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Merge pull request #2514 from oywg11/tersoff-shift

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Add a shift option to most Tersoff potential variants
This commit is contained in:
Axel Kohlmeyer
2021-01-15 13:59:56 -05:00
committed by GitHub
parent 8060a750d4 84ca5b53e3
commit 5e6411ea5a
41 changed files with 5339 additions and 1179 deletions
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98
doc/src/pair_tersoff.rst
View File

@ -16,14 +16,23 @@ pair_style tersoff/table command
Accelerator Variants: *tersoff/table/omp*
pair_style tersoff/shift command
================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style style
pair_style style keywords values
* style = *tersoff* or *tersoff/table* or *tersoff/gpu* or *tersoff/omp* or *tersoff/table/omp*
* keyword = *shift*
.. parsed-literal::
*shift* value = delta
delta = negative shift in equilibrium bond length
Examples
""""""""
@ -37,6 +46,9 @@ Examples
pair_style tersoff/table
pair_coeff * * SiCGe.tersoff Si(D)
pair_style tersoff shift 0.05
pair_coeff * * Si.tersoff Si
Description
"""""""""""
@ -46,7 +58,7 @@ The *tersoff* style computes a 3-body Tersoff potential
.. math::
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
V_{ij} & = f_C(r_{ij} + \delta) \left[ f_R(r_{ij} + \delta) + b_{ij} f_A(r_{ij} + \delta) \right] \\
f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
1 & r < R - D \\
\frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) &
@ -56,14 +68,15 @@ The *tersoff* style computes a 3-body Tersoff potential
f_R(r) & = A \exp (-\lambda_1 r) \\
f_A(r) & = -B \exp (-\lambda_2 r) \\
b_{ij} & = \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik} + \delta) g \left[ \theta_{ijk}(r_{ij}, r_{ik}) \right]
\exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
\frac{c^2}{\left[ d^2 + (\cos \theta - \cos \theta_0)^2\right]} \right)
where :math:`f_R` is a two-body term and :math:`f_A` includes three-body
interactions. The summations in the formula are over all neighbors
J and K of atom I within a cutoff distance = R + D.
J and K of atom I within a cutoff distance = R + D. :math:`\delta` is
an optional negative shift of the equilibrium bond length, as described below.
The *tersoff/table* style uses tabulated forms for the two-body,
environment and angular functions. Linear interpolation is performed
@ -167,6 +180,18 @@ Note that the twobody parameters in entries such as SiCC and CSiSi
are often the same, due to the common use of symmetric mixing rules,
but this is not always the case. For example, the beta and n parameters in
Tersoff_2 :ref:`(Tersoff_2) <Tersoff_21>` are not symmetric.
Similarly, the threebody parameters in entries such as SiCSi and SiSiC
are often the same, but this is not always the case, particularly
the value of R, which is sometimes typed on the
first and second elements, sometimes on the first and third elements.
Hence the need to specify R and D explicitly for all element triples.
For example, while Tersoff's notation
in Tersoff_2 :ref:`(Tersoff_2) <Tersoff_21>` is ambiguous on this point,
and properties of the zincblende lattice are the same for either choice,
Tersoff's results for rocksalt are consistent with typing on the first
and third elements. :ref:`Albe et al. <Albe>` adopts the same convention.
Conversely, the potential for B/N/C from the Cagin group
uses the opposite convention, typing on the first and second elements.
We chose the above form so as to enable users to define all commonly
used variants of the Tersoff potential. In particular, our form
@ -212,6 +237,37 @@ Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
for helping clarify how Tersoff parameters for alloys have been
defined in various papers.
The *shift* keyword computes the energy E of a system of atoms, whose
formula is the same as the Tersoff potential. The only modification is
that the original equilibrium bond length ( :math:`r_0`) of the system
is shifted to :math:`r_0-\delta`. The minus sign arises because each
radial distance :math:`r` is replaced by :math:`r+\delta`.
The *shift* keyword is designed for simulations of closely matched van
der Waals heterostructures. For instance, consider the case of a system
with few-layers graphene atop a thick hexagonal boron nitride (h-BN)
substrate simulated using periodic boundary conditions. The experimental
lattice mismatch of ~1.8% between graphene and h-BN is not well captured
by the equilibrium lattice constants of available potentials, thus a
small in-plane strain will be introduced in the system when building a
periodic supercell. To minimize the effect of strain on simulation
results, the *shift* keyword allows adjusting the equilibrium bond
length of one of the two materials (e.g., h-BN). Validation, benchmark
tests, and applications of the *shift* keyword can be found in
:ref:`(Mandelli_1) <Mandelli1>` and :ref:`(Ouyang_1) <Ouyang5>`.
For the specific case discussed above, the force field can be defined as
.. code-block:: LAMMPS
pair_style hybrid/overlay rebo tersoff shift -0.00407 ilp/graphene/hbn 16.0 coul/shield 16.0
pair_coeff * * rebo CH.rebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.695
pair_coeff 2 2 coul/shield 0.69
----------
.. include:: accel_styles.rst
@ -228,9 +284,10 @@ described above from values in the potential file.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart files <restart>`, 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.
This pair style does not write its information to :doc:`binary restart
files <restart>`, 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.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
@ -241,17 +298,24 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This pair style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
This pair style requires the :doc:`newton <newton>` setting to be "on"
for pair interactions.
The *shift* keyword is not supported by the *tersoff/gpu*,
*tersoff/intel*, *tersoff/kk*, *tersoff/table* or *tersoff/table/omp*
variants.
The Tersoff potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal :doc:`units <units>`. You can
use the Tersoff potential with any LAMMPS units, but you would need to
directory) are parameterized for :doc:`"metal" units <units>`. In addition
the pair style supports converting potential parameters on-the-fly between
"metal" and "real" units. You can use the *tersoff* pair style variants
with any LAMMPS units setting, but you would need to
create your own Tersoff potential file with coefficients listed in the
appropriate units if your simulation does not use "metal" units.
appropriate units if your simulation does not use "metal" or "real" units.
Related commands
""""""""""""""""
@ -261,7 +325,7 @@ Related commands
Default
"""""""
none
shift delta = 0.0
----------
@ -277,3 +341,11 @@ Condens. Matter, 15, 5649(2003).
.. _Tersoff_21:
**(Tersoff_2)** J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
.. _Mandelli1:
**(Mandelli_1)** D. Mandelli, W. Ouyang, M. Urbakh, and O. Hod, ACS Nano 13(7), 7603-7609 (2019).
.. _Ouyang5:
**(Ouyang_1)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).

33
doc/src/pair_tersoff_mod.rst
View File

@ -20,9 +20,15 @@ Syntax
.. code-block:: LAMMPS
pair_style tersoff/mod
pair_style style keywords values
pair_style tersoff/mod/c
* style = *tersoff/mod* or *tersoff/mod/c*
* keyword = *shift*
.. parsed-literal::
*shift* value = delta
delta = negative shift in equilibrium bond length
Examples
""""""""
@ -47,7 +53,7 @@ E of a system of atoms as
.. math::
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
V_{ij} & = f_C(r_{ij} + \delta) \left[ f_R(r_{ij} + \delta) + b_{ij} f_A(r_{ij} + \delta) \right] \\
f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
1 & r < R - D \\
\frac{1}{2} - \frac{9}{16} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) - \frac{1}{16} \sin \left( \frac{3\pi}{2} \frac{r-R}{D} \right) &
@ -57,13 +63,16 @@ E of a system of atoms as
f_R(r) & = A \exp (-\lambda_1 r) \\
f_A(r) & = -B \exp (-\lambda_2 r) \\
b_{ij} & = \left( 1 + {\zeta_{ij}}^\eta \right)^{-\frac{1}{2n}} \\
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik} + \delta) g(\theta_{ijk})
\exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\
g(\theta) & = c_1 + g_o(\theta) g_a(\theta) \\
g_o(\theta) & = \frac{c_2 (h - \cos \theta)^2}{c_3 + (h - \cos \theta)^2} \\
g_a(\theta) & = 1 + c_4 \exp \left[ -c_5 (h - \cos \theta)^2 \right] \\
where :math:`f_R` is a two-body term and :math:`f_A` includes three-body interactions.
:math:`\delta` is an optional negative shift of the
equilibrium bond length, as described below.
The summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = R + D.
The *tersoff/mod/c* style differs from *tersoff/mod* only in the
@ -71,7 +80,7 @@ formulation of the V_ij term, where it contains an additional c0 term.
.. math::
V_{ij} = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
V_{ij} = f_C(r_{ij} + \delta) \left[ f_R(r_{ij} + \delta) + b_{ij} f_A(r_{ij} + \delta) + c_0 \right] \\
The modified cutoff function :math:`f_C` proposed by :ref:`(Murty) <Murty>` and
having a continuous second-order differential is employed. The
@ -156,6 +165,12 @@ the center atom in a three-body interaction and it is bonded to the
second atom and the bond is influenced by the third atom. Thus an entry
for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
The *shift* keyword computes the energy E of a system of atoms, whose formula
is the same as the Tersoff potential. The only modification is that the original
equilibrium bond length ( :math:`r_0`) of the system is shifted to :math:`r_0-\delta`.
The minus sign arises because each radial distance :math:`r` is replaced by :math:`r+\delta`.
More information on this option is given on the main :doc:`pair_tersoff <pair_tersoff>` page.
----------
.. include:: accel_styles.rst
@ -187,9 +202,13 @@ if LAMMPS was built with that package. See the :doc:`Build package <Build_packa
This pair style requires the :doc:`newton <newton>` setting to be "on"
for pair interactions.
The Tersoff/MOD potential files provided with LAMMPS (see the potentials
The *shift* keyword is not supported by the *tersoff/gpu*,
*tersoff/intel*, *tersoff/kk*, *tersoff/table* or *tersoff/table/omp*
variants.
The *tersoff/mod* potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal :doc:`units <units>`. You can
use the Tersoff/MOD potential with any LAMMPS units, but you would need to
use the *tersoff/mod* pair style with any LAMMPS units, but you would need to
create your own Tersoff/MOD potential file with coefficients listed in the
appropriate units if your simulation does not use "metal" units.

