forked from lijiext/lammps
Update doc and examples due to the change of parameters
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Mingjian Wen
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24e41bc085
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@ -33,8 +33,8 @@ pair_coeff * * rebo CH.airebo C H :pre
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Style {drip} computes the interlayer interactions of layered materials using
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the dihedral-angle-corrected registry-dependent (DRIP) potential as described
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in "(Wen)"_#Wen1, which is based on the "(Kolmogorov)"_#Kolmogorov1 potential
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and provides an improvded prediction for forces.
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in "(Wen)"_#Wen2018, which is based on the "(Kolmogorov)"_#Kolmogorov2005
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potential and provides an improvded prediction for forces.
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The total potential energy of a system is
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:c,image(Eqs/pair_drip.jpg)
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@ -88,9 +88,10 @@ pair_style hybrid/overlay drip rebo
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pair_coeff * * drip C.drip C NULL
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pair_coeff * * rebo CH.airebo C H :pre
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NOTE: The parameter file developed in "(Wen)"_#Wen1 is provided with LAMMPS (see
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the "potentials" directory).
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NOTE: The potential parameters developed in "(Wen)"_#Wen2018 are provided with
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LAMMPS (see the "potentials" directory). Besides those in "Wen"_#Wen2018, an
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additional parameter "normal_cutoff", specific to the LAMMPS implementation, is
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used to find the three nearest neighbors of an atom to construct the normal.
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:line
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@ -131,9 +132,10 @@ simulation doesn't use "metal" units.
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:line
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:link(Wen1)
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[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018)
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:link(Wen2018)
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[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B,
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98, 235404 (2018)
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:link(Kolmogorov1)
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:link(Kolmogorov2005)
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[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
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@ -6,10 +6,14 @@
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# Cite as M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018).
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# C0 C2 C4 C delta lambda A z0 B eta rho_cut r_cut
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C C 1.1598e-02 1.2981e-02 3.2515e-02 7.8151e-03 8.3679e-01 2.7158 2.2216e-02 3.34 7.6799e-03 1.1432 1.562 12.0
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# C0 C2 C4 C delta lambda A z0 B eta rho_cut r_cut normal_cut
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C C 1.1598e-02 1.2981e-02 3.2515e-02 7.8151e-03 8.3679e-01 2.7158 2.2216e-02 3.34 7.6799e-03 1.1432 1.562 12.0 3.7
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# C0, C2, C4, C, A, and B in [eV]
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# delta, z0, eta, rho_cut, and r_cut in [Angstrom]
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# delta, z0, eta, rho_cut, r_cut, and normal_cut in [Angstrom]
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# lambda in [1/Angstrom]
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#
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# "normal_cut" is a parameter not present in the Wen paper, but specific to the
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# LAMMPS implementation, which is used to find the 3 nearest neighbors of an
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# atom to construct the normal.
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@ -16,8 +16,8 @@ read_data data.CH
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000135899 secs
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read_data CPU = 0.00296116 secs
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special bonds CPU = 0.000221014 secs
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read_data CPU = 0.00603986 secs
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# potential
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@ -44,9 +44,9 @@ WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimizat
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 4 1
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master list distance cutoff = 17.7
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ghost atom cutoff = 17.7
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binsize = 8.85, bins = 5 3 1
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair drip, perpetual, skip from (2)
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attributes: full, newton on, ghost
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@ -58,52 +58,52 @@ Neighbor list info ...
