forked from lijiext/lammps
198 lines
12 KiB
Groff
198 lines
12 KiB
Groff
LAMMPS (17 Feb 2022)
|
|
# Numerical difference calculation
|
|
# of error in forces, virial stress, and Born matrix
|
|
|
|
# adjustable parameters
|
|
|
|
variable nsteps index 500 # length of run
|
|
variable nthermo index 10 # thermo output interval
|
|
variable ndump index 500 # dump output interval
|
|
variable nlat index 3 # size of box
|
|
variable fdelta index 1.0e-4 # displacement size
|
|
variable vdelta index 1.0e-6 # strain size for numdiff/virial
|
|
variable bdelta index 1.0e-8 # strain size for numdiff Born matrix
|
|
variable temp index 10.0 # temperature
|
|
variable nugget equal 1.0e-6 # regularization for relerr
|
|
|
|
units metal
|
|
atom_style atomic
|
|
|
|
atom_modify map yes
|
|
lattice fcc 5.358000
|
|
Lattice spacing in x,y,z = 5.358 5.358 5.358
|
|
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
|
region box block 0 3 0 ${nlat} 0 ${nlat}
|
|
region box block 0 3 0 3 0 ${nlat}
|
|
region box block 0 3 0 3 0 3
|
|
create_box 1 box
|
|
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
|
1 by 2 by 2 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 108 atoms
|
|
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
|
create_atoms CPU = 0.000 seconds
|
|
mass 1 39.903
|
|
|
|
velocity all create ${temp} 2357 mom yes dist gaussian
|
|
velocity all create 10.0 2357 mom yes dist gaussian
|
|
|
|
pair_style lj/cut 5.0
|
|
pair_coeff 1 1 0.0102701 3.42
|
|
|
|
neighbor 0.0 bin
|
|
neigh_modify every 1 delay 0 check no
|
|
|
|
timestep 0.001
|
|
fix nve all nve
|
|
|
|
# define numerical force calculation
|
|
|
|
fix numforce all numdiff ${nthermo} ${fdelta}
|
|
fix numforce all numdiff 10 ${fdelta}
|
|
fix numforce all numdiff 10 1.0e-4
|
|
variable ferrx atom f_numforce[1]-fx
|
|
variable ferry atom f_numforce[2]-fy
|
|
variable ferrz atom f_numforce[3]-fz
|
|
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
|
compute faverrsq all reduce ave v_ferrsq
|
|
variable fsq atom fx^2+fy^2+fz^2
|
|
compute favsq all reduce ave v_fsq
|
|
variable frelerr equal sqrt(c_faverrsq/(c_favsq+${nugget}))
|
|
variable frelerr equal sqrt(c_faverrsq/(c_favsq+1e-06))
|
|
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
|
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
|
|
|
|
# define numerical virial stress tensor calculation
|
|
|
|
compute myvirial all pressure NULL virial
|
|
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
|
|
fix numvirial all numdiff/virial 10 ${vdelta}
|
|
fix numvirial all numdiff/virial 10 1.0e-6
|
|
variable errxx equal f_numvirial[1]-c_myvirial[1]
|
|
variable erryy equal f_numvirial[2]-c_myvirial[2]
|
|
variable errzz equal f_numvirial[3]-c_myvirial[3]
|
|
variable erryz equal f_numvirial[4]-c_myvirial[6]
|
|
variable errxz equal f_numvirial[5]-c_myvirial[5]
|
|
variable errxy equal f_numvirial[6]-c_myvirial[4]
|
|
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
|
|
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
|
|
variable vrelerr equal sqrt(v_verrsq/(v_vsq+${nugget}))
|
|
variable vrelerr equal sqrt(v_verrsq/(v_vsq+1e-06))
|
|
|
|
# define numerical Born matrix calculation
|
|
|
|
compute bornnum all born/matrix numdiff ${bdelta} myvirial
|
|
compute bornnum all born/matrix numdiff 1.0e-8 myvirial
|
|
compute born all born/matrix
|
|
variable berr vector c_bornnum-c_born
|
|
