fix_elec_drag.* name to fix_electron_stopping_fit.* to align with and distinguish from existing fix_electron_stopping.*

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jstewa
2020-09-23 17:14:14 -06:00
parent 6392d24411
commit f5635208e3
10 changed files with 7791 additions and 1 deletions
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7008
examples/USER/misc/electron_stopping_fit/CuNb_ZL4.eam.alloy Normal file
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examples/USER/misc/electron_stopping_fit/README Normal file
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// ---------------------------------------------------------------------
VERSION: JULY, 2018
// ---------------------------------------------------------------------
This package contains the commands necessary to calculate and apply
electronic stopping effects via an inelastic energy-loss (IEL) force.
A detailed description of this method can be found in the following
papers:
J.A. Stewart, G. Brookman, P. Price, M. Franco, W. Ji, K. Hattar,
R. Dingreville (2018) Characterizing single isolated radiation-damage
events from molecular dynamics via virtual diffraction methods.
Journal of Applied Physics, 123(16), 165902.
C.W. Lee, J.A. Stewart, S.M. Foiles, R. Dingreville, and A. Schleife
(2020) Multiscale simulations of electron and ion dynamics in
self-irradiated silicon. Physical Review B, 102(2), 024107.
// ---------------------------------------------------------------------
USAGE AND INPUT:
fix_elec_drag: Calculates electronic stopping power and cumulative
energy lost to the electron gas via a quadratic
functional and applies a drag force to the classical
equations of motion for atoms moving above some
cutoff velocity.
Usage : fix edrag all electron/stopping/fit 4.63 3.3e-3 4.0e-8
Input : - Lower energy cutoff (Upper cutoff is assumed
to be 2x this value for truncation)
- Linear coefficient
- Quadratic coefficient (Usually taken = 0)
// ---------------------------------------------------------------------
AUTHOR INFORMATION:
The primary contributors to this package are:
Stephen M. Foiles (Sandia National Laboratories)
James A. Stewart (Sandia National Laboratories)
// ---------------------------------------------------------------------
ACKNOWLEDGEMENTS:
Thanks for additional contributions and development goes to:
Remi Dingreville (Sandia National Laboratories)
Elton Y. Chen (Sandia National Laboratories)
// ---------------------------------------------------------------------

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examples/USER/misc/electron_stopping_fit/Si.tersoff.zbl Normal file
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# Tersoff pair style parameters for various elements and/or mixtures
# Multiple entries can be added to this file, LAMMPS reads the ones it needs
#
# The following entries are in LAMMPS "metal" units (all others are unitless):
# A, B = eV; lambda1, lambda2, lambda3 = 1/Angstroms; R, D, ZBLcut = Angstroms; Z_i, Z_j = electron charge units
#
# These parameters are from the following papers and adapted to be used in the LAMMPS formalism:
# Tersoff (1988) New empirical approach for the structure and energy of covlent systems. Phys Rev B, 37, 6991 - 7000.
# Devanathan et al. (1998) Displacement threshold energies in beta-SiC. J Nucl Mater, 253, 47 - 52.
#
# Z_i and Z_j are the charges of the ith and jth nuclei from the coulomb potential
# ZBLcut is the ZBL cutoff parameter (should be less than 1.0 angstrom), ZBLexpscale is the scaling parameter in the exponential of the smoothing function
#
#
# Format of a single entry (one or more lines):
# element 1, element 2, element 3, m, gamma, lambda3, c, d, h, n, beta, lambda2, X_ij*B, R, D, lambda1, A, Z_i, Z_j, ZBLcut, ZBLexpscale
Si Si Si 1.0 1.0 0.0 1.0039e5 1.6217e1 -5.9825e-1 7.8734e-1 1.1e-6 1.7322 4.7118e2 2.85 0.15 2.4799 1.8308e3 14 14 0.95 14