59
doc/src/pair_tersoff_zbl.rst
View File

@ -13,7 +13,14 @@ Syntax
.. code-block:: LAMMPS
pair_style tersoff/zbl
pair_style tersoff/zbl keywords values
* keyword = *shift*
.. parsed-literal::
*shift* value = delta
delta = negative shift in equilibrium bond length
Examples
""""""""
@ -35,16 +42,17 @@ system of atoms as
.. math::
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} & = (1 - f_F(r_{ij})) V^{ZBL}_{ij} + f_F(r_{ij}) V^{Tersoff}_{ij} \\
f_F(r_{ij}) & = \frac{1}{1 + e^{-A_F(r_{ij} - r_C)}}\\
V_{ij} & = (1 - f_F(r_{ij} + \delta)) V^{ZBL}(r_{ij} + \delta)
+ f_F(r_{ij} + \delta) V^{Tersoff}(r_{ij} + \delta) \\
f_F(r) & = \frac{1}{1 + e^{-A_F(r - r_C)}}\\
\\
\\
V^{ZBL}_{ij} & = \frac{1}{4\pi\epsilon_0} \frac{Z_1 Z_2 \,e^2}{r_{ij}} \phi(r_{ij}/a) \\
V^{ZBL}(r) & = \frac{1}{4\pi\epsilon_0} \frac{Z_1 Z_2 \,e^2}{r} \phi(r/a) \\
a & = \frac{0.8854\,a_0}{Z_{1}^{0.23} + Z_{2}^{0.23}}\\
\phi(x) & = 0.1818e^{-3.2x} + 0.5099e^{-0.9423x} + 0.2802e^{-0.4029x} + 0.02817e^{-0.2016x}\\
\\
\\
V^{Tersoff}_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
V^{Tersoff}(r) & = f_C(r) \left[ f_R(r) + b_{ij} f_A(r) \right] \\
f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
1 & r < R - D \\
\frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) &
@ -54,7 +62,7 @@ system of atoms as
f_R(r) & = A \exp (-\lambda_1 r) \\
f_A(r) & = -B \exp (-\lambda_2 r) \\
b_{ij} & = \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik} + \delta) g(\theta_{ijk})
\exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
g(\theta) & = \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
\frac{c^2}{\left[ d^2 + (\cos \theta - \cos \theta_0)^2\right]} \right)
@ -81,6 +89,9 @@ includes
three-body interactions. The summations in the formula are over all
neighbors J and K of atom I within a cutoff distance = R + D.
:math:`\delta` is an optional negative shift of the
equilibrium bond length, as described below.
Only a single pair_coeff command is used with the *tersoff/zbl* style
which specifies a Tersoff/ZBL potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
@ -228,6 +239,14 @@ for helping clarify how Tersoff parameters for alloys have been
defined in various papers. Also thanks to Ram Devanathan for
providing the base ZBL implementation.
The *shift* keyword computes the energy E of a system of atoms, whose
formula is the same as the Tersoff potential. The only modification is
that the original equilibrium bond length ( :math:`r_0`) of the system
is shifted to :math:`r_0-\delta`. The minus sign arises because each
radial distance :math:`r` is replaced by :math:`r+\delta`. More
information on this option is given on the main :doc:`pair_tersoff
<pair_tersoff>` page.
----------
.. include:: accel_styles.rst
@ -244,9 +263,10 @@ described above from values in the potential file.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart files <restart>`, 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.
This pair style does not write its information to :doc:`binary restart
files <restart>`, 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.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
@ -257,18 +277,23 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This pair style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
This pair style requires the :doc:`newton <newton>` setting to be "on"
for pair interactions.
The Tersoff/ZBL potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal :doc:`units <units>`.
You can use the Tersoff potential with any LAMMPS units, but you would
need to create your own Tersoff potential file with coefficients
listed in the appropriate units if your simulation does not use "metal"
units.
The *shift* keyword is currently not supported for the *tersoff/gpu* and
*tersoff/kk* variants of this pair style.
The tersoff/zbl potential files provided with LAMMPS (see the potentials
directory) are parameterized for :doc:`"metal" units <units>`. Also the
pair style supports converting potential file parameters on-the-fly
between "metal" and "real" units. You can use the tersoff/zbl pair
style with any LAMMPS units, but you would need to create your own
tersoff/zbl potential file with coefficients listed in the appropriate
units if your simulation does not use "metal" or "real" units.
Related commands
""""""""""""""""

4
doc/utils/sphinx-config/false_positives.txt
View File

@ -330,6 +330,7 @@ Buyl
Bybee
bz
cadetblue
Cagin
calc
calibre
caltech
@ -1219,6 +1220,7 @@ Herrmann
Hertizian
hertzian
Hertzsch
heterostructures
hexahedrons
hexatic
hexorder
@ -2729,6 +2731,7 @@ rNEMD
ro
Rochus
Rockett
rocksalt
Rodrigues
Rohart
Ronchetti
@ -3548,6 +3551,7 @@ zz
Zm
PowerShell
filesystems
zincblende
Zstandard
Zstd
zstd

3
examples/README
View File

@ -112,7 +112,8 @@ steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
streitz: Streitz-Mintmire potential for Al2O3
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
template: examples for using atom_style template and comparing to atom style molecular
threebody: regression test input for a variety of manybody potentials
tersoff: regression test input for Tersoff variants
threebody: regression test input for a variety of threebody potentials
vashishta: models using the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command
wall: use of reflective walls with different stochastic models