variable berrsq equal "v_berr[1]^2 + v_berr[2]^2 + v_berr[3]^2 + v_berr[4]^2 + v_berr[5]^2 + v_berr[6]^2 + v_berr[7]^2 + v_berr[8]^2 + v_berr[9]^2 + v_berr[10]^2 + v_berr[11]^2 + v_berr[12]^2 + v_berr[13]^2 + v_berr[14]^2 + v_berr[15]^2 + v_berr[16]^2 + v_berr[17]^2 + v_berr[18]^2 + v_berr[19]^2 + v_berr[20]^2 + v_berr[21]^2"
|
|
|
|
variable bsq equal "c_born[1]^2 + c_born[2]^2 + c_born[3]^2 + c_born[4]^2 + c_born[5]^2 + c_born[6]^2 + c_born[7]^2 + c_born[8]^2 + c_born[9]^2 + c_born[10]^2 + c_born[11]^2 + c_born[12]^2 + c_born[13]^2 + c_born[14]^2 + c_born[15]^2 + c_born[16]^2 + c_born[17]^2 + c_born[18]^2 + c_born[19]^2 + c_born[20]^2 + c_born[21]^2"
|
|
|
|
variable brelerr equal sqrt(v_berrsq/(v_bsq+${nugget}))
|
|
variable brelerr equal sqrt(v_berrsq/(v_bsq+1e-06))
|
|
|
|
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr v_brelerr
|
|
thermo ${nthermo}
|
|
thermo 10
|
|
run ${nsteps}
|
|
run 500
|
|
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check no
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 5
|
|
ghost atom cutoff = 5
|
|
binsize = 2.5, bins = 7 7 7
|
|
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
(2) compute born/matrix, occasional, copy from (1)
|
|
attributes: half, newton on
|
|
pair build: copy
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 6.816 | 6.816 | 6.816 Mbytes
|
|
Step Temp PotEng TotEng Press v_frelerr v_vrelerr v_brelerr
|
|
0 10 -6.6101864 -6.471878 947.70558 1.9110624e-09 9.4407596e-10 3.1867416e-09
|
|
10 9.9369961 -6.6093149 -6.471878 949.31222 1.3055176e-08 4.996456e-10 2.7421655e-09
|
|
20 9.7500224 -6.6067289 -6.4718779 954.07898 1.3721178e-08 5.6039795e-10 2.3689718e-09
|
|
30 9.4448115 -6.6025075 -6.4718779 961.85502 1.3813156e-08 6.8451692e-10 1.9844663e-09
|
|
40 9.0305392 -6.5967776 -6.4718777 972.39819 1.3961749e-08 3.1134064e-10 1.7915052e-09
|
|
50 8.5196068 -6.5897109 -6.4718776 985.38158 1.3996941e-08 7.0149406e-10 2.002272e-09
|
|
60 7.9273388 -6.5815192 -6.4718775 1000.4024 1.4000005e-08 3.5766629e-10 2.4944703e-09
|
|
70 7.2715879 -6.5724494 -6.4718773 1016.9932 1.3996503e-08 6.2731503e-10 1.7010533e-09
|
|
80 6.5722375 -6.5627766 -6.4718771 1034.6361 1.3973603e-08 3.1142917e-10 2.808524e-09
|
|
90 5.8505991 -6.5527956 -6.4718769 1052.7794 1.3983301e-08 3.9931135e-10 2.6118214e-09
|
|
100 5.128708 -6.542811 -6.4718767 1070.8561 1.395586e-08 2.3152413e-10 2.8742755e-09
|
|
110 4.4285344 -6.5331269 -6.4718766 1088.305 1.3938374e-08 4.2173005e-10 2.3059886e-09
|
|
120 3.7711361 -6.5240343 -6.4718764 1104.5919 1.3915264e-08 2.5458038e-10 1.4864012e-09
|
|
130 3.1757964 -6.5158002 -6.4718762 1119.2319 1.3858843e-08 5.7490448e-10 2.6191823e-09
|
|
140 2.6591997 -6.5086551 -6.4718761 1131.8095 1.3814891e-08 3.5434633e-10 2.2009364e-09
|
|
150 2.2347034 -6.5027839 -6.471876 1141.9961 1.3781115e-08 5.0639594e-10 2.9032558e-09
|
|
160 1.9117661 -6.4983173 -6.471876 1149.564 1.3734288e-08 3.1954962e-10 2.6097446e-09
|
|
170 1.6955808 -6.4953273 -6.471876 1154.3946 1.3682252e-08 3.5426781e-10 2.9605676e-09
|
|
180 1.586949 -6.4938249 -6.471876 1156.4812 1.363e-08 4.0804881e-10 2.1707904e-09
|
|
190 1.5824056 -6.4937621 -6.4718761 1155.925 1.3532637e-08 4.0767685e-10 3.0091462e-09
|
|
200 1.6745831 -6.4950371 -6.4718762 1152.926 1.3455927e-08 2.953369e-10 2.5029298e-09
|
|
210 1.8527803 -6.4975018 -6.4718763 1147.7684 1.335224e-08 3.5042319e-10 3.0550064e-09
|
|
220 2.1036825 -6.5009721 -6.4718764 1140.8026 1.3239176e-08 3.5988448e-10 2.6852683e-09