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# ***
# Example input for including electronic stopping effects using fix elec/drag
# Perfect Cu lattice with a single incident Nb atom - multiple species simulation
# ***
units metal
boundary p p p
lattice fcc 3.597
region box block -15 15 -15 15 -15 15
create_box 2 box
create_atoms 1 box
pair_style eam/alloy
pair_coeff * * CuNb_ZL4.eam.alloy Cu Nb
mass 1 63.546
mass 2 92.90638
velocity all create 300 42534 mom yes rot yes
set atom 1 type 2
group pka id 1
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
thermo 20
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
dump 0 all custom 200 dump.pka_* id type x y z vx vy vz fx fy fz
dump_modify 0 first yes
run 2000

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examples/USER/misc/electron_stopping_fit/in.cascade_SiSi Normal file
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# ***
# Example input for including electronic stopping effects using fix elec/drag
# Perfect Si lattice with one primary knock-on atom (PKA) - single species simulation
# ***
units metal
boundary p p p
lattice diamond 5.431
region box block -15 15 -15 15 -15 15
create_box 1 box
create_atoms 1 box
pair_style tersoff/zbl
pair_coeff * * Si.tersoff.zbl Si
mass 1 28.0855
velocity all create 300 42534 mom yes rot yes
group pka id 1
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
thermo 20
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
dump 0 all custom 200 dump.pka_* id type x y z vx vy vz fx fy fz
dump_modify 0 first yes
run 2000

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examples/USER/misc/electron_stopping_fit/log.cascase_CuNb Normal file
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LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix elec/drag
# Perfect Cu lattice with a single incident Nb atom - multiple species simulation
# ***
units metal
boundary p p p
lattice fcc 3.597
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
region box block -15 15 -15 15 -15 15
create_box 2 box
Created orthogonal box = (-53.955000 -53.955000 -53.955000) to (53.955000 53.955000 53.955000)
2 by 2 by 4 MPI processor grid
create_atoms 1 box
Created 108000 atoms
create_atoms CPU = 0.002 seconds
pair_style eam/alloy
pair_coeff * * CuNb_ZL4.eam.alloy Cu Nb
mass 1 63.546
mass 2 92.90638
velocity all create 300 42534 mom yes rot yes
set atom 1 type 2
Setting atom values ...
1 settings made for type
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all elec/drag 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
thermo 20
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
dump 0 all custom 200 dump.pka_* id type x y z vx vy vz fx fy fz
dump_modify 0 first yes
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.506786
ghost atom cutoff = 7.506786
binsize = 3.753393, bins = 29 29 29
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.20 | 10.47 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 18322 -382316.35 255774.5 0
20 2.6647604e-06 0.00022494231 18308.42 -382179.62 255584.93 52.356667
40 1.1679999e-06 0.00025990893 18297.517 -382035.55 255432.72 60.488565
60 7.7212205e-07 0.00027888914 18288.602 -381915.51 255308.27 64.900024
80 5.9617028e-07 0.0002924637 18281.252 -381816.05 255205.66 68.05358
100 5.0061743e-07 0.00030339238 18275.297 -381735.46 255122.53 70.591475
120 4.4398667e-07 0.00031281961 18270.646 -381672.72 255057.61 72.780023
140 4.0989229e-07 0.00032134586 18267.246 -381627.23 255010.13 74.758942
160 3.9088566e-07 0.00032934172 18265.061 -381598.59 254979.64 76.614452
180 3.8354475e-07 0.00033707186 18264.073 -381586.58 254965.84 78.408129
200 3.8666558e-07 0.00034475509 18264.267 -381591.08 254968.56 80.190876
220 4.007769e-07 0.00035260282 18265.643 -381612.1 254987.76 82.011874
