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Energy conservation for non-zero lambda3

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This commit is contained in:
Wengen Ouyang
2020-12-17 03:31:59 +02:00
parent f434797a3e
commit a01b376391
4 changed files with 248 additions and 12 deletions
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18
examples/USER/misc/tersoff_shift/Si.tersoff Normal file
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# 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

36
examples/USER/misc/tersoff_shift/in.Si_shift Normal file
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# 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

194
examples/USER/misc/tersoff_shift/log.30Nov20.Si_shift0.05.g++.1 Normal file
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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

12
src/USER-MISC/pair_tersoff_shift.h
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@ -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 *);
//
};
}