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Merge pull request #1453 from mjwen/pair_drip 

add pair style drip
This commit is contained in:
Axel Kohlmeyer 2019-05-10 20:44:28 -04:00 committed by GitHub
parent 03505a6c48 799f4061f4
commit a7c9560dc1
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28 changed files with 2937 additions and 7 deletions
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1
doc/src/Commands_pair.txt
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@ -80,6 +80,7 @@ OPT.
"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
"dpd/tstat (go)"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"drip"_pair_drip.html,
"eam (gikot)"_pair_eam.html,
"eam/alloy (gikot)"_pair_eam.html,
"eam/cd (o)"_pair_eam.html,

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doc/src/Eqs/pair_drip.tex Normal file
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\documentclass[12pt]{article}
\usepackage{amsmath}
\usepackage{bm}
\begin{document}
\begin{eqnarray*}
E &=& \frac{1}{2} \sum_{i} \sum_{j\notin\text{layer}\,i} \phi_{ij} \\\phi_{ij} &=& f_\text{c}(x_r) \left[ e^{-\lambda(r_{ij} - z_0 )} \left[C+f(\rho_{ij})+ g(\rho_{ij}, \{\alpha_{ij}^{(m)}\}) \right]- A\left (\frac{z_0}{r_{ij}} \right)^6 \right] \\
\end{eqnarray*}
\end{document}

1
doc/src/lammps.book
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@ -574,6 +574,7 @@ pair_dipole.html
pair_dpd.html
pair_dpd_fdt.html
pair_dsmc.html
pair_drip.html
pair_eam.html
pair_edip.html
pair_eff.html

141
doc/src/pair_drip.txt Normal file
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@ -0,0 +1,141 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style drip command :h3
[Syntax:]
pair_style hybrid/overlay drip \[styles ...\] :pre
styles = other styles to be overlayed with drip (optional) :ul
[Examples:]
pair_style hybrid/overlay drip
pair_coeff * * none
pair_coeff * * drip C.drip C :pre
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
pair_coeff * * rebo CH.airebo C :pre
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL
pair_coeff * * rebo CH.airebo C H :pre
[Description:]
Style {drip} computes the interlayer interactions of layered materials using
the dihedral-angle-corrected registry-dependent (DRIP) potential as described
in "(Wen)"_#Wen2018, which is based on the "(Kolmogorov)"_#Kolmogorov2005
potential and provides an improved prediction for forces.
The total potential energy of a system is
:c,image(Eqs/pair_drip.jpg)
where the {r^-6} term models the attractive London dispersion,
the exponential term is designed to capture the registry effect due to
overlapping {pi} bonds, and {fc} is a cutoff function.
This potential (DRIP) only provides the interlayer interactions between
graphene layers. So, to perform a realistic simulation, it should be used in
combination with an intralayer potential such as "REBO"_pair_airebo.html and
"Tersoff"_pair_tersoff.html.
To keep the intralayer interactions unaffected, we should avoid applying DRIP
to contribute energy to intralayer interactions. This can be achieved by
assigning different molecular IDs to atoms in different layers, and DRIP is
implemented such that only atoms with different molecular ID can interact with
each other. For this purpose, "atom style"_atom_style.html "molecular" or
"full" has to be used.
On the other way around, "REBO"_pair_airebo.html ("Tersoff"_pair_tersoff.html
or any other potential used to provide the intralayer interactions) should not
interfere with the interlayer interactions described by DRIP. This is typically
automatically achieved using the commands provided in the {Examples} section
above, since the cutoff distance for carbon-carbon interaction in the intralayer
potentials (e.g. 2 Angstrom for "REBO"_pair_airebo.html) is much smaller than
the equilibrium layer distance of graphene layers (about 3.4 Angstrom).
If you want, you can enforce this by assigning different atom types to atoms in
different layers, and apply an intralayer potential to one atom type.
See "pair_hybrid"_pair_hybrid.html for details.
:line
The "pair_coeff"_pair_coeff.html command for DRIP takes {4+N} arguments, where
{N} is the number of LAMMPS atom types. The fist three arguments must be fixed
to be {* * drip}, the fourth argument is the path to the DRIP parameter file,
and the remaining N arguments specifying the mapping between element in the
parameter file and atom types. For example, if your LAMMPS simulation has 3 atom
types and you want all of them to be C, you would use the following pair_coeff
command:
pair_coeff * * drip C.drip C C C :pre
If a mapping value is specified as NULL, the mapping is not performed. This
could be useful when DRIP is used to model part of the system where other
element exists. Suppose you have a hydrocarbon system, with C of atom type 1
and H of atom type 2, you can use the following command to inform DRIP not to
model H atoms:
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL
pair_coeff * * rebo CH.airebo C H :pre
NOTE: The potential parameters developed in "(Wen)"_#Wen2018 are provided with
LAMMPS (see the "potentials" directory). Besides those in "Wen"_#Wen2018, an
additional parameter "normal_cutoff", specific to the LAMMPS implementation, is
used to find the three nearest neighbors of an atom to construct the normal.
:line
[Mixing, shift, table, tail correction, and restart info]:
This pair style does not support the pair_modify mix, shift, table,
and tail options.
This pair style does not write their information to binary restart files, since
it is stored in potential files. Thus, you need to re-specify the pair_style and
pair_coeff commands in an input script that reads a restart file.
[Restrictions:]
This pair style is part of the USER-MISC package. It is only enabled if LAMMPS
was built with that package. See the "Build package"_Build_package.html doc
page for more info.
This pair potential requires the "newton"_newton.html setting to be "on" for
pair interactions.
The {C.drip} parameter file provided with LAMMPS (see the "potentials"
directory) is parameterized for metal "units"_units.html. You can use the DRIP
potential with any LAMMPS units, but you would need to create your own custom
parameter file with coefficients listed in the appropriate units, if your
simulation doesn't use "metal" units.
[Related commands:]
"pair_style lebedeva_z"_pair_lebedeva_z.html,
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
:line
:link(Wen2018)
[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B,
98, 235404 (2018)
:link(Kolmogorov2005)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

7
doc/src/pair_ilp_graphene_hbn.txt
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@ -50,11 +50,11 @@ calculating the normals.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.
To perform a realistic simulation, this potential must be used in combination with
intra-layer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intra-layer properties unaffected, the interlayer interaction
intralayer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intralayer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intra-layer potential and atoms residing on different layers
appropriate intralayer potential and atoms residing on different layers
interact via the ILP. Here, the molecule id is chosen as the layer identifier,
thus a data file with the "full" atom style is required to use this potential.
@ -117,6 +117,7 @@ units, if your simulation does not use {metal} units.
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,

7
doc/src/pair_kolmogorov_crespi_full.txt
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@ -44,12 +44,12 @@ can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene. To perform a realistic simulation, this potential
must be used in combination with intra-layer potential, such as
must be used in combination with intralayer potential, such as
"AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intra-layer properties unaffected, the interlayer interaction
To keep the intralayer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intra-layer potential and atoms residing on different layers
appropriate intralayer potential and atoms residing on different layers
interact via the ILP. Here, the molecule id is chosen as the layer identifier,
thus a data file with the "full" atom style is required to use this potential.
@ -106,6 +106,7 @@ units.
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.

1
doc/src/pair_kolmogorov_crespi_z.txt
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@ -59,6 +59,7 @@ package"_Build_package.html doc page for more info.
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
"pair_style lebedeva/z"_pair_lebedeva_z.html

1
doc/src/pair_lebedeva_z.txt
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@ -53,6 +53,7 @@ package"_Build_package.html doc page for more info.
"pair_coeff"_pair_coeff.html,
"pair_style none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html,
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html.