240 4.2835811e-07 0.00036085456 18268.204 -381649.77 255023.51 83.926836
260 4.7508573e-07 0.00036982649 18271.964 -381704.34 255076 86.009307
280 5.5330823e-07 0.00038000239 18276.946 -381776.25 255145.55 88.371814
300 6.9321904e-07 0.0003922506 18283.186 -381866.22 255232.67 91.216358
320 9.9050009e-07 0.00040850901 18290.744 -381975.51 255338.18 94.993734
340 2.0231145e-06 0.00043538567 18299.707 -382106.87 255463.3 101.24112
360 4.4734023e-06 0.00055311495 18304.008 -382193.31 255523.34 128.62138
380 8.7874706e-06 0.00064748812 18302.306 -382191.51 255499.58 150.56708
400 1.7106596e-06 0.00081274722 18292.538 -382095.51 255363.22 188.99556
420 8.1490654e-07 0.00083625178 18280.012 -381926.12 255188.35 194.45667
440 5.3697762e-07 0.00084952246 18268.337 -381766.23 255025.38 197.53782
460 4.0152518e-07 0.00085884162 18257.329 -381614.72 254871.7 199.70011
480 3.2168885e-07 0.00086605243 18246.914 -381471 254726.31 201.37217
500 2.6930333e-07 0.00087195548 18237.05 -381334.66 254588.6 202.7402
520 2.3246067e-07 0.00087697172 18227.709 -381205.43 254458.21 203.90207
540 2.0526276e-07 0.00088134976 18218.874 -381083.1 254334.87 204.91559
560 1.8445601e-07 0.00088524862 18210.529 -380967.5 254218.37 205.81773
580 1.6810201e-07 0.00088877616 18202.662 -380858.5 254108.55 206.63358
600 1.5497555e-07 0.0008920089 18195.265 -380755.99 254005.29 207.38093
620 1.4426609e-07 0.00089500317 18188.331 -380659.88 253908.49 208.07286
640 1.3541502e-07 0.00089780169 18181.853 -380570.09 253818.06 208.71932
660 1.280267e-07 0.00090043764 18175.826 -380486.56 253733.91 209.328
680 1.2181366e-07 0.00090293739 18170.244 -380409.22 253656 209.90504
700 1.165613e-07 0.00090532232 18165.106 -380338.04 253584.27 210.45541
720 1.1210827e-07 0.00090761002 18160.406 -380272.96 253518.66 210.9832
740 1.0833074e-07 0.00090981526 18156.143 -380213.96 253459.15 211.49183
760 1.0513259e-07 0.0009119506 18152.314 -380161 253405.7 211.98422
780 1.024387e-07 0.00091402688 18148.917 -380114.05 253358.28 212.4629
800 1.0019011e-07 0.00091605359 18145.95 -380073.1 253316.86 212.93007
820 9.8340559e-08 0.00091803919 18143.412 -380038.13 253281.42 213.38769
840 9.6853951e-08 0.0009199913 18141.301 -380009.11 253251.96 213.83753
860 9.5702524e-08 0.0009219169 18139.617 -379986.04 253228.45 214.28121
880 9.4865542e-08 0.00092382249 18138.358 -379968.91 253210.87 214.72025
900 9.4328102e-08 0.00092571421 18137.525 -379957.71 253199.24 215.15607
920 9.4080772e-08 0.00092759795 18137.116 -379952.43 253193.53 215.59003
940 9.411979e-08 0.00092947946 18137.131 -379953.08 253193.74 216.02348
960 9.4445831e-08 0.00093136447 18137.571 -379959.65 253199.88 216.45774
980 9.5064438e-08 0.00093325877 18138.435 -379972.15 253211.94 216.89415
1000 9.5986287e-08 0.0009351683 18139.723 -379990.58 253229.93 217.33411
1020 9.7227647e-08 0.00093709927 18141.437 -380014.95 253253.85 217.77904
1040 9.8811125e-08 0.00093905828 18143.576 -380045.26 253283.72 218.23048
1060 1.0076676e-07 0.00094105243 18146.142 -380081.54 253319.54 218.69009
1080 1.0313314e-07 0.00094308952 18149.136 -380123.8 253361.32 219.15967
1100 1.0595985e-07 0.00094517823 18152.558 -380172.05 253409.09 219.64123
1120 1.0930985e-07 0.00094732832 18156.41 -380226.32 253462.87 220.13705
1140 1.132636e-07 0.000949551 18160.694 -380286.64 253522.68 220.64974
1160 1.1792417e-07 0.00095185927 18165.412 -380353.04 253588.54 221.1823
1180 1.2342496e-07 0.00095426848 18170.567 -380425.55 253660.5 221.73831
1200 1.2994083e-07 0.00095679702 18176.161 -380504.23 253738.59 222.32204
1220 1.3770383e-07 0.00095946728 18182.197 -380589.11 253822.86 222.93869
1240 1.4702749e-07 0.00096230702 18188.679 -380680.26 253913.35 223.59472
1260 1.5834556e-07 0.00096535133 18195.613 -380777.75 254010.14 224.29828
1280 1.7227762e-07 0.00096864561 18203.002 -380881.67 254113.29 225.05993