892
examples/hBN-momolayer-5nm.data Normal file
View File

@ -0,0 +1,892 @@
Makeup graphene nanoribbon on hBN
880 atoms
2 atom types
0.000000000000000 46.152979739999999 xlo xhi
0.000000000000000 48.443364211584992 ylo yhi
0.000000000000000 100.000000000000000 zlo zhi
Atoms
1 1 0.420 0.000000000000000 0.000000000000000 0.000000000000000
2 2 -0.420 0.698900000000000 1.210530287683010 0.000000000000000
3 1 0.420 2.096700000000000 1.210530287683010 0.000000000000000
4 2 -0.420 2.795600000000000 0.000000000000000 0.000000000000000
5 1 0.420 4.193400000000000 0.000000000000000 0.000000000000000
6 2 -0.420 4.892300000000000 1.210530287683010 0.000000000000000
7 1 0.420 6.290100000000000 1.210530287683010 0.000000000000000
8 2 -0.420 6.989000000000000 0.000000000000000 0.000000000000000
9 1 0.420 8.386799999999999 0.000000000000000 0.000000000000000
10 2 -0.420 9.085699999999999 1.210530287683010 0.000000000000000
11 1 0.420 10.483499999999999 1.210530287683010 0.000000000000000
12 2 -0.420 11.182399999999999 0.000000000000000 0.000000000000000
13 1 0.420 12.580200000000000 0.000000000000000 0.000000000000000
14 2 -0.420 13.279100000000000 1.210530287683010 0.000000000000000
15 1 0.420 14.676900000000000 1.210530287683010 0.000000000000000
16 2 -0.420 15.375800000000000 0.000000000000000 0.000000000000000
17 1 0.420 16.773599999999998 0.000000000000000 0.000000000000000
18 2 -0.420 17.472500000000000 1.210530287683010 0.000000000000000
19 1 0.420 18.870300000000000 1.210530287683010 0.000000000000000
20 2 -0.420 19.569199999999999 0.000000000000000 0.000000000000000
21 1 0.420 20.966999999999999 0.000000000000000 0.000000000000000
22 2 -0.420 21.665900000000001 1.210530287683010 0.000000000000000
23 1 0.420 23.063699999999997 1.210530287683010 0.000000000000000
24 2 -0.420 23.762599999999999 0.000000000000000 0.000000000000000
25 1 0.420 25.160399999999999 0.000000000000000 0.000000000000000
26 2 -0.420 25.859299999999998 1.210530287683010 0.000000000000000
27 1 0.420 27.257099999999998 1.210530287683010 0.000000000000000
28 2 -0.420 27.956000000000000 0.000000000000000 0.000000000000000
29 1 0.420 29.353800000000000 0.000000000000000 0.000000000000000
30 2 -0.420 30.052699999999998 1.210530287683010 0.000000000000000
31 1 0.420 31.450499999999998 1.210530287683010 0.000000000000000
32 2 -0.420 32.149400000000000 0.000000000000000 0.000000000000000
33 1 0.420 33.547199999999997 0.000000000000000 0.000000000000000
34 2 -0.420 34.246099999999998 1.210530287683010 0.000000000000000
35 1 0.420 35.643899999999995 1.210530287683010 0.000000000000000
36 2 -0.420 36.342799999999997 0.000000000000000 0.000000000000000
37 1 0.420 37.740600000000001 0.000000000000000 0.000000000000000
38 2 -0.420 38.439499999999995 1.210530287683010 0.000000000000000
39 1 0.420 39.837299999999999 1.210530287683010 0.000000000000000
40 2 -0.420 40.536200000000001 0.000000000000000 0.000000000000000
41 1 0.420 41.933999999999997 0.000000000000000 0.000000000000000
42 2 -0.420 42.632899999999999 1.210530287683010 0.000000000000000
43 1 0.420 44.030699999999996 1.210530287683010 0.000000000000000
44 2 -0.420 44.729599999999998 0.000000000000000 0.000000000000000
45 1 0.420 0.000000000000000 2.421060575366020 0.000000000000000
46 2 -0.420 0.698900000000000 3.631590863049030 0.000000000000000
47 1 0.420 2.096700000000000 3.631590863049030 0.000000000000000
48 2 -0.420 2.795600000000000 2.421060575366020 0.000000000000000
49 1 0.420 4.193400000000000 2.421060575366020 0.000000000000000
50 2 -0.420 4.892300000000000 3.631590863049030 0.000000000000000
51 1 0.420 6.290100000000000 3.631590863049030 0.000000000000000
52 2 -0.420 6.989000000000000 2.421060575366020 0.000000000000000
53 1 0.420 8.386799999999999 2.421060575366020 0.000000000000000
54 2 -0.420 9.085699999999999 3.631590863049030 0.000000000000000
55 1 0.420 10.483499999999999 3.631590863049030 0.000000000000000
56 2 -0.420 11.182399999999999 2.421060575366020 0.000000000000000
57 1 0.420 12.580200000000000 2.421060575366020 0.000000000000000
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690 2 -0.420 30.052699999999998 37.526438918173312 0.000000000000000
691 1 0.420 31.450499999999998 37.526438918173312 0.000000000000000
692 2 -0.420 32.149400000000000 36.315908630490298 0.000000000000000
693 1 0.420 33.547199999999997 36.315908630490298 0.000000000000000
694 2 -0.420 34.246099999999998 37.526438918173312 0.000000000000000
695 1 0.420 35.643899999999995 37.526438918173312 0.000000000000000
696 2 -0.420 36.342799999999997 36.315908630490298 0.000000000000000
697 1 0.420 37.740600000000001 36.315908630490298 0.000000000000000
698 2 -0.420 38.439499999999995 37.526438918173312 0.000000000000000
699 1 0.420 39.837299999999999 37.526438918173312 0.000000000000000
700 2 -0.420 40.536200000000001 36.315908630490298 0.000000000000000
701 1 0.420 41.933999999999997 36.315908630490298 0.000000000000000
702 2 -0.420 42.632899999999999 37.526438918173312 0.000000000000000
703 1 0.420 44.030699999999996 37.526438918173312 0.000000000000000
704 2 -0.420 44.729599999999998 36.315908630490298 0.000000000000000
705 1 0.420 0.000000000000000 38.736969205856319 0.000000000000000
706 2 -0.420 0.698900000000000 39.947499493539325 0.000000000000000
707 1 0.420 2.096700000000000 39.947499493539325 0.000000000000000
708 2 -0.420 2.795600000000000 38.736969205856319 0.000000000000000
709 1 0.420 4.193400000000000 38.736969205856319 0.000000000000000
710 2 -0.420 4.892300000000000 39.947499493539325 0.000000000000000
711 1 0.420 6.290100000000000 39.947499493539325 0.000000000000000
712 2 -0.420 6.989000000000000 38.736969205856319 0.000000000000000
713 1 0.420 8.386799999999999 38.736969205856319 0.000000000000000
714 2 -0.420 9.085699999999999 39.947499493539325 0.000000000000000
715 1 0.420 10.483499999999999 39.947499493539325 0.000000000000000
716 2 -0.420 11.182399999999999 38.736969205856319 0.000000000000000
717 1 0.420 12.580200000000000 38.736969205856319 0.000000000000000
718 2 -0.420 13.279100000000000 39.947499493539325 0.000000000000000
719 1 0.420 14.676900000000000 39.947499493539325 0.000000000000000
720 2 -0.420 15.375800000000000 38.736969205856319 0.000000000000000
721 1 0.420 16.773599999999998 38.736969205856319 0.000000000000000
722 2 -0.420 17.472500000000000 39.947499493539325 0.000000000000000
723 1 0.420 18.870300000000000 39.947499493539325 0.000000000000000
724 2 -0.420 19.569199999999999 38.736969205856319 0.000000000000000
725 1 0.420 20.966999999999999 38.736969205856319 0.000000000000000
726 2 -0.420 21.665900000000001 39.947499493539325 0.000000000000000
727 1 0.420 23.063699999999997 39.947499493539325 0.000000000000000
728 2 -0.420 23.762599999999999 38.736969205856319 0.000000000000000
729 1 0.420 25.160399999999999 38.736969205856319 0.000000000000000
730 2 -0.420 25.859299999999998 39.947499493539325 0.000000000000000
731 1 0.420 27.257099999999998 39.947499493539325 0.000000000000000
732 2 -0.420 27.956000000000000 38.736969205856319 0.000000000000000
733 1 0.420 29.353800000000000 38.736969205856319 0.000000000000000
734 2 -0.420 30.052699999999998 39.947499493539325 0.000000000000000
735 1 0.420 31.450499999999998 39.947499493539325 0.000000000000000
736 2 -0.420 32.149400000000000 38.736969205856319 0.000000000000000
737 1 0.420 33.547199999999997 38.736969205856319 0.000000000000000
738 2 -0.420 34.246099999999998 39.947499493539325 0.000000000000000
739 1 0.420 35.643899999999995 39.947499493539325 0.000000000000000
740 2 -0.420 36.342799999999997 38.736969205856319 0.000000000000000
741 1 0.420 37.740600000000001 38.736969205856319 0.000000000000000
742 2 -0.420 38.439499999999995 39.947499493539325 0.000000000000000
743 1 0.420 39.837299999999999 39.947499493539325 0.000000000000000
744 2 -0.420 40.536200000000001 38.736969205856319 0.000000000000000
745 1 0.420 41.933999999999997 38.736969205856319 0.000000000000000
746 2 -0.420 42.632899999999999 39.947499493539325 0.000000000000000
747 1 0.420 44.030699999999996 39.947499493539325 0.000000000000000
748 2 -0.420 44.729599999999998 38.736969205856319 0.000000000000000
749 1 0.420 0.000000000000000 41.158029781222339 0.000000000000000
750 2 -0.420 0.698900000000000 42.368560068905346 0.000000000000000
751 1 0.420 2.096700000000000 42.368560068905346 0.000000000000000
752 2 -0.420 2.795600000000000 41.158029781222339 0.000000000000000
753 1 0.420 4.193400000000000 41.158029781222339 0.000000000000000
754 2 -0.420 4.892300000000000 42.368560068905346 0.000000000000000
755 1 0.420 6.290100000000000 42.368560068905346 0.000000000000000
756 2 -0.420 6.989000000000000 41.158029781222339 0.000000000000000
757 1 0.420 8.386799999999999 41.158029781222339 0.000000000000000
758 2 -0.420 9.085699999999999 42.368560068905346 0.000000000000000
759 1 0.420 10.483499999999999 42.368560068905346 0.000000000000000
760 2 -0.420 11.182399999999999 41.158029781222339 0.000000000000000
761 1 0.420 12.580200000000000 41.158029781222339 0.000000000000000
762 2 -0.420 13.279100000000000 42.368560068905346 0.000000000000000
763 1 0.420 14.676900000000000 42.368560068905346 0.000000000000000
764 2 -0.420 15.375800000000000 41.158029781222339 0.000000000000000
765 1 0.420 16.773599999999998 41.158029781222339 0.000000000000000
766 2 -0.420 17.472500000000000 42.368560068905346 0.000000000000000
767 1 0.420 18.870300000000000 42.368560068905346 0.000000000000000
768 2 -0.420 19.569199999999999 41.158029781222339 0.000000000000000
769 1 0.420 20.966999999999999 41.158029781222339 0.000000000000000
770 2 -0.420 21.665900000000001 42.368560068905346 0.000000000000000
771 1 0.420 23.063699999999997 42.368560068905346 0.000000000000000
772 2 -0.420 23.762599999999999 41.158029781222339 0.000000000000000
773 1 0.420 25.160399999999999 41.158029781222339 0.000000000000000
774 2 -0.420 25.859299999999998 42.368560068905346 0.000000000000000
775 1 0.420 27.257099999999998 42.368560068905346 0.000000000000000
776 2 -0.420 27.956000000000000 41.158029781222339 0.000000000000000
777 1 0.420 29.353800000000000 41.158029781222339 0.000000000000000
778 2 -0.420 30.052699999999998 42.368560068905346 0.000000000000000
779 1 0.420 31.450499999999998 42.368560068905346 0.000000000000000
780 2 -0.420 32.149400000000000 41.158029781222339 0.000000000000000
781 1 0.420 33.547199999999997 41.158029781222339 0.000000000000000
782 2 -0.420 34.246099999999998 42.368560068905346 0.000000000000000
783 1 0.420 35.643899999999995 42.368560068905346 0.000000000000000
784 2 -0.420 36.342799999999997 41.158029781222339 0.000000000000000
785 1 0.420 37.740600000000001 41.158029781222339 0.000000000000000
786 2 -0.420 38.439499999999995 42.368560068905346 0.000000000000000
787 1 0.420 39.837299999999999 42.368560068905346 0.000000000000000
788 2 -0.420 40.536200000000001 41.158029781222339 0.000000000000000
789 1 0.420 41.933999999999997 41.158029781222339 0.000000000000000
790 2 -0.420 42.632899999999999 42.368560068905346 0.000000000000000
791 1 0.420 44.030699999999996 42.368560068905346 0.000000000000000
792 2 -0.420 44.729599999999998 41.158029781222339 0.000000000000000
793 1 0.420 0.000000000000000 43.579090356588360 0.000000000000000
794 2 -0.420 0.698900000000000 44.789620644271366 0.000000000000000
795 1 0.420 2.096700000000000 44.789620644271366 0.000000000000000
796 2 -0.420 2.795600000000000 43.579090356588360 0.000000000000000
797 1 0.420 4.193400000000000 43.579090356588360 0.000000000000000
798 2 -0.420 4.892300000000000 44.789620644271366 0.000000000000000
799 1 0.420 6.290100000000000 44.789620644271366 0.000000000000000
800 2 -0.420 6.989000000000000 43.579090356588360 0.000000000000000
801 1 0.420 8.386799999999999 43.579090356588360 0.000000000000000
802 2 -0.420 9.085699999999999 44.789620644271366 0.000000000000000
803 1 0.420 10.483499999999999 44.789620644271366 0.000000000000000
804 2 -0.420 11.182399999999999 43.579090356588360 0.000000000000000
805 1 0.420 12.580200000000000 43.579090356588360 0.000000000000000
806 2 -0.420 13.279100000000000 44.789620644271366 0.000000000000000
807 1 0.420 14.676900000000000 44.789620644271366 0.000000000000000
808 2 -0.420 15.375800000000000 43.579090356588360 0.000000000000000
809 1 0.420 16.773599999999998 43.579090356588360 0.000000000000000
810 2 -0.420 17.472500000000000 44.789620644271366 0.000000000000000
811 1 0.420 18.870300000000000 44.789620644271366 0.000000000000000
812 2 -0.420 19.569199999999999 43.579090356588360 0.000000000000000
813 1 0.420 20.966999999999999 43.579090356588360 0.000000000000000
814 2 -0.420 21.665900000000001 44.789620644271366 0.000000000000000
815 1 0.420 23.063699999999997 44.789620644271366 0.000000000000000
816 2 -0.420 23.762599999999999 43.579090356588360 0.000000000000000
817 1 0.420 25.160399999999999 43.579090356588360 0.000000000000000
818 2 -0.420 25.859299999999998 44.789620644271366 0.000000000000000
819 1 0.420 27.257099999999998 44.789620644271366 0.000000000000000
820 2 -0.420 27.956000000000000 43.579090356588360 0.000000000000000
821 1 0.420 29.353800000000000 43.579090356588360 0.000000000000000
822 2 -0.420 30.052699999999998 44.789620644271366 0.000000000000000
823 1 0.420 31.450499999999998 44.789620644271366 0.000000000000000
824 2 -0.420 32.149400000000000 43.579090356588360 0.000000000000000
825 1 0.420 33.547199999999997 43.579090356588360 0.000000000000000
826 2 -0.420 34.246099999999998 44.789620644271366 0.000000000000000
827 1 0.420 35.643899999999995 44.789620644271366 0.000000000000000
828 2 -0.420 36.342799999999997 43.579090356588360 0.000000000000000
829 1 0.420 37.740600000000001 43.579090356588360 0.000000000000000
830 2 -0.420 38.439499999999995 44.789620644271366 0.000000000000000
831 1 0.420 39.837299999999999 44.789620644271366 0.000000000000000
832 2 -0.420 40.536200000000001 43.579090356588360 0.000000000000000
833 1 0.420 41.933999999999997 43.579090356588360 0.000000000000000
834 2 -0.420 42.632899999999999 44.789620644271366 0.000000000000000
835 1 0.420 44.030699999999996 44.789620644271366 0.000000000000000
836 2 -0.420 44.729599999999998 43.579090356588360 0.000000000000000
837 1 0.420 0.000000000000000 46.000150931954380 0.000000000000000
838 2 -0.420 0.698900000000000 47.210681219637387 0.000000000000000
839 1 0.420 2.096700000000000 47.210681219637387 0.000000000000000
840 2 -0.420 2.795600000000000 46.000150931954380 0.000000000000000
841 1 0.420 4.193400000000000 46.000150931954380 0.000000000000000
842 2 -0.420 4.892300000000000 47.210681219637387 0.000000000000000
843 1 0.420 6.290100000000000 47.210681219637387 0.000000000000000
844 2 -0.420 6.989000000000000 46.000150931954380 0.000000000000000
845 1 0.420 8.386799999999999 46.000150931954380 0.000000000000000
846 2 -0.420 9.085699999999999 47.210681219637387 0.000000000000000
847 1 0.420 10.483499999999999 47.210681219637387 0.000000000000000
848 2 -0.420 11.182399999999999 46.000150931954380 0.000000000000000
849 1 0.420 12.580200000000000 46.000150931954380 0.000000000000000
850 2 -0.420 13.279100000000000 47.210681219637387 0.000000000000000
851 1 0.420 14.676900000000000 47.210681219637387 0.000000000000000
852 2 -0.420 15.375800000000000 46.000150931954380 0.000000000000000
853 1 0.420 16.773599999999998 46.000150931954380 0.000000000000000
854 2 -0.420 17.472500000000000 47.210681219637387 0.000000000000000
855 1 0.420 18.870300000000000 47.210681219637387 0.000000000000000
856 2 -0.420 19.569199999999999 46.000150931954380 0.000000000000000
857 1 0.420 20.966999999999999 46.000150931954380 0.000000000000000
858 2 -0.420 21.665900000000001 47.210681219637387 0.000000000000000
859 1 0.420 23.063699999999997 47.210681219637387 0.000000000000000
860 2 -0.420 23.762599999999999 46.000150931954380 0.000000000000000
861 1 0.420 25.160399999999999 46.000150931954380 0.000000000000000
862 2 -0.420 25.859299999999998 47.210681219637387 0.000000000000000
863 1 0.420 27.257099999999998 47.210681219637387 0.000000000000000
864 2 -0.420 27.956000000000000 46.000150931954380 0.000000000000000
865 1 0.420 29.353800000000000 46.000150931954380 0.000000000000000
866 2 -0.420 30.052699999999998 47.210681219637387 0.000000000000000
867 1 0.420 31.450499999999998 47.210681219637387 0.000000000000000
868 2 -0.420 32.149400000000000 46.000150931954380 0.000000000000000
869 1 0.420 33.547199999999997 46.000150931954380 0.000000000000000
870 2 -0.420 34.246099999999998 47.210681219637387 0.000000000000000
871 1 0.420 35.643899999999995 47.210681219637387 0.000000000000000
872 2 -0.420 36.342799999999997 46.000150931954380 0.000000000000000
873 1 0.420 37.740600000000001 46.000150931954380 0.000000000000000
874 2 -0.420 38.439499999999995 47.210681219637387 0.000000000000000
875 1 0.420 39.837299999999999 47.210681219637387 0.000000000000000
876 2 -0.420 40.536200000000001 46.000150931954380 0.000000000000000
877 1 0.420 41.933999999999997 46.000150931954380 0.000000000000000
878 2 -0.420 42.632899999999999 47.210681219637387 0.000000000000000
879 1 0.420 44.030699999999996 47.210681219637387 0.000000000000000
880 2 -0.420 44.729599999999998 46.000150931954380 0.000000000000000