3
doc/src/pair_style.txt
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@ -147,6 +147,7 @@ accelerated styles exist.
"dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy
"dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting
"dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
"drip"_pair_drip.html - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
"eam"_pair_eam.html - embedded atom method (EAM)
"eam/alloy"_pair_eam.html - alloy EAM
"eam/cd"_pair_eam.html - concentration-dependent EAM
@ -174,7 +175,7 @@ accelerated styles exist.
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
"lebedeva/z"_pair_lebedeva_z.html - Lebedeva inter-layer potential for graphene with normals along z-axis
"lebedeva/z"_pair_lebedeva_z.html - Lebedeva interlayer potential for graphene with normals along z-axis
"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
"line/lj"_pair_line_lj.html - LJ potential between line segments
"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file

1
doc/src/pairs.txt
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@ -31,6 +31,7 @@ Pair Styles :h1
pair_dipole
pair_dpd
pair_dpd_fdt
pair_drip
pair_dsmc
pair_eam
pair_edip

2
doc/utils/sphinx-config/false_positives.txt
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@ -1160,6 +1160,7 @@ Interparticle
interstitials
Intr
intra
intralayer
intramolecular
ints
inv
@ -1276,6 +1277,7 @@ Katsnelson
Katsura
Kaufmann
Kawata
Kaxiras
Kayser
kb
kB

1
examples/USER/misc/drip/C.drip Symbolic link
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@ -0,0 +1 @@
../../../../potentials/C.drip

1
examples/USER/misc/drip/CH.rebo Symbolic link
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@ -0,0 +1 @@
../../../../potentials/CH.rebo

6
examples/USER/misc/drip/README.txt Normal file
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@ -0,0 +1,6 @@
in.C_drip:
Use DRIP and REBO to relax a bilayer graphene.
in.CH_drip:
Use DRIP and REBO to relax a bilayer graphene with additional hydrogen atoms
on top of it.