1300 1.897315e-07 0.00097225015 18210.853 -380992.1 254222.89 225.89367
1320 2.1209523e-07 0.00097624755 18219.173 -381109.18 254339.04 226.81871
1340 2.4160263e-07 0.00098075538 18227.971 -381233.03 254461.86 227.86238
1360 2.8207358e-07 0.00098594918 18237.256 -381363.86 254591.48 229.0655
1380 3.4063727e-07 0.00099210804 18247.042 -381501.9 254728.09 230.49294
1400 4.322825e-07 0.00099971618 18257.343 -381647.47 254871.9 232.25731
1420 5.9482769e-07 0.0010097306 18268.179 -381801.05 255023.16 234.58112
1440 9.6055241e-07 0.0010245153 18279.561 -381963.38 255182.06 238.01409
1460 2.6487585e-06 0.0010540252 18291.412 -382135.65 255347.49 244.87092
1480 1.6540131e-06 0.0011473577 18286.353 -382087.11 255276.87 266.56651
1500 7.7231163e-07 0.0011698578 18273.103 -381907.39 255091.9 271.79306
1520 5.0196808e-07 0.0011823587 18260.401 -381732.97 254914.58 274.69466
1540 3.7028814e-07 0.0011910172 18248.126 -381563.62 254743.22 276.70297
1560 2.9266906e-07 0.0011976261 18236.229 -381399.08 254577.14 278.23481
1580 2.4170771e-07 0.0012029632 18224.682 -381239.13 254415.96 279.47106
1600 2.0581226e-07 0.0012074372 18213.468 -381083.61 254259.4 280.50668
1620 1.7924561e-07 0.0012112887 18202.573 -380932.4 254107.31 281.39766
1640 1.5884307e-07 0.0012146714 18191.986 -380785.4 253959.52 282.1797
1660 1.4272115e-07 0.0012176891 18181.701 -380642.51 253815.94 282.87696
1680 1.2968815e-07 0.0012204153 18171.711 -380503.67 253676.47 283.5065
1700 1.1895537e-07 0.0012229038 18162.009 -380368.82 253541.04 284.08082
1720 1.0998022e-07 0.0012251951 18152.594 -380237.91 253409.6 284.60934
1740 1.0237742e-07 0.0012273205 18143.459 -380110.88 253282.08 285.09933
1760 9.5866108e-08 0.0012293045 18134.603 -379987.7 253158.44 285.55651
1780 9.0236829e-08 0.0012311671 18126.022 -379868.34 253038.65 285.98547
1800 8.5330251e-08 0.0012329241 18117.714 -379752.77 252922.68 286.38994
1820 8.1023028e-08 0.0012345889 18109.677 -379640.95 252810.48 286.77299
1840 7.7218826e-08 0.0012361724 18101.908 -379532.87 252702.03 287.13719
1860 7.384063e-08 0.0012376841 18094.407 -379428.5 252597.32 287.48469
1880 7.0826602e-08 0.0012391317 18087.172 -379327.83 252496.32 287.81735
1900 6.8126364e-08 0.0012405221 18080.201 -379230.84 252399 288.13672
1920 6.5698544e-08 0.0012418611 18073.494 -379137.51 252305.37 288.44417
1940 6.3508807e-08 0.0012431539 18067.049 -379047.83 252215.39 288.7409
1960 6.1528608e-08 0.0012444049 18060.865 -378961.79 252129.06 289.02794
1980 5.9733936e-08 0.0012456182 18054.941 -378879.37 252046.37 289.3062
2000 5.8104457e-08 0.0012467971 18049.277 -378800.57 251967.3 289.57652
Loop time of 32.2671 on 16 procs for 2000 steps with 108000 atoms
Performance: 0.000 ns/day, 77129.149 hours/ns, 61.983 timesteps/s
98.2% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 27.828 | 28.038 | 28.257 | 2.5 | 86.89
Neigh | 0.11693 | 0.119 | 0.1208 | 0.4 | 0.37
Comm | 1.1116 | 1.3315 | 1.5544 | 11.5 | 4.13
Output | 1.1689 | 1.1693 | 1.1739 | 0.1 | 3.62
Modify | 1.3304 | 1.3421 | 1.3515 | 0.6 | 4.16
Other | | 0.2677 | | | 0.83
Nlocal: 6750.00 ave 6782 max 6721 min
Histogram: 2 2 0 3 2 2 1 1 1 2
Nghost: 11502.0 ave 11531 max 11470 min
Histogram: 2 1 1 1 2 2 3 0 2 2
Neighs: 472501.0 ave 475010 max 470641 min
Histogram: 2 1 3 2 2 2 1 1 1 1
Total # of neighbors = 7560018
Ave neighs/atom = 70.000167
Neighbor list builds = 8
Dangerous builds = 1
Total wall time: 0:00:32

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LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix elec/drag
# Perfect Si lattice with one primary knock-on atom (PKA) - single species simulation
# ***
units metal
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block -15 15 -15 15 -15 15
create_box 1 box
Created orthogonal box = (-81.465000 -81.465000 -81.465000) to (81.465000 81.465000 81.465000)
2 by 2 by 4 MPI processor grid