37
examples/in.hBN_shift Normal file
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@ -0,0 +1,37 @@
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-momolayer-5nm.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 1000

1
examples/tersoff/BNC.tersoff Symbolic link
View File

@ -0,0 +1 @@
../../potentials/BNC.tersoff

1
examples/tersoff/Si.tersoff Symbolic link
View File

@ -0,0 +1 @@
../../potentials/Si.tersoff

0
examples/threebody/Si.tersoff.mod → examples/tersoff/Si.tersoff.mod
View File

0
examples/threebody/Si.tersoff.modc → examples/tersoff/Si.tersoff.modc
View File

892
examples/tersoff/hBN-monolayer-5nm.data Normal file
View File

@ -0,0 +1,892 @@
Makeup graphene nanoribbon on hBN
880 atoms
2 atom types
0.000000000000000 46.152979739999999 xlo xhi
0.000000000000000 48.443364211584992 ylo yhi
0.000000000000000 100.000000000000000 zlo zhi
Atoms
1 1 0.420 0.000000000000000 0.000000000000000 0.000000000000000
2 2 -0.420 0.698900000000000 1.210530287683010 0.000000000000000
3 1 0.420 2.096700000000000 1.210530287683010 0.000000000000000
4 2 -0.420 2.795600000000000 0.000000000000000 0.000000000000000
5 1 0.420 4.193400000000000 0.000000000000000 0.000000000000000
6 2 -0.420 4.892300000000000 1.210530287683010 0.000000000000000
7 1 0.420 6.290100000000000 1.210530287683010 0.000000000000000
8 2 -0.420 6.989000000000000 0.000000000000000 0.000000000000000
9 1 0.420 8.386799999999999 0.000000000000000 0.000000000000000
10 2 -0.420 9.085699999999999 1.210530287683010 0.000000000000000
11 1 0.420 10.483499999999999 1.210530287683010 0.000000000000000
12 2 -0.420 11.182399999999999 0.000000000000000 0.000000000000000
13 1 0.420 12.580200000000000 0.000000000000000 0.000000000000000
14 2 -0.420 13.279100000000000 1.210530287683010 0.000000000000000
15 1 0.420 14.676900000000000 1.210530287683010 0.000000000000000
16 2 -0.420 15.375800000000000 0.000000000000000 0.000000000000000
17 1 0.420 16.773599999999998 0.000000000000000 0.000000000000000
18 2 -0.420 17.472500000000000 1.210530287683010 0.000000000000000
19 1 0.420 18.870300000000000 1.210530287683010 0.000000000000000
20 2 -0.420 19.569199999999999 0.000000000000000 0.000000000000000
21 1 0.420 20.966999999999999 0.000000000000000 0.000000000000000
22 2 -0.420 21.665900000000001 1.210530287683010 0.000000000000000
23 1 0.420 23.063699999999997 1.210530287683010 0.000000000000000
24 2 -0.420 23.762599999999999 0.000000000000000 0.000000000000000
25 1 0.420 25.160399999999999 0.000000000000000 0.000000000000000
26 2 -0.420 25.859299999999998 1.210530287683010 0.000000000000000
27 1 0.420 27.257099999999998 1.210530287683010 0.000000000000000
28 2 -0.420 27.956000000000000 0.000000000000000 0.000000000000000
29 1 0.420 29.353800000000000 0.000000000000000 0.000000000000000
30 2 -0.420 30.052699999999998 1.210530287683010 0.000000000000000
31 1 0.420 31.450499999999998 1.210530287683010 0.000000000000000
32 2 -0.420 32.149400000000000 0.000000000000000 0.000000000000000
33 1 0.420 33.547199999999997 0.000000000000000 0.000000000000000
34 2 -0.420 34.246099999999998 1.210530287683010 0.000000000000000
35 1 0.420 35.643899999999995 1.210530287683010 0.000000000000000
36 2 -0.420 36.342799999999997 0.000000000000000 0.000000000000000
37 1 0.420 37.740600000000001 0.000000000000000 0.000000000000000
38 2 -0.420 38.439499999999995 1.210530287683010 0.000000000000000
39 1 0.420 39.837299999999999 1.210530287683010 0.000000000000000
40 2 -0.420 40.536200000000001 0.000000000000000 0.000000000000000
41 1 0.420 41.933999999999997 0.000000000000000 0.000000000000000
42 2 -0.420 42.632899999999999 1.210530287683010 0.000000000000000
43 1 0.420 44.030699999999996 1.210530287683010 0.000000000000000
44 2 -0.420 44.729599999999998 0.000000000000000 0.000000000000000
45 1 0.420 0.000000000000000 2.421060575366020 0.000000000000000
46 2 -0.420 0.698900000000000 3.631590863049030 0.000000000000000
47 1 0.420 2.096700000000000 3.631590863049030 0.000000000000000
48 2 -0.420 2.795600000000000 2.421060575366020 0.000000000000000
49 1 0.420 4.193400000000000 2.421060575366020 0.000000000000000
50 2 -0.420 4.892300000000000 3.631590863049030 0.000000000000000
51 1 0.420 6.290100000000000 3.631590863049030 0.000000000000000
52 2 -0.420 6.989000000000000 2.421060575366020 0.000000000000000
53 1 0.420 8.386799999999999 2.421060575366020 0.000000000000000
54 2 -0.420 9.085699999999999 3.631590863049030 0.000000000000000
55 1 0.420 10.483499999999999 3.631590863049030 0.000000000000000
56 2 -0.420 11.182399999999999 2.421060575366020 0.000000000000000
57 1 0.420 12.580200000000000 2.421060575366020 0.000000000000000
58 2 -0.420 13.279100000000000 3.631590863049030 0.000000000000000
59 1 0.420 14.676900000000000 3.631590863049030 0.000000000000000
60 2 -0.420 15.375800000000000 2.421060575366020 0.000000000000000
61 1 0.420 16.773599999999998 2.421060575366020 0.000000000000000
62 2 -0.420 17.472500000000000 3.631590863049030 0.000000000000000
63 1 0.420 18.870300000000000 3.631590863049030 0.000000000000000
64 2 -0.420 19.569199999999999 2.421060575366020 0.000000000000000
65 1 0.420 20.966999999999999 2.421060575366020 0.000000000000000
66 2 -0.420 21.665900000000001 3.631590863049030 0.000000000000000
67 1 0.420 23.063699999999997 3.631590863049030 0.000000000000000
68 2 -0.420 23.762599999999999 2.421060575366020 0.000000000000000
69 1 0.420 25.160399999999999 2.421060575366020 0.000000000000000
70 2 -0.420 25.859299999999998 3.631590863049030 0.000000000000000
71 1 0.420 27.257099999999998 3.631590863049030 0.000000000000000
72 2 -0.420 27.956000000000000 2.421060575366020 0.000000000000000
73 1 0.420 29.353800000000000 2.421060575366020 0.000000000000000
74 2 -0.420 30.052699999999998 3.631590863049030 0.000000000000000
75 1 0.420 31.450499999999998 3.631590863049030 0.000000000000000
76 2 -0.420 32.149400000000000 2.421060575366020 0.000000000000000
77 1 0.420 33.547199999999997 2.421060575366020 0.000000000000000
78 2 -0.420 34.246099999999998 3.631590863049030 0.000000000000000
79 1 0.420 35.643899999999995 3.631590863049030 0.000000000000000
80 2 -0.420 36.342799999999997 2.421060575366020 0.000000000000000
81 1 0.420 37.740600000000001 2.421060575366020 0.000000000000000
82 2 -0.420 38.439499999999995 3.631590863049030 0.000000000000000
83 1 0.420 39.837299999999999 3.631590863049030 0.000000000000000
84 2 -0.420 40.536200000000001 2.421060575366020 0.000000000000000
85 1 0.420 41.933999999999997 2.421060575366020 0.000000000000000
86 2 -0.420 42.632899999999999 3.631590863049030 0.000000000000000
87 1 0.420 44.030699999999996 3.631590863049030 0.000000000000000
88 2 -0.420 44.729599999999998 2.421060575366020 0.000000000000000
89 1 0.420 0.000000000000000 4.842121150732040 0.000000000000000
90 2 -0.420 0.698900000000000 6.052651438415050 0.000000000000000
91 1 0.420 2.096700000000000 6.052651438415050 0.000000000000000
92 2 -0.420 2.795600000000000 4.842121150732040 0.000000000000000
93 1 0.420 4.193400000000000 4.842121150732040 0.000000000000000
94 2 -0.420 4.892300000000000 6.052651438415050 0.000000000000000
95 1 0.420 6.290100000000000 6.052651438415050 0.000000000000000
96 2 -0.420 6.989000000000000 4.842121150732040 0.000000000000000
97 1 0.420 8.386799999999999 4.842121150732040 0.000000000000000
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730 2 -0.420 25.859299999999998 39.947499493539325 0.000000000000000
731 1 0.420 27.257099999999998 39.947499493539325 0.000000000000000
732 2 -0.420 27.956000000000000 38.736969205856319 0.000000000000000
733 1 0.420 29.353800000000000 38.736969205856319 0.000000000000000
734 2 -0.420 30.052699999999998 39.947499493539325 0.000000000000000
735 1 0.420 31.450499999999998 39.947499493539325 0.000000000000000
736 2 -0.420 32.149400000000000 38.736969205856319 0.000000000000000
737 1 0.420 33.547199999999997 38.736969205856319 0.000000000000000
738 2 -0.420 34.246099999999998 39.947499493539325 0.000000000000000
739 1 0.420 35.643899999999995 39.947499493539325 0.000000000000000
740 2 -0.420 36.342799999999997 38.736969205856319 0.000000000000000
741 1 0.420 37.740600000000001 38.736969205856319 0.000000000000000
742 2 -0.420 38.439499999999995 39.947499493539325 0.000000000000000
743 1 0.420 39.837299999999999 39.947499493539325 0.000000000000000
744 2 -0.420 40.536200000000001 38.736969205856319 0.000000000000000
745 1 0.420 41.933999999999997 38.736969205856319 0.000000000000000
746 2 -0.420 42.632899999999999 39.947499493539325 0.000000000000000
747 1 0.420 44.030699999999996 39.947499493539325 0.000000000000000
748 2 -0.420 44.729599999999998 38.736969205856319 0.000000000000000
749 1 0.420 0.000000000000000 41.158029781222339 0.000000000000000
750 2 -0.420 0.698900000000000 42.368560068905346 0.000000000000000
751 1 0.420 2.096700000000000 42.368560068905346 0.000000000000000