416
examples/USER/misc/drip/data.C Normal file
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@ -0,0 +1,416 @@
LAMMPS data file
400 atoms
1 atom types
0.0 2.465000000000000e+01 xlo xhi
0.0 2.134752620328641e+01 ylo yhi
0.0 3.000000000000000e+01 zlo zhi
1.232500000000000e+01 0.000000000000000e+00 0.000000000000000e+00 xy xz yz
Masses
1 12.011
Atoms # molecular
1 1 1 0.000000000000000e+00 0.000000000000000e+00 1.498097531971289e+01
2 1 1 9.859999999999999e+00 1.707802096262913e+01 1.489139792549795e+01
3 1 1 2.588250000000000e+01 6.404257860985923e+00 1.495586615731768e+01
4 1 1 2.711500000000000e+01 7.115842067762138e+00 1.501795235919980e+01
5 1 1 4.930000000000000e+00 8.539010481314564e+00 1.492827527515956e+01
6 1 1 6.162499999999999e+00 9.250594688090777e+00 1.500678649580791e+01
7 1 1 3.204499999999999e+01 1.565485254907670e+01 1.511662064028576e+01
8 1 1 3.081250000000000e+01 1.494326834230049e+01 1.505500683988625e+01
9 1 1 7.395000000000000e+00 8.539010481314564e+00 1.504923694256975e+01
10 1 1 8.627500000000000e+00 9.250594688090777e+00 1.503332570633445e+01
11 1 1 9.859999999999999e+00 8.539010481314564e+00 1.508137430939768e+01
12 1 1 1.109250000000000e+01 9.250594688090777e+00 1.510475862694483e+01
13 1 1 1.109250000000000e+01 1.778960516940534e+01 1.494613902888088e+01
14 1 1 2.958000000000000e+01 1.565485254907670e+01 1.516279958068751e+01
15 1 1 1.232500000000000e+01 8.539010481314564e+00 1.511276583208523e+01
16 1 1 1.355750000000000e+01 9.250594688090777e+00 1.495632206546155e+01
17 1 1 1.479000000000000e+01 8.539010481314564e+00 1.498291715828213e+01
18 1 1 1.602250000000000e+01 9.250594688090777e+00 1.509801558902469e+01
19 1 1 2.711499999999999e+01 1.565485254907670e+01 1.500089766276763e+01
20 1 1 2.588250000000000e+01 1.494326834230049e+01 1.505114888970355e+01
21 1 1 1.725500000000000e+01 8.539010481314564e+00 1.504495103103041e+01
22 1 1 1.848750000000000e+01 9.250594688090777e+00 1.513527732850389e+01
23 1 1 1.972000000000000e+01 8.539010481314564e+00 1.502400693288890e+01
24 1 1 2.095250000000000e+01 9.250594688090777e+00 1.490419939433632e+01
25 1 1 2.465000000000000e+01 1.565485254907670e+01 1.492998117758711e+01
26 1 1 2.834750000000000e+01 1.494326834230049e+01 1.496091474579883e+01
27 1 1 2.465000000000000e+01 7.115842067762138e+00 1.497394355694102e+01
28 1 1 2.341750000000000e+01 6.404257860985923e+00 1.500235588455933e+01
29 1 1 2.218500000000000e+01 7.115842067762138e+00 1.503766448268803e+01
30 1 1 2.465000000000000e+01 4.269505240657282e+00 1.488340764495658e+01
31 1 1 2.588250000000000e+01 4.981089447433495e+00 1.490587231994899e+01
32 1 1 3.697500000000000e+00 6.404257860985923e+00 1.500462204163887e+01
33 1 1 4.930000000000000e+00 7.115842067762138e+00 1.507823175629797e+01
34 1 1 2.095250000000000e+01 1.778960516940534e+01 1.485635836857104e+01
35 1 1 1.972000000000000e+01 1.707802096262913e+01 1.508733405608850e+01
36 1 1 6.162500000000000e+00 6.404257860985923e+00 1.495657175139946e+01
37 1 1 7.395000000000000e+00 7.115842067762138e+00 1.505630699893542e+01
38 1 1 8.627500000000000e+00 6.404257860985923e+00 1.493710859708546e+01
39 1 1 9.859999999999999e+00 7.115842067762138e+00 1.498031036104573e+01
40 1 1 1.848750000000000e+01 1.778960516940534e+01 1.492663969598082e+01
41 1 1 1.725500000000000e+01 1.707802096262913e+01 1.487928391741343e+01
42 1 1 2.218500000000000e+01 1.280851572197185e+01 1.493339893560164e+01
43 1 1 1.232500000000000e+01 7.115842067762138e+00 1.507943978677017e+01
44 1 1 1.355750000000000e+01 6.404257860985923e+00 1.484914917113341e+01
45 1 1 1.479000000000000e+01 7.115842067762138e+00 1.516663648122805e+01
46 1 1 1.602250000000000e+01 1.778960516940534e+01 1.494170266401908e+01
47 1 1 1.479000000000000e+01 1.707802096262913e+01 1.489834582180523e+01
48 1 1 1.602250000000000e+01 6.404257860985923e+00 1.502658138746657e+01
49 1 1 1.725500000000000e+01 7.115842067762138e+00 1.498697322036154e+01
50 1 1 1.848750000000000e+01 6.404257860985923e+00 1.504573856434245e+01
51 1 1 1.972000000000000e+01 7.115842067762138e+00 1.498510668772038e+01
52 1 1 1.355750000000000e+01 1.778960516940534e+01 1.503160986637731e+01
53 1 1 1.232500000000000e+01 1.707802096262913e+01 1.482446479934924e+01
54 1 1 2.095250000000000e+01 6.404257860985923e+00 1.510811524523195e+01
55 1 1 2.341750000000000e+01 1.494326834230049e+01 1.505440697642049e+01
56 1 1 2.218500000000000e+01 1.707802096262913e+01 1.489480063588714e+01
57 1 1 2.218500000000000e+01 8.539010481314564e+00 1.495045959051609e+01
58 1 1 2.465000000000000e+01 8.539010481314564e+00 1.512601015985335e+01
59 1 1 2.588250000000000e+01 1.067376310164321e+01 1.495691790117351e+01
60 1 1 2.711500000000000e+01 1.138534730841942e+01 1.496195578420333e+01
61 1 1 9.859999999999999e+00 1.565485254907670e+01 1.488138963237187e+01
62 1 1 8.627500000000000e+00 1.494326834230049e+01 1.498700505084123e+01
63 1 1 2.834750000000000e+01 1.067376310164321e+01 1.504459111637339e+01
64 1 1 2.958000000000000e+01 1.138534730841942e+01 1.495098625433358e+01
65 1 1 7.395000000000000e+00 1.280851572197185e+01 1.505608046573023e+01
66 1 1 8.627500000000000e+00 1.352009992874806e+01 1.484199719552881e+01
67 1 1 3.081250000000000e+01 1.352009992874806e+01 1.483451056838223e+01
68 1 1 2.958000000000000e+01 1.280851572197185e+01 1.502332948089694e+01
69 1 1 9.859999999999999e+00 1.280851572197185e+01 1.506286085730730e+01
70 1 1 2.465000000000000e+01 1.138534730841942e+01 1.506305034228861e+01
71 1 1 1.109250000000000e+01 1.352009992874806e+01 1.491918072685150e+01
72 1 1 1.355750000000000e+01 1.352009992874806e+01 1.494644661191470e+01
73 1 1 2.834750000000000e+01 1.352009992874806e+01 1.496099714517733e+01
74 1 1 2.711500000000000e+01 1.280851572197185e+01 1.498298656405413e+01
75 1 1 1.479000000000000e+01 1.280851572197185e+01 1.511808602386498e+01
76 1 1 1.602250000000000e+01 1.352009992874806e+01 1.509196186449678e+01
77 1 1 1.725500000000000e+01 1.280851572197185e+01 1.494017769280163e+01
78 1 1 1.848750000000000e+01 1.352009992874806e+01 1.486540173862453e+01
79 1 1 2.588250000000000e+01 1.352009992874806e+01 1.502414429870090e+01
80 1 1 2.465000000000000e+01 1.280851572197185e+01 1.491189258035136e+01
81 1 1 1.972000000000000e+01 1.280851572197185e+01 1.503451993485524e+01
82 1 1 2.095250000000000e+01 1.352009992874806e+01 1.503423133885440e+01
83 1 1 1.232500000000000e+01 1.280851572197185e+01 1.492432047742539e+01
84 1 1 2.341750000000000e+01 1.067376310164321e+01 1.500488865182437e+01
85 1 1 1.109250000000000e+01 1.494326834230049e+01 1.509530225402135e+01
86 1 1 1.232500000000000e+01 1.565485254907670e+01 1.500246060086581e+01
87 1 1 2.588250000000000e+01 9.250594688090777e+00 1.498734533172262e+01