|
|
230 2.4121721 -6.5052389 -6.4718766 1132.4243 1.3090019e-08 3.5004036e-10 2.8838602e-09
|
|
240 2.7621668 -6.5100798 -6.4718767 1123.0538 1.2946525e-08 4.1216361e-10 2.1105916e-09
|
|
250 3.1374274 -6.5152701 -6.4718768 1113.1152 1.277789e-08 5.9848318e-10 2.3087106e-09
|
|
260 3.5222906 -6.5205932 -6.471877 1103.0171 1.2591089e-08 2.0080182e-10 1.6969069e-09
|
|
270 3.9022942 -6.5258491 -6.4718771 1093.1369 1.2432232e-08 4.2494727e-10 1.7375594e-09
|
|
280 4.2646753 -6.5308612 -6.4718772 1083.8072 1.2268238e-08 6.1239266e-10 1.7005135e-09
|
|
290 4.598736 -6.5354816 -6.4718772 1075.306 1.2181179e-08 4.9338341e-10 2.1326848e-09
|
|
300 4.896078 -6.5395941 -6.4718773 1067.85 1.2098274e-08 3.4564838e-10 2.4199891e-09
|
|
310 5.150715 -6.543116 -6.4718773 1061.5918 1.2184958e-08 4.2383299e-10 2.2243759e-09
|
|
320 5.3590742 -6.5459978 -6.4718773 1056.6189 1.2312948e-08 3.5194185e-10 1.3856935e-09
|
|
330 5.5199009 -6.5482222 -6.4718773 1052.9565 1.2573918e-08 4.2401322e-10 2.9882e-09
|
|
340 5.6340787 -6.5498013 -6.4718773 1050.5719 1.2821551e-08 5.8802825e-10 2.7333289e-09
|
|
350 5.7043792 -6.5507736 -6.4718772 1049.3813 1.3067314e-08 4.0014945e-10 2.3564728e-09
|
|
360 5.7351548 -6.5511992 -6.4718772 1049.2581 1.331283e-08 4.1684815e-10 1.735621e-09
|
|
370 5.7319891 -6.5511553 -6.4718771 1050.042 1.354018e-08 3.8495426e-10 2.4460056e-09
|
|
380 5.7013193 -6.5507311 -6.4718771 1051.5496 1.3734888e-08 3.5333605e-10 2.5174342e-09
|
|
390 5.6500487 -6.5500219 -6.471877 1053.5847 1.3892287e-08 3.8154957e-10 1.77358e-09
|
|
400 5.5851679 -6.5491245 -6.471877 1055.9489 1.3988171e-08 5.8769536e-10 1.9262201e-09
|
|
410 5.5134009 -6.5481319 -6.4718769 1058.4508 1.4088779e-08 3.6754739e-10 2.7586362e-09
|
|
420 5.4408957 -6.547129 -6.4718769 1060.9152 1.4139924e-08 4.9030281e-10 3.2871245e-09
|
|
430 5.3729707 -6.5461895 -6.4718768 1063.1898 1.4173041e-08 5.2345074e-10 3.5995984e-09
|
|
440 5.3139284 -6.5453729 -6.4718768 1065.1506 1.4191516e-08 5.9481094e-10 2.5005297e-09
|
|
450 5.2669383 -6.5447229 -6.4718768 1066.7054 1.4168424e-08 3.0799668e-10 2.0864191e-09
|
|
460 5.2339881 -6.5442672 -6.4718768 1067.7958 1.4163444e-08 6.3927736e-10 2.2872669e-09
|
|
470 5.2158979 -6.544017 -6.4718768 1068.3968 1.413819e-08 5.5108262e-10 4.4334972e-09
|
|
480 5.2123873 -6.5439685 -6.4718768 1068.5155 1.4083227e-08 3.9249548e-10 2.5568235e-09
|
|
490 5.2221849 -6.544104 -6.4718768 1068.188 1.4035287e-08 2.1988631e-10 2.1264034e-09
|
|
500 5.2431716 -6.5443943 -6.4718768 1067.4759 1.3968666e-08 3.9100701e-10 3.290368e-09
|
|
Loop time of 0.170182 on 4 procs for 500 steps with 108 atoms
|
|
|
|
Performance: 253.846 ns/day, 0.095 hours/ns, 2938.035 timesteps/s
|
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.0012069 | 0.0012994 | 0.0013512 | 0.2 | 0.76
|
|
Neigh | 0.0048233 | 0.0050244 | 0.0053881 | 0.3 | 2.95
|
|
Comm | 0.0072462 | 0.0078013 | 0.008175 | 0.4 | 4.58
|
|
Output | 0.0080632 | 0.0081244 | 0.0082899 | 0.1 | 4.77
|
|
Modify | 0.1476 | 0.14764 | 0.14768 | 0.0 | 86.75
|
|
Other | | 0.0002961 | | | 0.17
|
|
|
|
Nlocal: 27 ave 31 max 24 min
|
|
Histogram: 1 0 1 0 1 0 0 0 0 1
|
|
Nghost: 135 ave 138 max 131 min
|
|
Histogram: 1 0 0 0 0 1 0 1 0 1
|
|
Neighs: 162 ave 191 max 148 min
|
|
Histogram: 1 2 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 648
|
|
Ave neighs/atom = 6
|
|
Neighbor list builds = 500
|
|
Dangerous builds not checked
|
|
Total wall time: 0:00:00
|