752 2 -0.420 2.795600000000000 41.158029781222339 0.000000000000000
753 1 0.420 4.193400000000000 41.158029781222339 0.000000000000000
754 2 -0.420 4.892300000000000 42.368560068905346 0.000000000000000
755 1 0.420 6.290100000000000 42.368560068905346 0.000000000000000
756 2 -0.420 6.989000000000000 41.158029781222339 0.000000000000000
757 1 0.420 8.386799999999999 41.158029781222339 0.000000000000000
758 2 -0.420 9.085699999999999 42.368560068905346 0.000000000000000
759 1 0.420 10.483499999999999 42.368560068905346 0.000000000000000
760 2 -0.420 11.182399999999999 41.158029781222339 0.000000000000000
761 1 0.420 12.580200000000000 41.158029781222339 0.000000000000000
762 2 -0.420 13.279100000000000 42.368560068905346 0.000000000000000
763 1 0.420 14.676900000000000 42.368560068905346 0.000000000000000
764 2 -0.420 15.375800000000000 41.158029781222339 0.000000000000000
765 1 0.420 16.773599999999998 41.158029781222339 0.000000000000000
766 2 -0.420 17.472500000000000 42.368560068905346 0.000000000000000
767 1 0.420 18.870300000000000 42.368560068905346 0.000000000000000
768 2 -0.420 19.569199999999999 41.158029781222339 0.000000000000000
769 1 0.420 20.966999999999999 41.158029781222339 0.000000000000000
770 2 -0.420 21.665900000000001 42.368560068905346 0.000000000000000
771 1 0.420 23.063699999999997 42.368560068905346 0.000000000000000
772 2 -0.420 23.762599999999999 41.158029781222339 0.000000000000000
773 1 0.420 25.160399999999999 41.158029781222339 0.000000000000000
774 2 -0.420 25.859299999999998 42.368560068905346 0.000000000000000
775 1 0.420 27.257099999999998 42.368560068905346 0.000000000000000
776 2 -0.420 27.956000000000000 41.158029781222339 0.000000000000000
777 1 0.420 29.353800000000000 41.158029781222339 0.000000000000000
778 2 -0.420 30.052699999999998 42.368560068905346 0.000000000000000
779 1 0.420 31.450499999999998 42.368560068905346 0.000000000000000
780 2 -0.420 32.149400000000000 41.158029781222339 0.000000000000000
781 1 0.420 33.547199999999997 41.158029781222339 0.000000000000000
782 2 -0.420 34.246099999999998 42.368560068905346 0.000000000000000
783 1 0.420 35.643899999999995 42.368560068905346 0.000000000000000
784 2 -0.420 36.342799999999997 41.158029781222339 0.000000000000000
785 1 0.420 37.740600000000001 41.158029781222339 0.000000000000000
786 2 -0.420 38.439499999999995 42.368560068905346 0.000000000000000
787 1 0.420 39.837299999999999 42.368560068905346 0.000000000000000
788 2 -0.420 40.536200000000001 41.158029781222339 0.000000000000000
789 1 0.420 41.933999999999997 41.158029781222339 0.000000000000000
790 2 -0.420 42.632899999999999 42.368560068905346 0.000000000000000
791 1 0.420 44.030699999999996 42.368560068905346 0.000000000000000
792 2 -0.420 44.729599999999998 41.158029781222339 0.000000000000000
793 1 0.420 0.000000000000000 43.579090356588360 0.000000000000000
794 2 -0.420 0.698900000000000 44.789620644271366 0.000000000000000
795 1 0.420 2.096700000000000 44.789620644271366 0.000000000000000
796 2 -0.420 2.795600000000000 43.579090356588360 0.000000000000000
797 1 0.420 4.193400000000000 43.579090356588360 0.000000000000000
798 2 -0.420 4.892300000000000 44.789620644271366 0.000000000000000
799 1 0.420 6.290100000000000 44.789620644271366 0.000000000000000
800 2 -0.420 6.989000000000000 43.579090356588360 0.000000000000000
801 1 0.420 8.386799999999999 43.579090356588360 0.000000000000000
802 2 -0.420 9.085699999999999 44.789620644271366 0.000000000000000
803 1 0.420 10.483499999999999 44.789620644271366 0.000000000000000
804 2 -0.420 11.182399999999999 43.579090356588360 0.000000000000000
805 1 0.420 12.580200000000000 43.579090356588360 0.000000000000000
806 2 -0.420 13.279100000000000 44.789620644271366 0.000000000000000
807 1 0.420 14.676900000000000 44.789620644271366 0.000000000000000
808 2 -0.420 15.375800000000000 43.579090356588360 0.000000000000000
809 1 0.420 16.773599999999998 43.579090356588360 0.000000000000000
810 2 -0.420 17.472500000000000 44.789620644271366 0.000000000000000
811 1 0.420 18.870300000000000 44.789620644271366 0.000000000000000
812 2 -0.420 19.569199999999999 43.579090356588360 0.000000000000000
813 1 0.420 20.966999999999999 43.579090356588360 0.000000000000000
814 2 -0.420 21.665900000000001 44.789620644271366 0.000000000000000
815 1 0.420 23.063699999999997 44.789620644271366 0.000000000000000
816 2 -0.420 23.762599999999999 43.579090356588360 0.000000000000000
817 1 0.420 25.160399999999999 43.579090356588360 0.000000000000000
818 2 -0.420 25.859299999999998 44.789620644271366 0.000000000000000
819 1 0.420 27.257099999999998 44.789620644271366 0.000000000000000
820 2 -0.420 27.956000000000000 43.579090356588360 0.000000000000000
821 1 0.420 29.353800000000000 43.579090356588360 0.000000000000000
822 2 -0.420 30.052699999999998 44.789620644271366 0.000000000000000
823 1 0.420 31.450499999999998 44.789620644271366 0.000000000000000
824 2 -0.420 32.149400000000000 43.579090356588360 0.000000000000000
825 1 0.420 33.547199999999997 43.579090356588360 0.000000000000000
826 2 -0.420 34.246099999999998 44.789620644271366 0.000000000000000
827 1 0.420 35.643899999999995 44.789620644271366 0.000000000000000
828 2 -0.420 36.342799999999997 43.579090356588360 0.000000000000000
829 1 0.420 37.740600000000001 43.579090356588360 0.000000000000000
830 2 -0.420 38.439499999999995 44.789620644271366 0.000000000000000
831 1 0.420 39.837299999999999 44.789620644271366 0.000000000000000
832 2 -0.420 40.536200000000001 43.579090356588360 0.000000000000000
833 1 0.420 41.933999999999997 43.579090356588360 0.000000000000000
834 2 -0.420 42.632899999999999 44.789620644271366 0.000000000000000
835 1 0.420 44.030699999999996 44.789620644271366 0.000000000000000
836 2 -0.420 44.729599999999998 43.579090356588360 0.000000000000000
837 1 0.420 0.000000000000000 46.000150931954380 0.000000000000000
838 2 -0.420 0.698900000000000 47.210681219637387 0.000000000000000
839 1 0.420 2.096700000000000 47.210681219637387 0.000000000000000
840 2 -0.420 2.795600000000000 46.000150931954380 0.000000000000000
841 1 0.420 4.193400000000000 46.000150931954380 0.000000000000000
842 2 -0.420 4.892300000000000 47.210681219637387 0.000000000000000
843 1 0.420 6.290100000000000 47.210681219637387 0.000000000000000
844 2 -0.420 6.989000000000000 46.000150931954380 0.000000000000000
845 1 0.420 8.386799999999999 46.000150931954380 0.000000000000000
846 2 -0.420 9.085699999999999 47.210681219637387 0.000000000000000
847 1 0.420 10.483499999999999 47.210681219637387 0.000000000000000
848 2 -0.420 11.182399999999999 46.000150931954380 0.000000000000000
849 1 0.420 12.580200000000000 46.000150931954380 0.000000000000000
850 2 -0.420 13.279100000000000 47.210681219637387 0.000000000000000
851 1 0.420 14.676900000000000 47.210681219637387 0.000000000000000
852 2 -0.420 15.375800000000000 46.000150931954380 0.000000000000000
853 1 0.420 16.773599999999998 46.000150931954380 0.000000000000000
854 2 -0.420 17.472500000000000 47.210681219637387 0.000000000000000
855 1 0.420 18.870300000000000 47.210681219637387 0.000000000000000
856 2 -0.420 19.569199999999999 46.000150931954380 0.000000000000000
857 1 0.420 20.966999999999999 46.000150931954380 0.000000000000000
858 2 -0.420 21.665900000000001 47.210681219637387 0.000000000000000
859 1 0.420 23.063699999999997 47.210681219637387 0.000000000000000
860 2 -0.420 23.762599999999999 46.000150931954380 0.000000000000000
861 1 0.420 25.160399999999999 46.000150931954380 0.000000000000000
862 2 -0.420 25.859299999999998 47.210681219637387 0.000000000000000
863 1 0.420 27.257099999999998 47.210681219637387 0.000000000000000
864 2 -0.420 27.956000000000000 46.000150931954380 0.000000000000000
865 1 0.420 29.353800000000000 46.000150931954380 0.000000000000000
866 2 -0.420 30.052699999999998 47.210681219637387 0.000000000000000
867 1 0.420 31.450499999999998 47.210681219637387 0.000000000000000
868 2 -0.420 32.149400000000000 46.000150931954380 0.000000000000000
869 1 0.420 33.547199999999997 46.000150931954380 0.000000000000000
870 2 -0.420 34.246099999999998 47.210681219637387 0.000000000000000
871 1 0.420 35.643899999999995 47.210681219637387 0.000000000000000
872 2 -0.420 36.342799999999997 46.000150931954380 0.000000000000000
873 1 0.420 37.740600000000001 46.000150931954380 0.000000000000000
874 2 -0.420 38.439499999999995 47.210681219637387 0.000000000000000
875 1 0.420 39.837299999999999 47.210681219637387 0.000000000000000
876 2 -0.420 40.536200000000001 46.000150931954380 0.000000000000000
877 1 0.420 41.933999999999997 46.000150931954380 0.000000000000000
878 2 -0.420 42.632899999999999 47.210681219637387 0.000000000000000
879 1 0.420 44.030699999999996 47.210681219637387 0.000000000000000
880 2 -0.420 44.729599999999998 46.000150931954380 0.000000000000000