88 1 1 2.218500000000000e+01 1.565485254907670e+01 1.504729297899704e+01
89 1 1 2.095250000000000e+01 1.494326834230049e+01 1.486622917148261e+01
90 1 1 2.711500000000000e+01 8.539010481314564e+00 1.494373650471835e+01
91 1 1 2.834750000000000e+01 9.250594688090777e+00 1.488792788684821e+01
92 1 1 6.162500000000000e+00 1.067376310164321e+01 1.486731884367082e+01
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316 2 1 8.627499999999998e+00 7.827426274538350e+00 1.840542860269897e+01
317 2 1 1.848750000000000e+01 7.115842067762137e-01 1.843036272469964e+01
318 2 1 2.095250000000000e+01 7.115842067762137e-01 1.828037025055374e+01
319 2 1 2.218500000000000e+01 1.423168413552427e+00 1.847794227938386e+01
320 2 1 2.341750000000000e+01 7.115842067762137e-01 1.836220929695125e+01
321 2 1 2.465000000000000e+01 1.423168413552427e+00 1.856129777428492e+01
322 2 1 2.465000000000000e+00 2.846336827104855e+00 1.828958750195393e+01
323 2 1 3.697500000000000e+00 3.557921033881068e+00 1.848583325162553e+01
324 2 1 4.930000000000000e+00 2.846336827104855e+00 1.838401024175294e+01
325 2 1 6.162499999999999e+00 3.557921033881068e+00 1.837437624437527e+01
326 2 1 7.395000000000000e+00 2.846336827104855e+00 1.841292915268399e+01
327 2 1 8.627500000000000e+00 3.557921033881068e+00 1.848557970160289e+01
328 2 1 9.859999999999999e+00 2.846336827104855e+00 1.842924761810127e+01
329 2 1 1.109250000000000e+01 3.557921033881068e+00 1.831004365073452e+01
330 2 1 1.232500000000000e+01 2.846336827104855e+00 1.818033371289823e+01
331 2 1 1.355750000000000e+01 3.557921033881068e+00 1.844566501118075e+01
332 2 1 1.972000000000000e+01 1.423168413552427e+00 1.846190975036447e+01
333 2 1 2.218500000000000e+01 1.423168413552428e+01 1.835322517893207e+01
334 2 1 9.859999999999999e+00 7.115842067762138e+00 1.839789371642158e+01
335 2 1 1.232500000000000e+01 7.115842067762138e+00 1.847537444410727e+01
336 2 1 8.627500000000000e+00 1.209693151519563e+01 1.829199174409380e+01
337 2 1 9.859999999999999e+00 1.138534730841942e+01 1.829413303647114e+01
338 2 1 1.109250000000000e+01 1.209693151519563e+01 1.856999584032139e+01
339 2 1 1.232500000000000e+01 1.138534730841942e+01 1.851349651735582e+01
340 2 1 1.355750000000000e+01 1.209693151519563e+01 1.831123823696192e+01
341 2 1 1.479000000000000e+01 1.138534730841942e+01 1.843448433334394e+01
342 2 1 1.602250000000000e+01 1.209693151519563e+01 1.839428881565063e+01
343 2 1 1.725500000000000e+01 1.138534730841942e+01 1.849178099784848e+01
344 2 1 1.848750000000000e+01 1.209693151519563e+01 1.824975358434335e+01
345 2 1 1.972000000000000e+01 1.138534730841942e+01 1.839694145030204e+01
346 2 1 2.095250000000000e+01 1.209693151519563e+01 1.829096787226717e+01
347 2 1 2.218500000000000e+01 1.138534730841942e+01 1.840263887228008e+01
348 2 1 2.341750000000000e+01 1.209693151519563e+01 1.837666030509410e+01
349 2 1 2.465000000000000e+01 1.138534730841942e+01 1.835828025909527e+01
350 2 1 2.588250000000000e+01 1.209693151519563e+01 1.833582168089864e+01
351 2 1 2.711500000000000e+01 1.138534730841942e+01 1.836353031742933e+01
352 2 1 2.834750000000000e+01 1.209693151519563e+01 1.845852602484125e+01
353 2 1 2.958000000000000e+01 1.138534730841942e+01 1.853888136458308e+01
354 2 1 3.081250000000000e+01 1.209693151519563e+01 1.831036168742244e+01
355 2 1 8.627500000000000e+00 1.352009992874806e+01 1.835261188649090e+01
356 2 1 9.859999999999999e+00 1.423168413552428e+01 1.821705864207346e+01
357 2 1 1.109250000000000e+01 1.352009992874806e+01 1.831524712388831e+01
358 2 1 1.232500000000000e+01 1.423168413552428e+01 1.852378179475058e+01
359 2 1 1.355750000000000e+01 1.352009992874806e+01 1.852309441840510e+01
360 2 1 1.479000000000000e+01 1.423168413552428e+01 1.836621027472939e+01
361 2 1 1.602250000000000e+01 1.352009992874806e+01 1.849039311610116e+01
362 2 1 1.725500000000000e+01 1.423168413552428e+01 1.842269825087092e+01
363 2 1 1.848750000000000e+01 1.352009992874806e+01 1.825468998789840e+01
364 2 1 1.972000000000000e+01 1.423168413552428e+01 1.849561590548242e+01
365 2 1 7.395000000000000e+00 1.138534730841942e+01 1.859813014678126e+01
366 2 1 3.451000000000000e+01 1.992435778973398e+01 1.813501916227946e+01
367 2 1 2.834750000000000e+01 9.250594688090777e+00 1.847653992697568e+01
368 2 1 2.711499999999999e+01 9.962178894866991e+00 1.849053529347614e+01
369 2 1 1.355750000000000e+01 7.827426274538350e+00 1.835096749618396e+01
370 2 1 1.479000000000000e+01 7.115842067762138e+00 1.844059942495262e+01
371 2 1 1.602250000000000e+01 7.827426274538350e+00 1.844461353068087e+01
372 2 1 1.725500000000000e+01 7.115842067762138e+00 1.836290600804645e+01
373 2 1 1.848750000000000e+01 7.827426274538350e+00 1.825818280452995e+01
374 2 1 1.972000000000000e+01 7.115842067762138e+00 1.837997086460227e+01
375 2 1 2.095250000000000e+01 7.827426274538350e+00 1.826491847987811e+01
376 2 1 2.218500000000000e+01 7.115842067762138e+00 1.841142851923555e+01
377 2 1 2.341750000000000e+01 7.827426274538350e+00 1.826594520665525e+01
378 2 1 2.465000000000000e+01 7.115842067762138e+00 1.838708488224049e+01
379 2 1 2.588250000000000e+01 7.827426274538350e+00 1.830434555380351e+01
380 2 1 2.711500000000000e+01 7.115842067762138e+00 1.859652575977937e+01
381 2 1 2.834750000000000e+01 7.827426274538350e+00 1.844094595194482e+01
382 2 1 6.162499999999999e+00 9.250594688090777e+00 1.856484810097502e+01
383 2 1 1.109250000000000e+01 7.827426274538350e+00 1.847502232204046e+01
384 2 1 7.395000000000000e+00 9.962178894866991e+00 1.854741705791729e+01
385 2 1 9.859999999999999e+00 9.962178894866991e+00 1.837074522628645e+01
386 2 1 1.109250000000000e+01 9.250594688090777e+00 1.846206781979952e+01
387 2 1 1.232500000000000e+01 9.962178894866991e+00 1.823251181425658e+01
388 2 1 1.355750000000000e+01 9.250594688090777e+00 1.834993099844037e+01
389 2 1 1.479000000000000e+01 9.962178894866991e+00 1.843248036437880e+01
390 2 1 1.602250000000000e+01 9.250594688090777e+00 1.855142577781635e+01
391 2 1 1.725500000000000e+01 9.962178894866991e+00 1.847587547064991e+01
392 2 1 1.848750000000000e+01 9.250594688090777e+00 1.850249139638135e+01
393 2 1 1.972000000000000e+01 9.962178894866991e+00 1.841266132895000e+01
394 2 1 2.095250000000000e+01 9.250594688090777e+00 1.837466808881276e+01
395 2 1 2.218500000000000e+01 9.962178894866991e+00 1.834587370280250e+01
396 2 1 2.341750000000000e+01 9.250594688090777e+00 1.846590574952954e+01
397 2 1 2.465000000000000e+01 9.962178894866991e+00 1.835650105398410e+01
398 2 1 2.588250000000000e+01 9.250594688090777e+00 1.838143174570202e+01
399 2 1 8.627500000000000e+00 9.250594688090777e+00 1.843904853716322e+01
400 2 1 3.574249999999999e+01 2.063594199651019e+01 1.839864514570517e+01

