diff --git a/examples/USER/misc/tersoff_shift/Si.tersoff b/examples/USER/misc/tersoff_shift/Si.tersoff new file mode 100644 index 0000000000..fa565df42b --- /dev/null +++ b/examples/USER/misc/tersoff_shift/Si.tersoff @@ -0,0 +1,18 @@ +# DATE: 2007-10-25 UNITS: metal CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Tersoff, Phys Rev B, 37, 6991 (1988) + +# Tersoff parameters for various elements and mixtures +# multiple entries can be added to this file, LAMMPS reads the ones it needs +# these entries are in LAMMPS "metal" units: +# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms +# other quantities are unitless + +# This is the Si parameterization from a particular Tersoff paper: +# J. Tersoff, PRB, 37, 6991 (1988) +# See the SiCGe.tersoff file for different Si variants. + +# format of a single entry (one or more lines): +# element 1, element 2, element 3, +# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A + +Si Si Si 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956 + 0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7 diff --git a/examples/USER/misc/tersoff_shift/in.Si_shift b/examples/USER/misc/tersoff_shift/in.Si_shift new file mode 100644 index 0000000000..4ef30e61e9 --- /dev/null +++ b/examples/USER/misc/tersoff_shift/in.Si_shift @@ -0,0 +1,36 @@ +# Generate tip +units metal +dimension 3 +boundary p p p +atom_style atomic + +variable xm equal 10 +variable ym equal 10 +variable zm equal 5 +lattice diamond 5.481 # Si-Si +region recbox block 0.0 ${xm} 0.0 ${ym} 0.0 ${zm} + +create_box 1 recbox +create_atoms 1 region recbox units box + +mass * 28.0855 +pair_style tersoff/shift 0.05 +pair_coeff * * Si.tersoff Si + +thermo_style custom step cpu etotal pe ke temp +thermo 100 +thermo_modify flush yes norm no lost warn +thermo_modify line one format float %20.15g + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 dist gaussian mom yes rot yes +fix thermostat all nve + +############# Output ############### +thermo 100 +thermo_style custom step etotal pe ke temp +thermo_modify lost warn + +###### Run molecular dynamics ###### +run 10000 diff --git a/examples/USER/misc/tersoff_shift/log.30Nov20.Si_shift0.05.g++.1 b/examples/USER/misc/tersoff_shift/log.30Nov20.Si_shift0.05.g++.1 new file mode 100644 index 0000000000..c0f4304afe --- /dev/null +++ b/examples/USER/misc/tersoff_shift/log.30Nov20.Si_shift0.05.g++.1 @@ -0,0 +1,194 @@ +LAMMPS (30 Nov 2020) +# Generate tip +units metal +dimension 3 +boundary p p p +atom_style atomic + +variable xm equal 10 +variable ym equal 10 +variable zm equal 5 +lattice diamond 5.481 # Si-Si +Lattice spacing in x,y,z = 5.4810000 5.4810000 5.4810000 +region recbox block 0.0 ${xm} 0.0 ${ym} 0.0 ${zm} +region recbox block 0.0 10 0.0 ${ym} 0.0 ${zm} +region recbox block 0.0 10 0.0 10 0.0 ${zm} +region recbox block 0.0 10 0.0 10 0.0 5 + +create_box 1 recbox +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (54.810000 54.810000 27.405000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region recbox units box +Created 4000 atoms + create_atoms CPU = 0.001 seconds + +mass * 28.0855 +pair_style tersoff/shift 0.05 +pair_coeff * * Si.tersoff Si +Reading tersoff potential file Si.tersoff with DATE: 2007-10-25 + +thermo_style custom step cpu etotal pe ke temp +thermo 100 +thermo_modify flush yes norm no lost warn +thermo_modify line one format float %20.15g + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 dist gaussian mom yes rot yes +fix thermostat all nve + +############# Output ############### +thermo 100 +thermo_style custom step etotal pe ke temp +WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:693) +thermo_modify lost warn + +###### Run molecular dynamics ###### +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.2 + ghost atom cutoff = 5.2 + binsize = 2.6, bins = 22 22 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff/shift, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.802 | 3.802 | 3.802 Mbytes +Step TotEng PotEng KinEng Temp + 0 -18183.755 -18338.829 155.0734 300 + 100 -18183.66 -18247.917 64.256597 124.30874 + 200 -18183.654 -18242.513 58.858225 113.86523 + 300 -18183.683 -18265.139 81.456543 157.58321 + 400 -18183.671 -18258.798 75.12695 145.33818 + 500 -18183.679 -18261.264 77.585257 150.09394 + 600 -18183.673 -18258.411 74.737378 144.58453 + 700 -18183.674 -18257.786 74.11252 143.3757 + 800 -18183.679 -18263.045 79.365484 153.53791 + 900 -18183.672 -18259.796 76.123779 147.26661 + 1000 -18183.674 -18258.87 75.195714 145.47121 + 1100 -18183.676 -18261.269 77.59265 150.10824 + 1200 -18183.675 -18263.291 79.615576 154.02173 + 1300 -18183.677 -18261.085 77.408599 149.75218 + 1400 -18183.67 -18257.368 73.697265 142.57236 + 1500 -18183.677 -18261.04 77.363754 149.66543 + 1600 -18183.678 -18265.003 81.325058 157.32884 + 1700 -18183.674 -18257.983 74.308506 143.75484 + 1800 -18183.674 -18259.601 75.927205 146.88633 + 1900 -18183.676 -18263.228 79.551563 153.89789 + 2000 -18183.676 -18260.861 77.185151 149.31991 + 2100 -18183.674 -18261.109 77.434845 149.80296 + 2200 -18183.674 -18259.775 76.101422 147.22336 + 2300 -18183.675 -18261.459 77.78369 150.47782 + 2400 -18183.677 -18262.108 78.430533 151.72918 + 2500 -18183.673 -18257.276 73.603 142.38999 + 2600 -18183.675 -18257.815 74.139593 143.42807 + 2700 -18183.676 -18262.311 78.634382 152.12354 + 2800 -18183.675 -18262.031 78.35564 151.5843 + 2900 -18183.676 -18260.662 76.985337 148.93336 + 3000 -18183.675 -18259.627 75.95239 146.93505 + 3100 -18183.674 -18258.689 75.015243 145.12207 + 3200 -18183.677 -18264.078 80.401279 155.54173 + 3300 -18183.675 -18260.502 76.827262 148.62755 + 3400 -18183.674 -18259.322 75.648519 146.34719 + 3500 -18183.677 -18262.575 78.89745 152.63247 + 3600 -18183.674 -18259.703 76.028748 147.08277 + 3700 -18183.675 -18260.132 76.456781 147.91083 + 3800 -18183.676 -18261.159 77.482985 149.89609 + 3900 -18183.676 -18261.78 78.104238 151.09794 + 4000 -18183.674 -18261.154 77.479339 149.88903 + 4100 -18183.674 -18258.407 74.73235 144.5748 + 4200 -18183.675 -18260.478 76.80323 148.58106 + 4300 -18183.675 -18261.958 78.283002 151.44378 + 4400 -18183.675 -18259.458 75.782601 146.60658 + 4500 -18183.676 -18261.565 77.888353 150.6803 + 4600 -18183.675 -18262.439 78.763787 152.37389 + 4700 -18183.674 -18259.736 76.062328 147.14773 + 4800 -18183.675 -18259.507 75.831695 146.70156 + 4900 -18183.674 -18260.095 76.420852 147.84132 + 5000 -18183.676 -18261.031 77.35533 149.64913 + 5100 -18183.675 -18261.154 77.479231 149.88883 + 5200 -18183.675 -18260.91 77.234546 149.41547 + 5300 -18183.675 -18259.096 75.421551 145.9081 + 5400 -18183.675 -18261.272 77.597794 150.1182 + 5500 -18183.676 -18261.628 77.951733 150.80291 + 5600 -18183.676 -18261.346 77.669986 150.25786 + 5700 -18183.674 -18259.838 76.163516 147.34349 + 5800 -18183.675 -18261.268 77.592366 150.10769 + 5900 -18183.676 -18260.091 76.415502 147.83097 + 6000 -18183.676 -18260.681 77.004995 148.97138 + 6100 -18183.675 -18260.836 77.161235 149.27364 + 6200 -18183.676 -18260.737 77.060829 149.0794 + 6300 -18183.675 -18261.271 77.595943 150.11461 + 6400 -18183.675 -18261.07 77.394756 149.7254 + 6500 -18183.675 -18260.183 76.507456 148.00886 + 6600 -18183.674 -18259.407 75.732739 146.51012 + 6700 -18183.675 -18263.584 79.908585 154.58858 + 6800 -18183.675 -18258.898 75.223189 145.52436 + 6900 -18183.675 -18259.668 75.992353 147.01236 + 7000 -18183.675 -18261.005 77.32958 149.59932 + 7100 -18183.674 -18257.606 73.93173 143.02594 + 7200 -18183.675 -18262.243 78.567797 151.99473 + 7300 -18183.675 -18262.45 78.774503 152.39462 + 7400 -18183.675 -18261.601 77.926008 150.75315 + 7500 -18183.676 -18259.617 75.941677 146.91432 + 7600 -18183.676 -18259.857 76.181093 147.37749 + 7700 -18183.675 -18260.876 77.201101 149.35076 + 7800 -18183.675 -18261.473 77.797809 150.50514 + 7900 -18183.673 -18259.886 76.212823 147.43887 + 8000 -18183.676 -18260.24 76.563571 148.11742 + 8100 -18183.678 -18262.645 78.966698 152.76643 + 8200 -18183.674 -18259.053 75.379541 145.82683 + 8300 -18183.674 -18259.443 75.769016 146.5803 + 8400 -18183.676 -18261.296 77.619894 150.16095 + 8500 -18183.677 -18261.539 77.862555 150.63039 + 8600 -18183.673 -18259.912 76.239027 147.48957 + 8700 -18183.676 -18260.747 77.071153 149.09937 + 8800 -18183.677 -18261.441 77.763508 150.43878 + 8900 -18183.675 -18260.339 76.663677 148.31108 + 9000 -18183.674 -18260.772 77.098384 149.15205 + 9100 -18183.675 -18259.284 75.608629 146.27002 + 9200 -18183.676 -18261.033 77.356514 149.65142 + 9300 -18183.676 -18261.538 77.86202 150.62936 + 9400 -18183.676 -18260.932 77.256598 149.45813 + 9500 -18183.675 -18261.609 77.934109 150.76882 + 9600 -18183.675 -18259.409 75.734665 146.51385 + 9700 -18183.676 -18260.011 76.335226 147.67567 + 9800 -18183.676 -18260.877 77.200654 149.3499 + 9900 -18183.675 -18260.68 77.005143 148.97167 + 10000 -18183.677 -18261.794 78.117487 151.12358 +Loop time of 166.716 on 1 procs for 10000 steps with 4000 atoms + +Performance: 5.182 ns/day, 4.631 hours/ns, 59.982 timesteps/s +96.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 165.04 | 165.04 | 165.04 | 0.0 | 99.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.46039 | 0.46039 | 0.46039 | 0.0 | 0.28 +Output | 0.027102 | 0.027102 | 0.027102 | 0.0 | 0.02 +Modify | 0.78734 | 0.78734 | 0.78734 | 0.0 | 0.47 +Other | | 0.3996 | | | 0.24 + +Nlocal: 4000.00 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3470.00 ave 3470 max 3470 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 112000.0 ave 112000 max 112000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 112000 +Ave neighs/atom = 28.000000 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:47 diff --git a/src/USER-MISC/pair_tersoff_shift.h b/src/USER-MISC/pair_tersoff_shift.h index 82e5c86171..29e0049d76 100644 --- a/src/USER-MISC/pair_tersoff_shift.h +++ b/src/USER-MISC/pair_tersoff_shift.h @@ -28,18 +28,6 @@ class PairTersoffShift : public PairTersoff { public: PairTersoffShift(class LAMMPS *); ~PairTersoffShift() {} -// void settings(int, char **); - -// protected: -// virtual void repulsive(Param *, double, double &, int, double &); -// virtual double zeta(Param *, double, double, double *, double *); -// virtual void force_zeta(Param *, double, double, double &, -// double &, int, double &); -// void attractive(Param *, double, double, double, double *, double *, -// double *, double *, double *); -// void costheta_d(double *, double, double *, double, -// double *, double *, double *); -// }; }