37
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# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-monolayer-5nm.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 1000

135
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# Simple regression tests for Tersoff potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a &
a1 1.0 0.0 0.0 &
a2 0.0 1.0 0.0 &
a3 0.0 0.0 1.0 &
basis 0.0 0.0 0.0 &
basis 0.0 0.5 0.5 &
basis 0.5 0.0 0.5 &
basis 0.5 0.5 0.0 &
basis 0.25 0.25 0.25 &
basis 0.25 0.75 0.75 &
basis 0.75 0.25 0.75 &
basis 0.75 0.75 0.25
region myreg block 0 4 &
0 4 &
0 4
create_box 8 myreg
create_atoms 1 region myreg &
basis 1 1 &
basis 2 2 &
basis 3 3 &
basis 4 4 &
basis 5 5 &
basis 6 6 &
basis 7 7 &
basis 8 8
mass * 28.06
velocity all create $t 5287287 loop geom
# Equilibrate using Tersoff model for silicon
pair_style tersoff
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
write_restart restart.equil
# Test Tersoff/Mod model for Si
clear
read_restart restart.equil
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
# Test Tersoff/Mod/C model for Si
clear
read_restart restart.equil
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
# Test Tersoff model for B/N/C
clear
read_restart restart.equil
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
# Test Tersoff model for B/N/C
clear
read_restart restart.equil
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff N N N C B B C B
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100

101
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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-monolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.003 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.545 | 3.545 | 3.545 Mbytes
Step TotEng PotEng KinEng Temp
0 -6570.525999324201 -6604.6118995607 34.0859002365 300
100 -6570.310828576855 -6584.788128201216 14.47729962436115 127.4189579026448
200 -6570.372315727984 -6587.98140230295 17.60908657496611 154.9827329140911
300 -6570.341402414283 -6587.005611017601 16.66420860331832 146.6665849019345
400 -6570.373381655075 -6587.812074340169 17.43869268509366 153.48304633967
500 -6570.357279692746 -6587.139105628337 16.78182593559217 147.7017695218898
600 -6570.364533408486 -6588.199043380888 17.83450997240158 156.9667503160497
700 -6570.362000654088 -6587.514376495223 17.15237584113499 150.9630878644169
800 -6570.358394689025 -6587.200486866491 16.84209217746576 148.2321903832028
900 -6570.372035122432 -6588.096861613308 17.72482649087559 156.0013938422734
1000 -6570.355748883583 -6587.399428461676 17.04367957809225 150.0064201899072
Loop time of 0.998048 on 1 procs for 1000 steps with 880 atoms
Performance: 86.569 ns/day, 0.277 hours/ns, 1001.956 timesteps/s
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.98001 | 0.98001 | 0.98001 | 0.0 | 98.19
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.006538 | 0.006538 | 0.006538 | 0.0 | 0.66
Output | 0.000224 | 0.000224 | 0.000224 | 0.0 | 0.02
Modify | 0.00781 | 0.00781 | 0.00781 | 0.0 | 0.78
Other | | 0.003467 | | | 0.35
Nlocal: 880.000 ave 880 max 880 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1518.00 ave 1518 max 1518 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: 15840.0 ave 15840 max 15840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