562
examples/USER/misc/drip/data.CH Normal file
View File

@ -0,0 +1,562 @@
LAMMPS data file
545 atoms
2 atom types
0.0 2.465000000000000e+01 xlo xhi
0.0 2.134752620328641e+01 ylo yhi
0.0 3.000000000000000e+01 zlo zhi
1.232500000000000e+01 0.000000000000000e+00 0.000000000000000e+00 xy xz yz
Masses
1 12.011
2 1.0
Atoms # molecular
1 1 1 0.000000000000000e+00 0.000000000000000e+00 1.498097531971289e+01
2 1 1 9.859999999999999e+00 1.707802096262913e+01 1.489139792549795e+01
3 1 1 2.588250000000000e+01 6.404257860985923e+00 1.495586615731768e+01
4 1 1 2.711500000000000e+01 7.115842067762138e+00 1.501795235919980e+01
5 1 1 4.930000000000000e+00 8.539010481314564e+00 1.492827527515956e+01
6 1 1 6.162499999999999e+00 9.250594688090777e+00 1.500678649580791e+01
7 1 1 3.204499999999999e+01 1.565485254907670e+01 1.511662064028576e+01
8 1 1 3.081250000000000e+01 1.494326834230049e+01 1.505500683988625e+01
9 1 1 7.395000000000000e+00 8.539010481314564e+00 1.504923694256975e+01
10 1 1 8.627500000000000e+00 9.250594688090777e+00 1.503332570633445e+01
11 1 1 9.859999999999999e+00 8.539010481314564e+00 1.508137430939768e+01
12 1 1 1.109250000000000e+01 9.250594688090777e+00 1.510475862694483e+01
13 1 1 1.109250000000000e+01 1.778960516940534e+01 1.494613902888088e+01
14 1 1 2.958000000000000e+01 1.565485254907670e+01 1.516279958068751e+01
15 1 1 1.232500000000000e+01 8.539010481314564e+00 1.511276583208523e+01
16 1 1 1.355750000000000e+01 9.250594688090777e+00 1.495632206546155e+01
17 1 1 1.479000000000000e+01 8.539010481314564e+00 1.498291715828213e+01
18 1 1 1.602250000000000e+01 9.250594688090777e+00 1.509801558902469e+01
19 1 1 2.711499999999999e+01 1.565485254907670e+01 1.500089766276763e+01
20 1 1 2.588250000000000e+01 1.494326834230049e+01 1.505114888970355e+01
21 1 1 1.725500000000000e+01 8.539010481314564e+00 1.504495103103041e+01
22 1 1 1.848750000000000e+01 9.250594688090777e+00 1.513527732850389e+01
23 1 1 1.972000000000000e+01 8.539010481314564e+00 1.502400693288890e+01
24 1 1 2.095250000000000e+01 9.250594688090777e+00 1.490419939433632e+01
25 1 1 2.465000000000000e+01 1.565485254907670e+01 1.492998117758711e+01
26 1 1 2.834750000000000e+01 1.494326834230049e+01 1.496091474579883e+01
27 1 1 2.465000000000000e+01 7.115842067762138e+00 1.497394355694102e+01
28 1 1 2.341750000000000e+01 6.404257860985923e+00 1.500235588455933e+01
29 1 1 2.218500000000000e+01 7.115842067762138e+00 1.503766448268803e+01
30 1 1 2.465000000000000e+01 4.269505240657282e+00 1.488340764495658e+01
31 1 1 2.588250000000000e+01 4.981089447433495e+00 1.490587231994899e+01
32 1 1 3.697500000000000e+00 6.404257860985923e+00 1.500462204163887e+01
33 1 1 4.930000000000000e+00 7.115842067762138e+00 1.507823175629797e+01
34 1 1 2.095250000000000e+01 1.778960516940534e+01 1.485635836857104e+01
35 1 1 1.972000000000000e+01 1.707802096262913e+01 1.508733405608850e+01
36 1 1 6.162500000000000e+00 6.404257860985923e+00 1.495657175139946e+01
37 1 1 7.395000000000000e+00 7.115842067762138e+00 1.505630699893542e+01
38 1 1 8.627500000000000e+00 6.404257860985923e+00 1.493710859708546e+01
39 1 1 9.859999999999999e+00 7.115842067762138e+00 1.498031036104573e+01
40 1 1 1.848750000000000e+01 1.778960516940534e+01 1.492663969598082e+01
41 1 1 1.725500000000000e+01 1.707802096262913e+01 1.487928391741343e+01
42 1 1 2.218500000000000e+01 1.280851572197185e+01 1.493339893560164e+01
43 1 1 1.232500000000000e+01 7.115842067762138e+00 1.507943978677017e+01
44 1 1 1.355750000000000e+01 6.404257860985923e+00 1.484914917113341e+01
45 1 1 1.479000000000000e+01 7.115842067762138e+00 1.516663648122805e+01
46 1 1 1.602250000000000e+01 1.778960516940534e+01 1.494170266401908e+01
47 1 1 1.479000000000000e+01 1.707802096262913e+01 1.489834582180523e+01
48 1 1 1.602250000000000e+01 6.404257860985923e+00 1.502658138746657e+01
49 1 1 1.725500000000000e+01 7.115842067762138e+00 1.498697322036154e+01
50 1 1 1.848750000000000e+01 6.404257860985923e+00 1.504573856434245e+01
51 1 1 1.972000000000000e+01 7.115842067762138e+00 1.498510668772038e+01
52 1 1 1.355750000000000e+01 1.778960516940534e+01 1.503160986637731e+01
53 1 1 1.232500000000000e+01 1.707802096262913e+01 1.482446479934924e+01
54 1 1 2.095250000000000e+01 6.404257860985923e+00 1.510811524523195e+01
55 1 1 2.341750000000000e+01 1.494326834230049e+01 1.505440697642049e+01
56 1 1 2.218500000000000e+01 1.707802096262913e+01 1.489480063588714e+01
57 1 1 2.218500000000000e+01 8.539010481314564e+00 1.495045959051609e+01
58 1 1 2.465000000000000e+01 8.539010481314564e+00 1.512601015985335e+01
59 1 1 2.588250000000000e+01 1.067376310164321e+01 1.495691790117351e+01
60 1 1 2.711500000000000e+01 1.138534730841942e+01 1.496195578420333e+01
61 1 1 9.859999999999999e+00 1.565485254907670e+01 1.488138963237187e+01
62 1 1 8.627500000000000e+00 1.494326834230049e+01 1.498700505084123e+01
63 1 1 2.834750000000000e+01 1.067376310164321e+01 1.504459111637339e+01
64 1 1 2.958000000000000e+01 1.138534730841942e+01 1.495098625433358e+01
65 1 1 7.395000000000000e+00 1.280851572197185e+01 1.505608046573023e+01
66 1 1 8.627500000000000e+00 1.352009992874806e+01 1.484199719552881e+01
67 1 1 3.081250000000000e+01 1.352009992874806e+01 1.483451056838223e+01
68 1 1 2.958000000000000e+01 1.280851572197185e+01 1.502332948089694e+01
69 1 1 9.859999999999999e+00 1.280851572197185e+01 1.506286085730730e+01
70 1 1 2.465000000000000e+01 1.138534730841942e+01 1.506305034228861e+01
71 1 1 1.109250000000000e+01 1.352009992874806e+01 1.491918072685150e+01
72 1 1 1.355750000000000e+01 1.352009992874806e+01 1.494644661191470e+01
73 1 1 2.834750000000000e+01 1.352009992874806e+01 1.496099714517733e+01
74 1 1 2.711500000000000e+01 1.280851572197185e+01 1.498298656405413e+01
75 1 1 1.479000000000000e+01 1.280851572197185e+01 1.511808602386498e+01
76 1 1 1.602250000000000e+01 1.352009992874806e+01 1.509196186449678e+01
77 1 1 1.725500000000000e+01 1.280851572197185e+01 1.494017769280163e+01
78 1 1 1.848750000000000e+01 1.352009992874806e+01 1.486540173862453e+01
79 1 1 2.588250000000000e+01 1.352009992874806e+01 1.502414429870090e+01
80 1 1 2.465000000000000e+01 1.280851572197185e+01 1.491189258035136e+01
81 1 1 1.972000000000000e+01 1.280851572197185e+01 1.503451993485524e+01
82 1 1 2.095250000000000e+01 1.352009992874806e+01 1.503423133885440e+01
83 1 1 1.232500000000000e+01 1.280851572197185e+01 1.492432047742539e+01
84 1 1 2.341750000000000e+01 1.067376310164321e+01 1.500488865182437e+01
85 1 1 1.109250000000000e+01 1.494326834230049e+01 1.509530225402135e+01
86 1 1 1.232500000000000e+01 1.565485254907670e+01 1.500246060086581e+01
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92 1 1 6.162500000000000e+00 1.067376310164321e+01 1.486731884367082e+01
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103 1 1 1.479000000000000e+01 1.138534730841942e+01 1.499843298302028e+01
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107 1 1 1.355750000000000e+01 1.494326834230049e+01 1.476511580670247e+01
108 1 1 1.848750000000000e+01 1.067376310164321e+01 1.483733215135541e+01
109 1 1 1.972000000000000e+01 1.138534730841942e+01 1.483307878319485e+01
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111 1 1 2.218500000000000e+01 1.138534730841942e+01 1.494032335018560e+01
112 1 1 2.341750000000000e+01 9.250594688090777e+00 1.511930030385710e+01