create_atoms 1 box
Created 216000 atoms
create_atoms CPU = 0.004 seconds
pair_style tersoff/zbl
pair_coeff * * Si.tersoff.zbl Si
mass 1 28.0855
velocity all create 300 42534 mom yes rot yes
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all elec/drag 4.63 3.3e-3 4.0e-8
thermo 20
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
dump 0 all custom 200 dump.pka_* id type x y z vx vy vz fx fy fz
dump_modify 0 first yes
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 66 66 66
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/zbl, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.68 | 10.68 | 10.68 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 6509.9241 -999992.11 181757.49 0
20 5.8535376e-06 0.00018285984 6504.2109 -999911.08 181597.97 78.573248
40 7.3437077e-06 0.00032558782 6501.6468 -999900.7 181526.38 139.85652
60 5.7782387e-06 0.00048338337 6499.9817 -999922.1 181479.89 207.59157
80 1.7803041e-05 0.00062201376 6498.3851 -999937.11 181435.31 267.07596
100 5.7695724e-06 0.0008764226 6491.6929 -999859.81 181248.47 376.21265
120 1.4719757e-06 0.00092268759 6488.491 -999790.21 181159.07 396.03972
140 2.040106e-06 0.0009541283 6488.9044 -999815.23 181170.61 409.51037
160 1.1709752e-05 0.0011249721 6489.6218 -999908.14 181190.64 482.73616
180 1.4052166e-06 0.0012237574 6482.8292 -999761.21 181000.99 525.05834
200 7.0645649e-07 0.0012432698 6478.465 -999647.7 180879.15 533.40945
220 5.3086492e-07 0.0012554161 6475.6927 -999575.49 180801.74 538.60481
240 4.7640655e-07 0.0012653882 6474.3494 -999542.24 180764.24 542.86876
260 4.8787977e-07 0.0012749228 6474.3825 -999547.24 180765.16 546.9453
280 5.7550217e-07 0.0012853466 6475.7725 -999590.51 180803.97 551.40265
300 8.4917452e-07 0.0012989169 6478.5144 -999672.88 180880.52 557.20767
320 3.2530619e-06 0.0013265212 6482.5081 -999796.2 180992.03 569.02383
340 9.1659616e-06 0.0014955314 6481.8343 -999849.09 180973.22 641.40448
360 1.3432453e-05 0.0017808405 6476.4943 -999822.19 180824.12 763.54528
380 8.0104844e-06 0.0020958913 6469.4698 -999760.52 180628 898.31998
400 3.3669621e-06 0.0022009729 6464.0253 -999653.36 180475.99 943.23198
420 1.4887493e-05 0.0024115306 6462.9467 -999712.65 180445.87 1033.2068
440 7.6182614e-06 0.0025715115 6457.6166 -999632.22 180297.06 1101.5392
460 2.4972112e-05 0.0029551455 6450.3406 -999593.38 180093.91 1265.318
480 2.3561752e-05 0.0032880532 6442.0409 -999503.89 179862.18 1407.3073
500 1.4420455e-05 0.0035074129 6433.361 -999354.82 179619.84 1500.7814
520 1.1816914e-05 0.0038239154 6427.2604 -999318.69 179449.51 1635.5741
540 1.3748768e-05 0.0042004194 6417.4523 -999205.3 179175.67 1795.789
560 7.52018e-06 0.0043887882 6409.6827 -999068.82 178958.74 1875.8751
580 1.257523e-05 0.004616805 6405.6624 -999053.63 178846.49 1972.7564
600 1.9968416e-06 0.00472482 6398.5405 -998900.91 178647.65 2018.6254
620 1.5482324e-06 0.0047571463 6396.6815 -998862.7 178595.74 2032.3426
640 1.011291e-05 0.0048098552 6397.7948 -998915.97 178626.83 2054.7096
660 9.8205405e-06 0.0051044128 6390.8702 -998847.14 178433.49 2179.7236
680 7.6429983e-06 0.0053365884 6383.8042 -998748.69 178236.21 2278.1889
700 6.3388347e-06 0.0054927256 6378.4359 -998665.06 178086.33 2344.3656
720 2.3522106e-06 0.0056227115 6372.253 -998548.02 177913.7 2399.4307
740 6.4757544e-07 0.0056460538 6365.5083 -998369.63 177725.39 2409.3096
760 3.8324351e-07 0.005656035 6359.7035 -998211.79 177563.32 2413.5291
780 2.7394838e-07 0.005662533 6354.5359 -998070.25 177419.04 2416.2735
800 2.1564956e-07 0.0056674054 6349.9385 -997943.95 177290.68 2418.3296
820 1.8023193e-07 0.0056713554 6345.8823 -997832.36 177177.43 2419.9952
840 1.5702192e-07 0.0056747244 6342.3522 -997735.22 177078.87 2421.4148
860 1.4112901e-07 0.0056777042 6339.3392 -997652.35 176994.74 2422.6698
880 1.3002216e-07 0.0056804148 6336.838 -997583.66 176924.91 2423.8107