101
examples/tersoff/log.13Jan21.hBN_shift.g++.4 Normal file
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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style charge
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN-monolayer-5nm.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
2 by 2 by 1 MPI processor grid
reading atoms ...
880 atoms
read_data CPU = 0.010 seconds
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
######################## Potential defition ########################
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff B N
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 4928459 loop geom
fix thermostat all nve
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke temp
#thermo_modify lost warn
thermo_modify line one format float %20.16g lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.1
ghost atom cutoff = 4.1
binsize = 2.05, bins = 23 24 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.297 | 3.297 | 3.297 Mbytes
Step TotEng PotEng KinEng Temp
0 -6570.525999324095 -6604.611899560595 34.08590023650001 300.0000000000001
100 -6570.310828576847 -6584.788128201208 14.47729962436078 127.4189579026416
200 -6570.372315727983 -6587.981402302948 17.60908657496569 154.9827329140874
300 -6570.341402414288 -6587.005611017607 16.66420860331862 146.6665849019371
400 -6570.373381655087 -6587.81207434018 17.43869268509319 153.4830463396659
500 -6570.357279692746 -6587.139105628339 16.78182593559348 147.7017695219013
600 -6570.364533408483 -6588.199043380885 17.83450997240217 156.9667503160549
700 -6570.362000654081 -6587.514376495217 17.15237584113621 150.9630878644276
800 -6570.358394689017 -6587.200486866481 16.84209217746396 148.2321903831871
900 -6570.372035122433 -6588.096861613309 17.72482649087623 156.001393842279
1000 -6570.355748883587 -6587.399428461678 17.0436795780913 150.0064201898988
Loop time of 0.32051 on 4 procs for 1000 steps with 880 atoms
Performance: 269.571 ns/day, 0.089 hours/ns, 3120.030 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24483 | 0.26461 | 0.28741 | 2.9 | 82.56
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026425 | 0.049039 | 0.068616 | 6.8 | 15.30
Output | 0.000126 | 0.00016475 | 0.000248 | 0.0 | 0.05
Modify | 0.002472 | 0.002794 | 0.002933 | 0.4 | 0.87
Other | | 0.003905 | | | 1.22
Nlocal: 220.000 ave 241 max 199 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 563.000 ave 583 max 543 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3960.00 ave 4338 max 3582 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 15840
Ave neighs/atom = 18.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for Tersoff potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
create_atoms CPU = 0.000 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Tersoff model for silicon
pair_style tersoff
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.2
ghost atom cutoff = 4.2
binsize = 2.1, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2370.771 0 -2251.8775 12511.419
10 1144.7447 -2327.3227 0 -2251.7759 21852.599
20 770.19243 -2302.1547 0 -2251.7633 22286.587
30 1059.4324 -2320.1988 0 -2251.8159 6242.222
40 1000.972 -2314.6531 0 -2251.796 -3069.9273
50 803.91758 -2300.1702 0 -2251.7834 -7154.1383
60 761.38639 -2296.1731 0 -2251.7928 -14520.921
70 750.57677 -2294.3086 0 -2251.7965 -21400.198
80 676.66672 -2288.2634 0 -2251.7899 -23480.201
90 640.24103 -2284.6678 0 -2251.7848 -20659.983
100 742.67188 -2290.0616 0 -2251.7855 -16211.799
Loop time of 0.107338 on 1 procs for 100 steps with 512 atoms
Performance: 80.493 ns/day, 0.298 hours/ns, 931.637 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10455 | 0.10455 | 0.10455 | 0.0 | 97.40
Neigh | 0.001115 | 0.001115 | 0.001115 | 0.0 | 1.04
Comm | 0.000482 | 0.000482 | 0.000482 | 0.0 | 0.45
Output | 0.000194 | 0.000194 | 0.000194 | 0.0 | 0.18
Modify | 0.000787 | 0.000787 | 0.000787 | 0.0 | 0.73
Other | | 0.000209 | | | 0.19
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 857.000 ave 857 max 857 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: 8404.00 ave 8404 max 8404 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8404
Ave neighs/atom = 16.414062
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Tersoff/Mod model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style tersoff stores no restart info
512 atoms
read_restart CPU = 0.006 seconds
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
Step Temp E_pair E_mol TotEng Press
100 742.67188 -2210.6446 0 -2172.3685 -6444.2163
110 1135.5853 -2234.6974 0 -2172.3908 113.80404
120 1462.8415 -2253.8186 0 -2172.3853 10922.229
130 1755.9617 -2270.5152 0 -2172.3964 18780.707
140 1895.1939 -2277.1484 0 -2172.3965 22357.106
150 1869.5375 -2273.2734 0 -2172.3851 22616.492
160 1824.0448 -2268.4342 0 -2172.393 19254.299
170 1637.9038 -2254.5219 0 -2172.3815 15904.928
180 1451.9871 -2240.7199 0 -2172.3771 12064.754
190 1362.8248 -2233.1942 0 -2172.3789 7970.534
200 1341.1467 -2229.8951 0 -2172.3717 6244.8542
Loop time of 0.128972 on 1 procs for 100 steps with 512 atoms
Performance: 66.991 ns/day, 0.358 hours/ns, 775.362 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12498 | 0.12498 | 0.12498 | 0.0 | 96.91
Neigh | 0.002322 | 0.002322 | 0.002322 | 0.0 | 1.80
Comm | 0.000537 | 0.000537 | 0.000537 | 0.0 | 0.42
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.14
Modify | 0.000761 | 0.000761 | 0.000761 | 0.0 | 0.59
Other | | 0.000192 | | | 0.15
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 960.000 ave 960 max 960 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: 9244.00 ave 9244 max 9244 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9244
Ave neighs/atom = 18.054688
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style tersoff stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.205694
ghost atom cutoff = 4.205694
binsize = 2.102847, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.976 | 2.976 | 2.976 Mbytes
Step Temp E_pair E_mol TotEng Press
100 742.67188 -2221.9308 0 -2183.6547 -11721.269
110 1106.895 -2244.1196 0 -2183.6843 -2359.7819
120 1327.6674 -2256.3155 0 -2183.6767 7904.6604
130 1487.0219 -2264.3656 0 -2183.6707 14660.783
140 1709.1746 -2276.4761 0 -2183.6886 19298.791
150 1710.6528 -2274.1129 0 -2183.6764 22026.559
160 1651.0659 -2267.9877 0 -2183.6699 20916.722
170 1632.7705 -2264.7081 0 -2183.6777 17339.031
180 1477.693 -2252.4683 0 -2183.6706 12563.594
190 1310.8768 -2239.5419 0 -2183.6581 9591.0484
200 1356.7172 -2240.5315 0 -2183.668 5584.6734
Loop time of 0.133106 on 1 procs for 100 steps with 512 atoms
Performance: 64.911 ns/day, 0.370 hours/ns, 751.281 timesteps/s
96.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1291 | 0.1291 | 0.1291 | 0.0 | 96.99
Neigh | 0.002343 | 0.002343 | 0.002343 | 0.0 | 1.76
Comm | 0.0005 | 0.0005 | 0.0005 | 0.0 | 0.38
Output | 0.000186 | 0.000186 | 0.000186 | 0.0 | 0.14
Modify | 0.000786 | 0.000786 | 0.000786 | 0.0 | 0.59
Other | | 0.000191 | | | 0.14
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 903.000 ave 903 max 903 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: 8414.00 ave 8414 max 8414 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8414
Ave neighs/atom = 16.433594
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style tersoff stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
Step Temp E_pair E_mol TotEng Press
100 742.67188 -2973.8527 0 -2935.5766 3438975.9
110 4061.1085 -3183.2489 0 -2930.1208 2211712.7
120 4120.3231 -3187.0108 0 -2928.3047 2166764.3
130 3602.7602 -3158.5939 0 -2926.6167 2244475.7
140 3222.7773 -3141.7275 0 -2925.5369 2161607
150 3487.4703 -3163.7495 0 -2921.2462 2222150.2
160 3436.3009 -3169.4234 0 -2920.8775 2144368.7
170 3308.1796 -3170.3773 0 -2920.8967 2223612.9
180 3304.3776 -3178.7805 0 -2920.102 2072546.6
190 3217.3561 -3180.7963 0 -2918.4548 2118776.2
200 3041.6832 -3176.1794 0 -2916.5787 2130124.6
Loop time of 0.134621 on 1 procs for 100 steps with 512 atoms
Performance: 64.180 ns/day, 0.374 hours/ns, 742.826 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12837 | 0.12837 | 0.12837 | 0.0 | 95.35
Neigh | 0.004553 | 0.004553 | 0.004553 | 0.0 | 3.38
Comm | 0.000601 | 0.000601 | 0.000601 | 0.0 | 0.45
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.13
Modify | 0.000742 | 0.000742 | 0.000742 | 0.0 | 0.55
Other | | 0.000181 | | | 0.13
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1051.00 ave 1051 max 1051 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: 14760.0 ave 14760 max 14760 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14760
Ave neighs/atom = 28.828125
Neighbor list builds = 6
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style tersoff stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.985 | 2.985 | 2.985 Mbytes
Step Temp E_pair E_mol TotEng Press
100 742.67188 -3294.0266 0 -3255.7505 1615779.4
110 2870.7114 -3432.8485 0 -3257.629 1053310.6
120 2898.0798 -3431.4968 0 -3256.6851 1223402.3
130 2708.4483 -3419.0142 0 -3256.436 1105893.8
140 2307.8661 -3394.1268 0 -3256.1686 1148075.8
150 2215.3423 -3390.1427 0 -3255.8733 1138540
160 2515.488 -3412.6704 0 -3255.1731 1122902.8
170 2485.7109 -3415.0402 0 -3255.3787 1097748.5
180 2327.476 -3408.2463 0 -3254.6537 1061602.6
190 2339.5966 -3413.3961 0 -3254.7496 1088059
200 2260.5961 -3411.477 0 -3254.0771 1104581.5
Loop time of 0.120764 on 1 procs for 100 steps with 512 atoms
Performance: 71.545 ns/day, 0.335 hours/ns, 828.061 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11521 | 0.11521 | 0.11521 | 0.0 | 95.40
Neigh | 0.003874 | 0.003874 | 0.003874 | 0.0 | 3.21
Comm | 0.000542 | 0.000542 | 0.000542 | 0.0 | 0.45
Output | 0.000177 | 0.000177 | 0.000177 | 0.0 | 0.15
Modify | 0.000774 | 0.000774 | 0.000774 | 0.0 | 0.64
Other | | 0.00019 | | | 0.16
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1037.00 ave 1037 max 1037 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: 14676.0 ave 14676 max 14676 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14676
Ave neighs/atom = 28.664062
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:00:00