113 1 1 2.341750000000000e+01 1.778960516940534e+01 1.506163255648677e+01
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125 1 1 1.972000000000000e+01 1.992435778973398e+01 1.505808760634221e+01
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127 1 1 2.218500000000000e+01 0.000000000000000e+00 1.501312853963581e+01
128 1 1 8.627500000000000e+00 2.134752620328641e+00 1.505205628279858e+01
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353 2 1 2.958000000000000e+01 1.138534730841942e+01 1.853888136458308e+01
354 2 1 3.081250000000000e+01 1.209693151519563e+01 1.831036168742244e+01
355 2 1 8.627500000000000e+00 1.352009992874806e+01 1.835261188649090e+01
356 2 1 9.859999999999999e+00 1.423168413552428e+01 1.821705864207346e+01
357 2 1 1.109250000000000e+01 1.352009992874806e+01 1.831524712388831e+01
358 2 1 1.232500000000000e+01 1.423168413552428e+01 1.852378179475058e+01
359 2 1 1.355750000000000e+01 1.352009992874806e+01 1.852309441840510e+01
360 2 1 1.479000000000000e+01 1.423168413552428e+01 1.836621027472939e+01
361 2 1 1.602250000000000e+01 1.352009992874806e+01 1.849039311610116e+01
362 2 1 1.725500000000000e+01 1.423168413552428e+01 1.842269825087092e+01
363 2 1 1.848750000000000e+01 1.352009992874806e+01 1.825468998789840e+01
364 2 1 1.972000000000000e+01 1.423168413552428e+01 1.849561590548242e+01
365 2 1 7.395000000000000e+00 1.138534730841942e+01 1.859813014678126e+01
366 2 1 3.451000000000000e+01 1.992435778973398e+01 1.813501916227946e+01
367 2 1 2.834750000000000e+01 9.250594688090777e+00 1.847653992697568e+01
368 2 1 2.711499999999999e+01 9.962178894866991e+00 1.849053529347614e+01
369 2 1 1.355750000000000e+01 7.827426274538350e+00 1.835096749618396e+01
370 2 1 1.479000000000000e+01 7.115842067762138e+00 1.844059942495262e+01
371 2 1 1.602250000000000e+01 7.827426274538350e+00 1.844461353068087e+01
372 2 1 1.725500000000000e+01 7.115842067762138e+00 1.836290600804645e+01
373 2 1 1.848750000000000e+01 7.827426274538350e+00 1.825818280452995e+01
374 2 1 1.972000000000000e+01 7.115842067762138e+00 1.837997086460227e+01
375 2 1 2.095250000000000e+01 7.827426274538350e+00 1.826491847987811e+01
376 2 1 2.218500000000000e+01 7.115842067762138e+00 1.841142851923555e+01
377 2 1 2.341750000000000e+01 7.827426274538350e+00 1.826594520665525e+01
378 2 1 2.465000000000000e+01 7.115842067762138e+00 1.838708488224049e+01
379 2 1 2.588250000000000e+01 7.827426274538350e+00 1.830434555380351e+01
380 2 1 2.711500000000000e+01 7.115842067762138e+00 1.859652575977937e+01
381 2 1 2.834750000000000e+01 7.827426274538350e+00 1.844094595194482e+01
382 2 1 6.162499999999999e+00 9.250594688090777e+00 1.856484810097502e+01
383 2 1 1.109250000000000e+01 7.827426274538350e+00 1.847502232204046e+01
384 2 1 7.395000000000000e+00 9.962178894866991e+00 1.854741705791729e+01
385 2 1 9.859999999999999e+00 9.962178894866991e+00 1.837074522628645e+01
386 2 1 1.109250000000000e+01 9.250594688090777e+00 1.846206781979952e+01
387 2 1 1.232500000000000e+01 9.962178894866991e+00 1.823251181425658e+01
388 2 1 1.355750000000000e+01 9.250594688090777e+00 1.834993099844037e+01
389 2 1 1.479000000000000e+01 9.962178894866991e+00 1.843248036437880e+01
390 2 1 1.602250000000000e+01 9.250594688090777e+00 1.855142577781635e+01
391 2 1 1.725500000000000e+01 9.962178894866991e+00 1.847587547064991e+01
392 2 1 1.848750000000000e+01 9.250594688090777e+00 1.850249139638135e+01
393 2 1 1.972000000000000e+01 9.962178894866991e+00 1.841266132895000e+01
394 2 1 2.095250000000000e+01 9.250594688090777e+00 1.837466808881276e+01
395 2 1 2.218500000000000e+01 9.962178894866991e+00 1.834587370280250e+01
396 2 1 2.341750000000000e+01 9.250594688090777e+00 1.846590574952954e+01
397 2 1 2.465000000000000e+01 9.962178894866991e+00 1.835650105398410e+01
398 2 1 2.588250000000000e+01 9.250594688090777e+00 1.838143174570202e+01
399 2 1 8.627500000000000e+00 9.250594688090777e+00 1.843904853716322e+01
400 2 1 3.574249999999999e+01 2.063594199651019e+01 1.839864514570517e+01
401 2 2 2.958000000000000e+01 1.423168413552428e+01 2.000000000000000e+01
402 2 2 1.725500000000000e+01 1.850118937618155e+01 2.000000000000000e+01
403 2 2 3.204500000000000e+01 1.992435778973398e+01 2.000000000000000e+01
404 2 2 1.109250000000000e+01 1.636643675585292e+01 2.000000000000000e+01
405 2 2 9.859999999999999e+00 1.565485254907670e+01 2.000000000000000e+01
406 2 2 2.341750000000000e+01 1.352009992874806e+01 2.000000000000000e+01
407 2 2 2.465000000000000e+01 1.423168413552428e+01 2.000000000000000e+01
408 2 2 2.341750000000000e+01 1.778960516940534e+01 2.000000000000000e+01
409 2 2 2.711499999999999e+01 1.992435778973398e+01 2.000000000000000e+01
410 2 2 2.834750000000000e+01 2.063594199651019e+01 2.000000000000000e+01
411 2 2 2.465000000000000e+01 1.850118937618155e+01 2.000000000000000e+01
412 2 2 2.711500000000000e+01 1.423168413552428e+01 2.000000000000000e+01
413 2 2 2.588250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
414 2 2 3.204499999999999e+01 1.423168413552428e+01 2.000000000000000e+01
415 2 2 3.327750000000000e+01 2.063594199651019e+01 2.000000000000000e+01
416 2 2 2.218500000000000e+01 1.850118937618155e+01 2.000000000000000e+01
417 2 2 2.095250000000000e+01 1.778960516940534e+01 2.000000000000000e+01
418 2 2 2.711500000000000e+01 1.850118937618155e+01 2.000000000000000e+01
419 2 2 1.848750000000000e+01 1.778960516940534e+01 2.000000000000000e+01
420 2 2 1.972000000000000e+01 1.850118937618155e+01 2.000000000000000e+01
421 2 2 1.602250000000000e+01 1.778960516940534e+01 2.000000000000000e+01
422 2 2 2.958000000000000e+01 1.992435778973398e+01 2.000000000000000e+01
423 2 2 3.081250000000000e+01 2.063594199651019e+01 2.000000000000000e+01
424 2 2 2.588250000000000e+01 1.778960516940534e+01 2.000000000000000e+01
425 2 2 2.834750000000000e+01 1.352009992874806e+01 2.000000000000000e+01
426 2 2 3.081250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
427 2 2 1.355750000000000e+01 2.063594199651019e+01 2.000000000000000e+01
428 2 2 2.588250000000000e+01 2.063594199651019e+01 2.000000000000000e+01
429 2 2 1.109250000000000e+01 1.778960516940534e+01 2.000000000000000e+01
430 2 2 2.341750000000000e+01 1.636643675585292e+01 2.000000000000000e+01
431 2 2 3.327750000000000e+01 1.778960516940534e+01 2.000000000000000e+01
432 2 2 3.327750000000000e+01 1.636643675585292e+01 2.000000000000000e+01
433 2 2 3.204499999999999e+01 1.565485254907670e+01 2.000000000000000e+01
434 2 2 2.588250000000000e+01 1.636643675585292e+01 2.000000000000000e+01
435 2 2 1.602250000000000e+01 2.063594199651019e+01 2.000000000000000e+01
436 2 2 1.479000000000000e+01 1.992435778973398e+01 2.000000000000000e+01
437 2 2 2.711499999999999e+01 1.565485254907670e+01 2.000000000000000e+01
438 2 2 2.465000000000000e+01 1.565485254907670e+01 2.000000000000000e+01
439 2 2 2.834750000000000e+01 1.778960516940534e+01 2.000000000000000e+01
440 2 2 1.972000000000000e+01 1.565485254907670e+01 2.000000000000000e+01
441 2 2 1.972000000000000e+01 1.992435778973398e+01 2.000000000000000e+01
442 2 2 2.958000000000000e+01 1.850118937618155e+01 2.000000000000000e+01
443 2 2 1.232500000000000e+01 1.992435778973398e+01 2.000000000000000e+01
444 2 2 1.479000000000000e+01 1.850118937618155e+01 2.000000000000000e+01
445 2 2 1.479000000000000e+01 1.565485254907670e+01 2.000000000000000e+01