900 1.2228805e-07 0.0056829369 6334.8452 -997529.08 176869.27 2424.872
920 1.1709975e-07 0.0056853297 6333.3582 -997488.57 176827.75 2425.8784
940 1.1397036e-07 0.0056876388 6332.3755 -997462.1 176800.32 2426.8495
960 1.1263139e-07 0.0056899026 6331.8956 -997449.65 176786.92 2427.8014
980 1.1297372e-07 0.0056921557 6331.9175 -997451.21 176787.53 2428.7487
1000 1.1502522e-07 0.0056944318 6332.44 -997466.76 176802.12 2429.7058
1020 1.1895651e-07 0.0056967663 6333.4621 -997496.27 176830.65 2430.6875
1040 1.2511681e-07 0.0056991998 6334.9825 -997539.75 176873.11 2431.711
1060 1.3411487e-07 0.0057017822 6337.0003 -997597.17 176929.44 2432.7975
1080 1.4698231e-07 0.0057045791 6339.514 -997668.53 176999.62 2433.9747
1100 1.6551147e-07 0.0057076833 6342.5222 -997753.83 177083.61 2435.2818
1120 1.9300845e-07 0.0057112358 6346.0234 -997853.08 177181.37 2436.7785
1140 2.3618478e-07 0.0057154712 6350.015 -997966.31 177292.81 2438.564
1160 3.108468e-07 0.0057208289 6354.4922 -998093.58 177417.82 2440.8243
1180 4.6429306e-07 0.0057282929 6359.4421 -998234.93 177556.02 2443.9758
1200 9.2816707e-07 0.0057409335 6364.8148 -998390.27 177706.03 2449.3178
1220 2.0979021e-05 0.0058204095 6369.2961 -998548.29 177831.14 2482.9438
1240 3.2882081e-06 0.0060039745 6361.0026 -998394.02 177599.59 2560.609
1260 3.6924049e-06 0.0060569852 6359.1486 -998364.67 177547.82 2583.0193
1280 9.1658886e-06 0.0063262182 6353.595 -998323.02 177392.77 2696.8502
1300 6.8768211e-06 0.0064666219 6347.4618 -998210.93 177221.53 2756.1664
1320 6.9121863e-06 0.0066088699 6342.5533 -998134.15 177084.48 2816.2408
1340 7.0074085e-06 0.0067699237 6337.3331 -998056.53 176938.73 2884.2214
1360 1.6151257e-06 0.0068943644 6330.8472 -997929.72 176757.65 2936.7264
1380 5.1421721e-07 0.0069122062 6323.1882 -997723.46 176543.81 2944.2462
1400 2.9444595e-07 0.0069200351 6315.8333 -997521.42 176338.46 2947.5417
1420 2.0082068e-07 0.0069249277 6308.579 -997320.95 176135.92 2949.5985
1440 1.4987791e-07 0.0069284157 6301.3823 -997121.48 175934.99 2951.0631
1460 1.1822986e-07 0.0069310902 6294.2263 -996922.81 175735.19 2952.1847
1480 9.683654e-08 0.0069332389 6287.1024 -996724.81 175536.29 2953.0847
1500 8.1500357e-08 0.0069350221 6280.0061 -996527.43 175338.16 2953.8306
1520 7.0019944e-08 0.0069365379 6272.9345 -996330.63 175140.72 2954.464
1540 6.1135299e-08 0.0069378503 6265.8856 -996134.37 174943.92 2955.0117
1560 5.4075905e-08 0.0069390034 6258.8583 -995938.65 174747.71 2955.4923
1580 4.8345462e-08 0.0069400286 6251.8517 -995743.45 174552.09 2955.9191
1600 4.3610621e-08 0.0069409491 6244.8652 -995548.77 174357.03 2956.3019
1620 3.9639615e-08 0.0069417824 6237.8984 -995354.6 174162.51 2956.648
1640 3.6266563e-08 0.0069425423 6230.951 -995160.95 173968.54 2956.9632
1660 3.3369776e-08 0.0069432394 6224.0227 -994967.8 173775.1 2957.2521
1680 3.0858062e-08 0.0069438824 6217.1135 -994775.16 173582.2 2957.5182
1700 2.8661809e-08 0.0069444782 6210.2233 -994583.03 173389.82 2957.7644
1720 2.6727002e-08 0.0069450326 6203.3521 -994391.41 173197.98 2957.9934
1740 2.5011123e-08 0.0069455505 6196.4998 -994200.31 173006.66 2958.2069
1760 2.3480268e-08 0.0069460359 6189.6665 -994009.73 172815.87 2958.4068
1780 2.2107089e-08 0.0069464923 6182.8523 -993819.66 172625.62 2958.5946
1800 2.0869294e-08 0.0069469224 6176.0571 -993630.11 172435.9 2958.7713
1820 1.9748543e-08 0.006947329 6169.2811 -993441.1 172246.71 2958.9382
1840 1.8729611e-08 0.0069477141 6162.5244 -993252.61 172058.06 2959.0961
1860 1.7799764e-08 0.0069480797 6155.787 -993064.65 171869.96 2959.2458
1880 1.6948273e-08 0.0069484275 6149.0691 -992877.23 171682.39 2959.388
1900 1.6166034e-08 0.006948759 6142.3708 -992690.34 171495.37 2959.5234
1920 1.5445281e-08 0.0069490753 6135.6922 -992504.01 171308.91 2959.6525
1940 1.4779344e-08 0.0069493778 6129.0335 -992318.22 171123 2959.7757
