176 lines
9.3 KiB
Groff
176 lines
9.3 KiB
Groff
LAMMPS (7 Jan 2022)
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# Numerical difference calculation
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# of error in forces and virial stress
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# adjustable parameters
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variable nsteps index 500 # length of run
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variable nthermo index 10 # thermo output interval
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variable ndump index 500 # dump output interval
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variable nlat index 3 # size of box
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variable fdelta index 1.0e-4 # displacement size
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variable vdelta index 1.0e-6 # strain size
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variable temp index 10.0 # temperature
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units metal
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atom_style atomic
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atom_modify map yes
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lattice fcc 5.358000
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Lattice spacing in x,y,z = 5.358 5.358 5.358
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region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
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region box block 0 3 0 ${nlat} 0 ${nlat}
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region box block 0 3 0 3 0 ${nlat}
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region box block 0 3 0 3 0 3
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create_box 1 box
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Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 108 atoms
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using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
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create_atoms CPU = 0.000 seconds
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mass 1 39.903
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velocity all create ${temp} 2357 mom yes dist gaussian
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velocity all create 10.0 2357 mom yes dist gaussian
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pair_style lj/cubic
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pair_coeff * * 0.0102701 3.42
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neighbor 0.0 bin
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neigh_modify every 1 delay 0 check no
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timestep 0.001
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fix nve all nve
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# define numerical force calculation
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fix numforce all numdiff ${nthermo} ${fdelta}
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fix numforce all numdiff 10 ${fdelta}
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fix numforce all numdiff 10 1.0e-4
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variable ferrx atom f_numforce[1]-fx
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variable ferry atom f_numforce[2]-fy
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variable ferrz atom f_numforce[3]-fz
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variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
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compute faverrsq all reduce ave v_ferrsq
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variable fsq atom fx^2+fy^2+fz^2
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compute favsq all reduce ave v_fsq
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variable frelerr equal sqrt(c_faverrsq/c_favsq)
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dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
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dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
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# define numerical virial stress tensor calculation
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compute myvirial all pressure NULL virial
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fix numvirial all numdiff/virial ${nthermo} ${vdelta}
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fix numvirial all numdiff/virial 10 ${vdelta}
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fix numvirial all numdiff/virial 10 1.0e-6
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variable errxx equal f_numvirial[1]-c_myvirial[1]
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variable erryy equal f_numvirial[2]-c_myvirial[2]
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variable errzz equal f_numvirial[3]-c_myvirial[3]
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variable erryz equal f_numvirial[4]-c_myvirial[6]
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variable errxz equal f_numvirial[5]-c_myvirial[5]
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variable errxy equal f_numvirial[6]-c_myvirial[4]
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variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
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variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
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variable vrelerr equal sqrt(v_verrsq/v_vsq)
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thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
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thermo ${nthermo}
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thermo 10
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run ${nsteps}
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run 500
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.9407173
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ghost atom cutoff = 5.9407173
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binsize = 2.9703587, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cubic, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.083 | 6.083 | 6.083 Mbytes
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Step Temp PotEng TotEng Press v_frelerr v_vrelerr
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0 10 -7.0259569 -6.8876486 28.564278 19203.344 1.5660292e-06
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10 9.9376583 -7.0250947 -6.8876486 30.254762 1.5040965e-08 2.1991382e-07
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20 9.7520139 -7.022527 -6.8876485 35.28505 1.4756358e-08 2.6265315e-06
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30 9.4477557 -7.0183188 -6.8876485 43.519863 1.4688198e-08 2.6356166e-07
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40 9.0330215 -7.0125826 -6.8876484 54.727797 1.4637921e-08 5.2292327e-08
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50 8.5192918 -7.0054772 -6.8876483 68.585553 1.4587854e-08 7.1324716e-08