446 2 2 2.218500000000000e+01 1.992435778973398e+01 2.000000000000000e+01
447 2 2 1.725500000000000e+01 1.565485254907670e+01 2.000000000000000e+01
448 2 2 1.848750000000000e+01 1.636643675585292e+01 2.000000000000000e+01
449 2 2 3.081250000000000e+01 1.778960516940534e+01 2.000000000000000e+01
450 2 2 3.204499999999999e+01 1.850118937618155e+01 2.000000000000000e+01
451 2 2 2.957999999999999e+01 9.962178894866991e+00 2.000000000000000e+01
452 2 2 2.095250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
453 2 2 1.972000000000000e+01 2.846336827104855e+00 2.000000000000000e+01
454 2 2 2.095250000000000e+01 3.557921033881068e+00 2.000000000000000e+01
455 2 2 2.218500000000000e+01 2.846336827104855e+00 2.000000000000000e+01
456 2 2 3.697500000000000e+00 4.981089447433495e+00 2.000000000000000e+01
457 2 2 4.930000000000000e+00 5.692673654209710e+00 2.000000000000000e+01
458 2 2 6.162500000000000e+00 4.981089447433495e+00 2.000000000000000e+01
459 2 2 7.395000000000000e+00 5.692673654209710e+00 2.000000000000000e+01
460 2 2 8.627500000000000e+00 4.981089447433495e+00 2.000000000000000e+01
461 2 2 1.355750000000000e+01 4.981089447433495e+00 2.000000000000000e+01
462 2 2 1.479000000000000e+01 5.692673654209710e+00 2.000000000000000e+01
463 2 2 1.602250000000000e+01 4.981089447433495e+00 2.000000000000000e+01
464 2 2 1.725500000000000e+01 5.692673654209710e+00 2.000000000000000e+01
465 2 2 1.848750000000000e+01 4.981089447433495e+00 2.000000000000000e+01
466 2 2 2.341750000000000e+01 4.981089447433495e+00 2.000000000000000e+01
467 2 2 2.465000000000000e+01 5.692673654209710e+00 2.000000000000000e+01
468 2 2 6.162500000000000e+00 7.827426274538350e+00 2.000000000000000e+01
469 2 2 7.395000000000000e+00 7.115842067762138e+00 2.000000000000000e+01
470 2 2 1.848750000000000e+01 3.557921033881068e+00 2.000000000000000e+01
471 2 2 1.725500000000000e+01 2.846336827104855e+00 2.000000000000000e+01
472 2 2 1.602250000000000e+01 3.557921033881068e+00 2.000000000000000e+01
473 2 2 1.479000000000000e+01 2.846336827104855e+00 2.000000000000000e+01
474 2 2 1.232500000000000e+00 7.115842067762137e-01 2.000000000000000e+01
475 2 2 2.465000000000000e+00 1.423168413552427e+00 2.000000000000000e+01
476 2 2 3.697500000000000e+00 7.115842067762137e-01 2.000000000000000e+01
477 2 2 4.929999999999999e+00 1.423168413552427e+00 2.000000000000000e+01
478 2 2 9.859999999999999e+00 1.423168413552427e+00 2.000000000000000e+01
479 2 2 1.109250000000000e+01 7.115842067762137e-01 2.000000000000000e+01
480 2 2 1.232500000000000e+01 1.423168413552427e+00 2.000000000000000e+01
481 2 2 1.355750000000000e+01 7.115842067762137e-01 2.000000000000000e+01
482 2 2 1.479000000000000e+01 1.423168413552427e+00 2.000000000000000e+01
483 2 2 1.602250000000000e+01 7.115842067762137e-01 2.000000000000000e+01
484 2 2 2.095250000000000e+01 7.115842067762137e-01 2.000000000000000e+01
485 2 2 2.218500000000000e+01 1.423168413552427e+00 2.000000000000000e+01
486 2 2 2.341750000000000e+01 7.115842067762137e-01 2.000000000000000e+01
487 2 2 2.465000000000000e+01 1.423168413552427e+00 2.000000000000000e+01
488 2 2 2.465000000000000e+00 2.846336827104855e+00 2.000000000000000e+01
489 2 2 3.697500000000000e+00 3.557921033881068e+00 2.000000000000000e+01
490 2 2 8.627500000000000e+00 3.557921033881068e+00 2.000000000000000e+01
491 2 2 9.859999999999999e+00 2.846336827104855e+00 2.000000000000000e+01
492 2 2 1.109250000000000e+01 3.557921033881068e+00 2.000000000000000e+01
493 2 2 1.232500000000000e+01 2.846336827104855e+00 2.000000000000000e+01
494 2 2 1.355750000000000e+01 3.557921033881068e+00 2.000000000000000e+01
495 2 2 1.972000000000000e+01 1.423168413552427e+00 2.000000000000000e+01
496 2 2 8.627500000000000e+00 1.209693151519563e+01 2.000000000000000e+01
497 2 2 9.859999999999999e+00 1.138534730841942e+01 2.000000000000000e+01
498 2 2 1.109250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
499 2 2 1.232500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
500 2 2 1.355750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
501 2 2 1.479000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
502 2 2 1.602250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
503 2 2 2.095250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
504 2 2 2.218500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
505 2 2 2.341750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
506 2 2 2.465000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
507 2 2 2.588250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
508 2 2 2.711500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
509 2 2 2.834750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
510 2 2 2.958000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
511 2 2 3.081250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
512 2 2 8.627500000000000e+00 1.352009992874806e+01 2.000000000000000e+01
513 2 2 9.859999999999999e+00 1.423168413552428e+01 2.000000000000000e+01
514 2 2 1.109250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
515 2 2 1.602250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
516 2 2 1.725500000000000e+01 1.423168413552428e+01 2.000000000000000e+01
517 2 2 1.848750000000000e+01 1.352009992874806e+01 2.000000000000000e+01
518 2 2 1.972000000000000e+01 1.423168413552428e+01 2.000000000000000e+01
519 2 2 7.395000000000000e+00 1.138534730841942e+01 2.000000000000000e+01
520 2 2 3.451000000000000e+01 1.992435778973398e+01 2.000000000000000e+01
521 2 2 2.834750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
522 2 2 2.711499999999999e+01 9.962178894866991e+00 2.000000000000000e+01
523 2 2 1.355750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
524 2 2 1.479000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
525 2 2 1.972000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
526 2 2 2.095250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
527 2 2 2.218500000000000e+01 7.115842067762138e+00 2.000000000000000e+01
528 2 2 2.341750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
529 2 2 2.465000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
530 2 2 2.588250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
531 2 2 2.711500000000000e+01 7.115842067762138e+00 2.000000000000000e+01
532 2 2 2.834750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
533 2 2 6.162499999999999e+00 9.250594688090777e+00 2.000000000000000e+01
534 2 2 1.109250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
535 2 2 1.232500000000000e+01 9.962178894866991e+00 2.000000000000000e+01
536 2 2 1.355750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
537 2 2 1.479000000000000e+01 9.962178894866991e+00 2.000000000000000e+01
538 2 2 1.602250000000000e+01 9.250594688090777e+00 2.000000000000000e+01
539 2 2 1.725500000000000e+01 9.962178894866991e+00 2.000000000000000e+01
540 2 2 1.848750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
541 2 2 2.341750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
542 2 2 2.465000000000000e+01 9.962178894866991e+00 2.000000000000000e+01
543 2 2 2.588250000000000e+01 9.250594688090777e+00 2.000000000000000e+01
544 2 2 8.627500000000000e+00 9.250594688090777e+00 2.000000000000000e+01
545 2 2 3.574249999999999e+01 2.063594199651019e+01 2.000000000000000e+01