1960 1.4162469e-08 0.0069496675 6122.3947 -992132.98 170937.64 2959.8936
1980 1.3589666e-08 0.0069499452 6115.776 -991948.3 170752.85 2960.0066
2000 1.3056587e-08 0.0069502119 6109.1776 -991764.18 170568.62 2960.1149
Loop time of 102.285 on 16 procs for 2000 steps with 216000 atoms
Performance: 0.000 ns/day, 1088049.652 hours/ns, 19.553 timesteps/s
99.5% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 86.624 | 87.611 | 88.388 | 6.4 | 85.65
Neigh | 0.88619 | 0.90996 | 0.92467 | 1.3 | 0.89
Comm | 7.3456 | 8.144 | 9.1588 | 21.2 | 7.96
Output | 2.2851 | 2.2855 | 2.2903 | 0.1 | 2.23
Modify | 3.0244 | 3.0283 | 3.0332 | 0.1 | 2.96
Other | | 0.3064 | | | 0.30
Nlocal: 13500.0 ave 13528 max 13447 min
Histogram: 1 0 0 2 1 2 2 2 3 3
Nghost: 7282.56 ave 7336 max 7254 min
Histogram: 3 3 2 2 2 1 2 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 16 0 0 0 0 0 0 0 0 0
FullNghs: 378000.0 ave 378780 max 376516 min
Histogram: 1 0 0 2 1 2 2 2 3 3
Total # of neighbors = 6048000
Ave neighs/atom = 28.000000
Neighbor list builds = 56
Dangerous builds = 24
Total wall time: 0:01:42

2
src/USER-MISC/README
View File

@ -51,7 +51,7 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18
fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
fix elec/drag, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020
fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020
fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019
fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018
fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017

202
src/USER-MISC/fix_electron_stopping_fit.cpp Normal file
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@ -0,0 +1,202 @@
/* ---------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------ */
/* ---------------------------------------------------------------------
Contributing authors: Stephen M. Foiles (SNL)
James A. Stewart (SNL)
------------------------------------------------------------------ */
#include "fix_electron_stopping_fit.h"
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "error.h"
#include "citeme.h"
using namespace LAMMPS_NS;
using namespace FixConst;
// ---------------------------------------------------------------------
static const char cite_fix_electron_stopping_fit_c[] =
"fix_elec_drag command:\n\n"
"@Article{Stewart2018,\n"
" author = { J.A. Stewart and G. Brookman and P. Price and M. Franco and W. Ji and K. Hattar and R. Dingreville },\n"
" title = { Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods },\n"
" journal = { Journal of Applied Physics },\n"
" year = { 2018 },\n"
" volume = { 123 },\n"
" number = { 16 },\n"
" pages = { 165902 }\n"
"}\n\n"
"@Article{Lee2020,\n"
" author = { C.W. Lee and J.A. Stewart and S.M. Foiles and R. Dingreville and A. Schleife },\n"
" title = { Multiscale simulations of electron and ion dynamics in self-irradiated silicon },\n"
" journal = { Physical Review B },\n"
" year = { 2020 },\n"
" volume = { 102 },\n"
" number = { 2 },\n"
" pages = { 024107 }\n"
"}\n\n";
// ---------------------------------------------------------------------
FixElectronStoppingFit::FixElectronStoppingFit(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp,narg,arg)
{
if (narg < 3 + 3*atom->ntypes) {
error->all(FLERR,"Incorrect number of fix electron/stopping/fit arguments");
}
scalar_flag = 1;
global_freq = 1;
energy_coh_in = new double[atom->ntypes+1];
drag_fac_in_1 = new double[atom->ntypes+1];
drag_fac_in_2 = new double[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) {
energy_coh_in[i] = atof(arg[3*i]);
drag_fac_in_1[i] = atof(arg[3*i+1]);
drag_fac_in_2[i] = atof(arg[3*i+2]);
};
v_min_sq = new double[atom->ntypes+1];
v_max_sq = new double[atom->ntypes+1];
drag_fac_1 = new double[atom->ntypes+1];
drag_fac_2 = new double[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) {