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60 7.9212026 -6.997205 -6.8876481 84.684636 1.4525561e-08 3.1108149e-08
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70 7.2562592 -6.9880081 -6.8876479 102.54088 1.450885e-08 3.2311094e-08
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80 6.5444294 -6.9781627 -6.8876478 121.60715 1.4444738e-08 2.1776998e-08
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90 5.8075961 -6.9679715 -6.8876476 141.2895 1.4493562e-08 2.0400898e-08
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100 5.0688629 -6.957754 -6.8876474 160.9668 1.445455e-08 1.2636688e-08
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110 4.3517145 -6.947835 -6.8876472 180.0135 1.4460371e-08 1.2528038e-08
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120 3.6790589 -6.9385314 -6.887647 197.82486 1.4371757e-08 1.4489522e-08
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130 3.0721984 -6.9301379 -6.8876468 213.84331 1.4364708e-08 1.2461922e-08
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140 2.5497991 -6.9229125 -6.8876467 227.58429 1.4330926e-08 9.3913926e-09
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150 2.1269443 -6.917064 -6.8876466 238.6596 1.4287002e-08 4.1510266e-09
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160 1.8143642 -6.9127407 -6.8876465 246.79599 1.4282669e-08 7.7048281e-09
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170 1.6179191 -6.9100237 -6.8876465 251.84748 1.42726e-08 1.2719973e-08
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180 1.5383946 -6.9089239 -6.8876466 253.79991 1.4236534e-08 8.1200831e-09
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190 1.5716287 -6.9093836 -6.8876467 252.76745 1.41706e-08 6.5670612e-09
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200 1.7089493 -6.911283 -6.8876468 248.98142 1.4096463e-08 1.1685863e-08
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210 1.9378716 -6.9144493 -6.8876469 242.77289 1.4008978e-08 1.1226902e-08
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220 2.2429731 -6.9186692 -6.887647 234.55055 1.3886901e-08 9.9914102e-09
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230 2.606862 -6.9237023 -6.8876472 224.77626 1.3864576e-08 1.1540228e-08
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240 3.0111524 -6.9292941 -6.8876474 213.93996 1.3696314e-08 1.1697747e-08
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250 3.4373794 -6.9351893 -6.8876475 202.53583 1.3626701e-08 1.0398197e-08
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260 3.8678047 -6.9411426 -6.8876476 191.04084 1.3489489e-08 6.6603364e-09
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270 4.2860853 -6.9469279 -6.8876478 179.89646 1.3312014e-08 1.1687917e-08
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280 4.6777954 -6.9523457 -6.8876479 169.49404 1.3081144e-08 1.1336675e-08
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290 5.030805 -6.9572282 -6.887648 160.16371 1.2947385e-08 1.7342825e-08
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300 5.3355278 -6.9614428 -6.887648 152.16682 1.2893673e-08 1.7510534e-08
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310 5.5850532 -6.964894 -6.887648 145.69148 1.2842022e-08 1.2782546e-08
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320 5.7751794 -6.9675236 -6.8876481 140.85102 1.2903488e-08 1.5319437e-08
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330 5.9043601 -6.9693103 -6.887648 137.68497 1.3076809e-08 1.1208999e-08
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340 5.9735784 -6.9702676 -6.887648 136.16232 1.3296904e-08 1.891087e-08
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350 5.9861549 -6.9704415 -6.887648 136.18679 1.3504051e-08 2.5783601e-08
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360 5.947496 -6.9699067 -6.8876479 137.60397 1.3731112e-08 2.0556839e-08
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370 5.8647874 -6.9687627 -6.8876478 140.2101 1.4009878e-08 2.1771736e-08
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380 5.7466376 -6.9671285 -6.8876477 143.76234 1.4092054e-08 1.1085162e-08
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390 5.6026773 -6.9651374 -6.8876477 147.99019 1.4282872e-08 2.0221602e-08
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400 5.4431231 -6.9629305 -6.8876476 152.60787 1.4317739e-08 1.7076065e-08
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410 5.2783192 -6.960651 -6.8876475 157.32722 1.4415075e-08 2.5031776e-08
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420 5.1182723 -6.9584374 -6.8876474 161.87063 1.4441435e-08 2.2519289e-08
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430 4.9722 -6.956417 -6.8876473 165.98344 1.4550624e-08 2.4512613e-08
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440 4.8481153 -6.9547008 -6.8876473 169.44527 1.4544672e-08 1.4758301e-08
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450 4.7524707 -6.9533779 -6.8876472 172.07964 1.4546492e-08 1.324687e-08
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460 4.6898817 -6.9525122 -6.8876472 173.76132 1.4537475e-08 1.351367e-08
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470 4.6629495 -6.9521397 -6.8876472 174.42109 1.4530458e-08 1.521106e-08
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480 4.6721922 -6.9522675 -6.8876472 174.04742 1.4543785e-08 1.0905422e-08
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490 4.7160887 -6.9528747 -6.8876473 172.68525 1.4545591e-08 2.0128525e-08
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500 4.7912313 -6.953914 -6.8876473 170.43183 1.4438981e-08 1.6062775e-08
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Loop time of 0.837333 on 1 procs for 500 steps with 108 atoms
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Performance: 51.592 ns/day, 0.465 hours/ns, 597.134 timesteps/s
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99.8% 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 | 0.0097726 | 0.0097726 | 0.0097726 | 0.0 | 1.17
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Neigh | 0.03095 | 0.03095 | 0.03095 | 0.0 | 3.70
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Comm | 0.005564 | 0.005564 | 0.005564 | 0.0 | 0.66
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Output | 0.0042451 | 0.0042451 | 0.0042451 | 0.0 | 0.51
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Modify | 0.78618 | 0.78618 | 0.78618 | 0.0 | 93.89
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Other | | 0.0006258 | | | 0.07
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Nlocal: 108 ave 108 max 108 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 558 ave 558 max 558 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 972 ave 972 max 972 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 972
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Ave neighs/atom = 9
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Neighbor list builds = 500
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Dangerous builds not checked
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Total wall time: 0:00:00
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