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# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.CH
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100

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# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.C
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
pair_coeff * * rebo CH.rebo C
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100

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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.CH
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
545 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000152826 secs
read_data CPU = 0.000973701 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.92 | 12.92 | 12.92 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956
10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956
20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956
30 0 -3282.2176 0 -3282.2176 -19187.215 2779.5956
40 0 -3282.4004 0 -3282.4004 -21740.059 2779.5956
50 0 -3282.4755 0 -3282.4755 -22659.554 2779.5956
57 0 -3282.5011 0 -3282.5011 -23313.198 2779.5956
Loop time of 3.04218 on 1 procs for 57 steps with 545 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2884.37307546 -3282.49993222 -3282.5010627
Force two-norm initial, final = 115.342 0.193154
Force max component initial, final = 12.0934 0.03617
Final line search alpha, max atom move = 1 0.03617
Iterations, force evaluations = 57 100
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0291 | 3.0291 | 3.0291 | 0.0 | 99.57
Bond | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0016081 | 0.0016081 | 0.0016081 | 0.0 | 0.05
Output | 0.0079796 | 0.0079796 | 0.0079796 | 0.0 | 0.26
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003517 | | | 0.12
Nlocal: 545 ave 545 max 545 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3175 ave 3175 max 3175 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 294122 ave 294122 max 294122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 294122
Ave neighs/atom = 539.673
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.CH
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
545 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000135422 secs
read_data CPU = 0.00368595 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.03 | 11.1 | 11.16 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956
10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956
20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956
30 0 -3282.2176 0 -3282.2176 -19187.216 2779.5956
40 0 -3282.4004 0 -3282.4004 -21740.027 2779.5956
50 0 -3282.4753 0 -3282.4753 -22682.604 2779.5956
57 0 -3282.5023 0 -3282.5023 -23355.081 2779.5956
Loop time of 1.66218 on 4 procs for 57 steps with 545 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2884.37307546 -3282.50070864 -3282.50227121
Force two-norm initial, final = 115.342 0.228488
Force max component initial, final = 12.0934 0.03365
Final line search alpha, max atom move = 1 0.03365
Iterations, force evaluations = 57 100
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5571 | 1.5945 | 1.6314 | 2.3 | 95.93
Bond | 2.265e-05 | 2.9087e-05 | 3.4571e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.020248 | 0.05608 | 0.092328 | 11.8 | 3.37
Output | 0.0053282 | 0.0054213 | 0.0056982 | 0.2 | 0.33
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006172 | | | 0.37
Nlocal: 136.25 ave 177 max 100 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 2874.75 ave 2912 max 2835 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 73530.5 ave 73544 max 73517 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 294122
Ave neighs/atom = 539.673
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.C
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
400 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000912905 secs
read_data CPU = 0.00252986 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair rebo, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.21 | 12.21 | 12.21 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534
10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534
20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534
30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534
40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
Loop time of 2.93337 on 1 procs for 51 steps with 400 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2941.05486197 -2967.08958376 -2967.08962073
Force two-norm initial, final = 35.5666 0.0471918
Force max component initial, final = 6.23617 0.0050012
Final line search alpha, max atom move = 1 0.0050012
Iterations, force evaluations = 51 101
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9239 | 2.9239 | 2.9239 | 0.0 | 99.68
Bond | 1.2398e-05 | 1.2398e-05 | 1.2398e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0010808 | 0.0010808 | 0.0010808 | 0.0 | 0.04
Output | 0.0059283 | 0.0059283 | 0.0059283 | 0.0 | 0.20
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.002466 | | | 0.08
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2357 ave 2357 max 2357 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 294122 ave 294122 max 294122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 294122
Ave neighs/atom = 735.305
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.C
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
400 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.0003407 secs
read_data CPU = 0.00411105 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair rebo, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:934)
Per MPI rank memory allocation (min/avg/max) = 10.7 | 10.77 | 10.83 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534
10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534
20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534
30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534
40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
Loop time of 1.47901 on 4 procs for 51 steps with 400 atoms
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2941.05486197 -2967.08958376 -2967.08962073
Force two-norm initial, final = 35.5666 0.0471918
Force max component initial, final = 6.23617 0.0050012
Final line search alpha, max atom move = 1 0.0050012
Iterations, force evaluations = 51 101
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4314 | 1.4405 | 1.4548 | 0.8 | 97.40
Bond | 1.955e-05 | 2.265e-05 | 2.4796e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014506 | 0.029363 | 0.038964 | 5.5 | 1.99
Output | 0.00424 | 0.0043345 | 0.0046172 | 0.2 | 0.29
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.004772 | | | 0.32
Nlocal: 100 ave 100 max 100 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2132 ave 2132 max 2132 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 73530.5 ave 73544 max 73517 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 294122
Ave neighs/atom = 735.305
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

19
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@ -0,0 +1,19 @@
# DATE: 2019-04-19 CONTRIBUTOR: Mingjian Wen, wenxx151@umn.edu
#
# Parameters of the Dihedral-angle-corrected registry-dependent interlayer (DRIP)
# potential for multilayer graphene structures.
#
# Cite as M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018).
# C0 C2 C4 C delta lambda A z0 B eta rho_cut r_cut normal_cut
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
# C0, C2, C4, C, A, and B in [eV]
# delta, z0, eta, rho_cut, r_cut, and normal_cut in [Angstrom]
# lambda in [1/Angstrom]
#
# normal_cut is a parameter not present in the Wen paper, but specific to the
# LAMMPS implementation, which is used to find the 3 nearest neighbors of an
# atom to construct the normal.

2
src/.gitignore vendored
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@ -806,6 +806,8 @@
/pair_dpd_mt.h
/pair_dsmc.cpp
/pair_dsmc.h
/pair_drip.cpp
/pair_drip.h
/pair_eam.cpp
/pair_eam.h
/pair_eam_alloy.cpp

1
src/USER-MISC/README
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@ -70,6 +70,7 @@ pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11

1107
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mingjian Wen (University of Minnesota)
e-mail: wenxx151@umn.edu
This implements the DRIP model as described in
M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor,
Phys. Rev. B, 98, 235404 (2018).
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(drip, PairDRIP)
#else
#ifndef LMP_PAIR_DRIP_H
#define LMP_PAIR_DRIP_H
#include "pair.h"
#include "my_page.h"
#include <cmath>
namespace LAMMPS_NS {
#define DIM 3
typedef double V3[3];
class PairDRIP : public Pair {
public:
PairDRIP(class LAMMPS *);
virtual ~PairDRIP();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
protected:
struct Param
{
int ielement, jelement;
double C0, C2, C4, C, delta, lambda, A, z0, B, eta, rhocut, rcut, ncut;
double rhocutsq, rcutsq, ncutsq;
};
Param *params; // parameter set for I-J interactions
int **nearest3neigh; // nearest 3 neighbors of atoms
char **elements; // names of unique elements
int **elem2param; // mapping from element pairs to parameters
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
double cutmax; // max cutoff for all species
void read_file(char *);
void allocate();
// DRIP specific functions
double calc_attractive(Param&, double const, double const *,
double *const, double *const);
double calc_repulsive(int const, int const, Param&, double const,
double const *, double const *, V3 const *, V3 const *, V3 const *,
V3 const *, double *const, double *const);
void find_nearest3neigh();
void calc_normal(int const, double *const, V3 *const, V3 *const, V3 *const,
V3 *const);
void get_drhosqij(double const *, double const *, V3 const *, V3 const *,
V3 const *, V3 const *, double *const, double *const, double *const,
double *const, double *const);
double td(double, double, double, double, double const *const, double,
const double *const, double&, double&);
double dihedral(const int, const int, Param&, double const, double&,
double *const, double *const, double *const, double *const, double *const,
double *const, double *const, double *const);
double deriv_cos_omega(double const *, double const *, double const *,
double const *, double *const, double *const, double *const,
double *const);
double tap(double, double, double&);
double tap_rho(double, double, double&);
void deriv_cross(double const *, double const *, double const *,
double *const, V3 *const, V3 *const, V3 *const);
// inline functions
inline double dot(double const *x, double const *y) const
{
return x[0]*y[0]+x[1]*y[1]+x[2]*y[2];
}
inline void mat_dot_vec(V3 const *X, double const *y, double *const z) const
{
for (int k = 0; k < 3; k++) {
z[k] = X[k][0]*y[0]+X[k][1]*y[1]+X[k][2]*y[2];
}
}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: No enough neighbors to construct normal
Cannot find three neighbors within cutoff of the target atom.
Check the configuration.
*/