double mvv;
mvv = 2.0*energy_coh_in[i]/force->mvv2e;
v_min_sq[i] = 1.0*mvv/atom->mass[i];
v_max_sq[i] = 2.0*mvv/atom->mass[i];
drag_fac_1[i] = drag_fac_in_1[i];
drag_fac_2[i] = drag_fac_in_2[i];
};
};
// ---------------------------------------------------------------------
FixElectronStoppingFit::~FixElectronStoppingFit()
{
delete [] drag_fac_in_1;
delete [] drag_fac_in_2;
delete [] drag_fac_1;
delete [] drag_fac_2;
delete [] v_min_sq;
delete [] v_max_sq;
};
// ---------------------------------------------------------------------
int FixElectronStoppingFit::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
};
// ---------------------------------------------------------------------
void FixElectronStoppingFit::init()
{
electronic_loss_this_node = 0.;
electronic_loss = 0.;
f_dot_v_prior = 0.;
f_dot_v_current = 0.;
last_step = update->ntimestep;
};
// ---------------------------------------------------------------------
void FixElectronStoppingFit::setup(int vflag)
{
if (strcmp(update->integrate_style,"verlet") == 0)
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
};
};
// ---------------------------------------------------------------------
void FixElectronStoppingFit::post_force(int vflag)
{
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
f_dot_v_current = 0.0;
for (int i = 0; i < nlocal; i++) {
double vv = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (vv > v_min_sq[type[i]]) {
double gamma_x;
double gamma_y;
double gamma_z;
double v_mag = sqrt(vv);
if (vv < v_max_sq[type[i]]) {
double frac = (vv - v_min_sq[type[i]])/(v_max_sq[type[i]] - v_min_sq[type[i]]);
gamma_x = frac*(drag_fac_2[type[i]]*v[i][0] + drag_fac_1[type[i]]);
gamma_y = frac*(drag_fac_2[type[i]]*v[i][1] + drag_fac_1[type[i]]);
gamma_z = frac*(drag_fac_2[type[i]]*v[i][2] + drag_fac_1[type[i]]);
} else {
gamma_x = drag_fac_2[type[i]]*v[i][0] + drag_fac_1[type[i]];
gamma_y = drag_fac_2[type[i]]*v[i][1] + drag_fac_1[type[i]];
gamma_z = drag_fac_2[type[i]]*v[i][2] + drag_fac_1[type[i]];
};
f[i][0] -= gamma_x*v[i][0];
f[i][1] -= gamma_y*v[i][1];
f[i][2] -= gamma_z*v[i][2];
f_dot_v_current += sqrt(pow(gamma_x*v[i][0], 2.0) + pow(gamma_y*v[i][1], 2.0) + pow(gamma_z*v[i][2], 2.0))*v_mag;
};
};
this_step = update->ntimestep;
electronic_loss_this_node += (this_step - last_step)*update->dt*0.5*(f_dot_v_prior + f_dot_v_current);
last_step = this_step;
f_dot_v_prior = f_dot_v_current;
};
// ---------------------------------------------------------------------
void FixElectronStoppingFit::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
};
// ---------------------------------------------------------------------
double FixElectronStoppingFit::compute_scalar()
{
MPI_Allreduce(&electronic_loss_this_node,&electronic_loss,1,MPI_DOUBLE,MPI_SUM,world);
return electronic_loss;
};
// ---------------------------------------------------------------------

54
src/USER-MISC/fix_electron_stopping_fit.h Normal file
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@ -0,0 +1,54 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Stephen M. Foiles (SNL)
James A. Stewart (SNL)
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(electron/stopping/fit,FixElectronStoppingFit)
#else
#ifndef LMP_FIX_ELECTRON_STOPPING_FIT_H
#define LMP_FIX_ELECTRON_STOPPING_FIT_H
#include "fix.h"
namespace LAMMPS_NS {
class FixElectronStoppingFit : public Fix {
public:
FixElectronStoppingFit(class LAMMPS *, int, char **);
~FixElectronStoppingFit();
int setmask();
void init();
void setup(int);
void post_force(int);
void post_force_respa(int, int, int);
double compute_scalar();
private:
double *energy_coh_in,*v_min_sq,*v_max_sq,*drag_fac_in_1,*drag_fac_in_2,*drag_fac_1,*drag_fac_2;
double electronic_loss,electronic_loss_this_node;
double f_dot_v_prior,f_dot_v_current;
int last_step,this_step;
int nlevels_respa;
};
}
#endif
#endif