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 11.71 | 11.71 | 11.71 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 12.92 | 12.92 | 12.92 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0 -2883.1071 0 -2883.1071 366130.38 2779.5956
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10 0 -3229.1892 0 -3229.1892 -19780.166 2779.5956
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20 0 -3268.3574 0 -3268.3574 -15169.468 2779.5956
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30 0 -3270.013 0 -3270.013 -19827.419 2779.5956
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40 0 -3270.1341 0 -3270.1341 -20652.573 2779.5956
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50 0 -3270.2612 0 -3270.2612 -22644.203 2779.5956
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57 0 -3270.2821 0 -3270.2821 -23259.55 2779.5956
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Loop time of 2.88099 on 1 procs for 57 steps with 545 atoms
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40 0 -3270.1341 0 -3270.1341 -20652.569 2779.5956
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50 0 -3270.2612 0 -3270.2612 -22644.747 2779.5956
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57 0 -3270.2819 0 -3270.2819 -23254.995 2779.5956
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Loop time of 3.06624 on 1 procs for 57 steps with 545 atoms
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99.0% CPU use with 1 MPI tasks x no OpenMP threads
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99.3% CPU use with 1 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = max force evaluations
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Energy initial, next-to-last, final =
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-2883.10712045 -3270.28053776 -3270.28206154
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Force two-norm initial, final = 114.766 0.235923
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Force max component initial, final = 12.0195 0.0426664
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Final line search alpha, max atom move = 1 0.0426664
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-2883.10712045 -3270.28039929 -3270.28192718
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Force two-norm initial, final = 114.766 0.235428
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Force max component initial, final = 12.0195 0.0484347
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Final line search alpha, max atom move = 1 0.0484347
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Iterations, force evaluations = 57 101
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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 | 2.8692 | 2.8692 | 2.8692 | 0.0 | 99.59
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Bond | 3.5524e-05 | 3.5524e-05 | 3.5524e-05 | 0.0 | 0.00
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Pair | 3.0539 | 3.0539 | 3.0539 | 0.0 | 99.60
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Bond | 4.1485e-05 | 4.1485e-05 | 4.1485e-05 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0014327 | 0.0014327 | 0.0014327 | 0.0 | 0.05
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Output | 0.0069089 | 0.0069089 | 0.0069089 | 0.0 | 0.24
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Comm | 0.0019863 | 0.0019863 | 0.0019863 | 0.0 | 0.06
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Output | 0.0070152 | 0.0070152 | 0.0070152 | 0.0 | 0.23
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.003388 | | | 0.12
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Other | | 0.003321 | | | 0.11
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Nlocal: 545 ave 545 max 545 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2346 ave 2346 max 2346 min
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Nghost: 3175 ave 3175 max 3175 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 180462 ave 180462 max 180462 min
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FullNghs: 294122 ave 294122 max 294122 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 180462
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Ave neighs/atom = 331.123
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Total # of neighbors = 294122
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Ave neighs/atom = 539.673
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:02
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Total wall time: 0:00:03
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@ -16,8 +16,8 @@ read_data data.C
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000100136 secs
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read_data CPU = 0.00110912 secs
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special bonds CPU = 0.000164032 secs
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read_data CPU = 0.00137401 secs
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# potential
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@ -43,9 +43,9 @@ WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimizat
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 4 1
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master list distance cutoff = 17.7
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ghost atom cutoff = 17.7
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binsize = 8.85, bins = 5 3 1
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair drip, perpetual
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attributes: full, newton on, ghost
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@ -57,7 +57,7 @@ Neighbor list info ...
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 11.4 | 11.4 | 11.4 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 12.21 | 12.21 | 12.21 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534
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10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534
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@ -66,9 +66,9 @@ Step Temp E_pair E_mol TotEng Press Volume
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40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
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50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
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51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
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Loop time of 2.8619 on 1 procs for 51 steps with 400 atoms
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Loop time of 2.89944 on 1 procs for 51 steps with 400 atoms
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98.9% CPU use with 1 MPI tasks x no OpenMP threads
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99.6% CPU use with 1 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = max force evaluations
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@ -82,25 +82,25 @@ Minimization stats:
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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 | 2.8529 | 2.8529 | 2.8529 | 0.0 | 99.69
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Bond | 3.314e-05 | 3.314e-05 | 3.314e-05 | 0.0 | 0.00
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Pair | 2.8899 | 2.8899 | 2.8899 | 0.0 | 99.67
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Bond | 3.171e-05 | 3.171e-05 | 3.171e-05 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0010927 | 0.0010927 | 0.0010927 | 0.0 | 0.04
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Output | 0.0053217 | 0.0053217 | 0.0053217 | 0.0 | 0.19
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Comm | 0.001483 | 0.001483 | 0.001483 | 0.0 | 0.05
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Output | 0.0055339 | 0.0055339 | 0.0055339 | 0.0 | 0.19
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.002526 | | | 0.09
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Other | | 0.002449 | | | 0.08
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Nlocal: 400 ave 400 max 400 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1716 ave 1716 max 1716 min
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Nghost: 2357 ave 2357 max 2357 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 180462 ave 180462 max 180462 min
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FullNghs: 294122 ave 294122 max 294122 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 180462
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Ave neighs/atom = 451.155
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Total # of neighbors = 294122
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Ave neighs/atom = 735.305
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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@ -700,7 +700,8 @@ void PairDRIP::find_nearest3neigh()
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// store neighbors to be used later to compute normal
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if (nb3_rsq >= 1.0e10) {
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if (i<inum) {
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error->one(FLERR, "No enough neighbors to construct normal.");
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error->one(FLERR, "No enough neighbors to construct normal. Check the "
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"configuration to see whether atoms fly away.");
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} else {
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// This only happens for ghost atoms that are near the boundary of the
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// domain (i.e. r > r_cut + n_cut). These ghost atoms will not be
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