472
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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for Tersoff potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
create_atoms CPU = 0.000 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Tersoff model for silicon
pair_style tersoff
pair_coeff * * Si.tersoff Si Si Si Si Si Si Si Si
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.2
ghost atom cutoff = 4.2
binsize = 2.1, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2370.771 0 -2251.8775 12511.419
10 1144.7447 -2327.3227 0 -2251.7759 21852.599
20 770.19243 -2302.1547 0 -2251.7633 22286.587
30 1059.4324 -2320.1988 0 -2251.8159 6242.222
40 1000.972 -2314.6531 0 -2251.796 -3069.9273
50 803.91758 -2300.1702 0 -2251.7834 -7154.1383
60 761.38639 -2296.1731 0 -2251.7928 -14520.921
70 750.57677 -2294.3086 0 -2251.7965 -21400.198
80 676.66672 -2288.2634 0 -2251.7899 -23480.201
90 640.24103 -2284.6678 0 -2251.7848 -20659.983
100 742.67188 -2290.0616 0 -2251.7855 -16211.799
Loop time of 0.0321762 on 4 procs for 100 steps with 512 atoms
Performance: 268.521 ns/day, 0.089 hours/ns, 3107.882 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.026599 | 0.02712 | 0.027602 | 0.2 | 84.28
Neigh | 0.000285 | 0.00028875 | 0.000294 | 0.0 | 0.90
Comm | 0.003471 | 0.0039375 | 0.004446 | 0.6 | 12.24
Output | 0.000112 | 0.00013675 | 0.000203 | 0.0 | 0.43
Modify | 0.000443 | 0.0004555 | 0.000471 | 0.0 | 1.42
Other | | 0.000238 | | | 0.74
Nlocal: 128.000 ave 131 max 126 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 447.750 ave 453 max 440 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2101.00 ave 2152 max 2032 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8404
Ave neighs/atom = 16.414062
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Tersoff/Mod model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style tersoff stores no restart info
512 atoms
read_restart CPU = 0.002 seconds
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.949 | 2.950 | 2.950 Mbytes
Step Temp E_pair E_mol TotEng Press
100 742.67188 -2210.6446 0 -2172.3685 -6444.2163
110 1135.5853 -2234.6974 0 -2172.3908 113.80404
120 1462.8415 -2253.8186 0 -2172.3853 10922.229
130 1755.9617 -2270.5152 0 -2172.3964 18780.707
140 1895.1939 -2277.1484 0 -2172.3965 22357.106
150 1869.5375 -2273.2734 0 -2172.3851 22616.492
160 1824.0448 -2268.4342 0 -2172.393 19254.299
170 1637.9038 -2254.5219 0 -2172.3815 15904.928
180 1451.9871 -2240.7199 0 -2172.3771 12064.754
190 1362.8248 -2233.1942 0 -2172.3789 7970.534
200 1341.1467 -2229.8951 0 -2172.3717 6244.8542
Loop time of 0.0389003 on 4 procs for 100 steps with 512 atoms
Performance: 222.107 ns/day, 0.108 hours/ns, 2570.678 timesteps/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031362 | 0.032656 | 0.033605 | 0.5 | 83.95
Neigh | 0.000575 | 0.000599 | 0.000613 | 0.0 | 1.54
Comm | 0.003768 | 0.004733 | 0.006014 | 1.2 | 12.17
Output | 0.000207 | 0.00022525 | 0.000276 | 0.0 | 0.58
Modify | 0.000445 | 0.00047975 | 0.0005 | 0.0 | 1.23
Other | | 0.0002077 | | | 0.53
Nlocal: 128.000 ave 135 max 123 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 491.500 ave 499 max 486 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2311.00 ave 2457 max 2192 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 9244
Ave neighs/atom = 18.054688
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style tersoff stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.205694
ghost atom cutoff = 4.205694
binsize = 2.102847, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.949 | 2.949 | 2.949 Mbytes
Step Temp E_pair E_mol TotEng Press
100 742.67188 -2221.9308 0 -2183.6547 -11721.269
110 1106.895 -2244.1196 0 -2183.6843 -2359.7819
120 1327.6674 -2256.3155 0 -2183.6767 7904.6604
130 1487.0219 -2264.3656 0 -2183.6707 14660.783
140 1709.1746 -2276.4761 0 -2183.6886 19298.791
150 1710.6528 -2274.1129 0 -2183.6764 22026.559
160 1651.0659 -2267.9877 0 -2183.6699 20916.722
170 1632.7705 -2264.7081 0 -2183.6777 17339.031
180 1477.693 -2252.4683 0 -2183.6706 12563.594
190 1310.8768 -2239.5419 0 -2183.6581 9591.0484
200 1356.7172 -2240.5315 0 -2183.668 5584.6734
Loop time of 0.039244 on 4 procs for 100 steps with 512 atoms
Performance: 220.161 ns/day, 0.109 hours/ns, 2548.160 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.03126 | 0.032782 | 0.033915 | 0.5 | 83.53
Neigh | 0.000599 | 0.000707 | 0.000821 | 0.0 | 1.80
Comm | 0.00363 | 0.004893 | 0.006493 | 1.5 | 12.47
Output | 0.000122 | 0.0001425 | 0.000192 | 0.0 | 0.36
Modify | 0.000497 | 0.00050925 | 0.000522 | 0.0 | 1.30
Other | | 0.0002105 | | | 0.54
Nlocal: 128.000 ave 133 max 124 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 459.000 ave 470 max 452 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2103.50 ave 2204 max 2014 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 8414
Ave neighs/atom = 16.433594
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style tersoff stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.952 | 2.952 | 2.952 Mbytes
Step Temp E_pair E_mol TotEng Press
100 742.67188 -2973.8527 0 -2935.5766 3438975.9
110 4061.1085 -3183.2489 0 -2930.1208 2211712.7
120 4120.3231 -3187.0108 0 -2928.3047 2166764.3
130 3602.7602 -3158.5939 0 -2926.6167 2244475.7
140 3222.7773 -3141.7275 0 -2925.5369 2161607
150 3487.4703 -3163.7495 0 -2921.2462 2222150.2
160 3436.3009 -3169.4234 0 -2920.8775 2144368.7
170 3308.1796 -3170.3773 0 -2920.8967 2223612.9
180 3304.3776 -3178.7805 0 -2920.102 2072546.6
190 3217.3561 -3180.7963 0 -2918.4548 2118776.2
200 3041.6832 -3176.1794 0 -2916.5787 2130124.6
Loop time of 0.0488862 on 4 procs for 100 steps with 512 atoms
Performance: 176.737 ns/day, 0.136 hours/ns, 2045.565 timesteps/s
93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037364 | 0.039346 | 0.041066 | 0.8 | 80.49
Neigh | 0.001207 | 0.0012568 | 0.00136 | 0.2 | 2.57
Comm | 0.005218 | 0.007064 | 0.009117 | 1.9 | 14.45
Output | 0.000173 | 0.00020325 | 0.000277 | 0.0 | 0.42
Modify | 0.000709 | 0.000715 | 0.000723 | 0.0 | 1.46
Other | | 0.0003008 | | | 0.62
Nlocal: 128.000 ave 132 max 123 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 543.000 ave 548 max 535 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3690.00 ave 3811 max 3529 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 14760
Ave neighs/atom = 28.828125
Neighbor list builds = 6
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style tersoff stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff shift 0.05
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.952 | 2.952 | 2.952 Mbytes
Step Temp E_pair E_mol TotEng Press
100 742.67188 -3294.0266 0 -3255.7505 1615779.4
110 2870.7114 -3432.8485 0 -3257.629 1053310.6
120 2898.0798 -3431.4968 0 -3256.6851 1223402.3
130 2708.4483 -3419.0142 0 -3256.436 1105893.8
140 2307.8661 -3394.1268 0 -3256.1686 1148075.8
150 2215.3423 -3390.1427 0 -3255.8733 1138540
160 2515.488 -3412.6704 0 -3255.1731 1122902.8
170 2485.7109 -3415.0402 0 -3255.3787 1097748.5
180 2327.476 -3408.2463 0 -3254.6537 1061602.6
190 2339.5966 -3413.3961 0 -3254.7496 1088059
200 2260.5961 -3411.477 0 -3254.0771 1104581.5
Loop time of 0.0409132 on 4 procs for 100 steps with 512 atoms
Performance: 211.179 ns/day, 0.114 hours/ns, 2444.196 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.03285 | 0.033327 | 0.03406 | 0.3 | 81.46
Neigh | 0.000975 | 0.0010677 | 0.001184 | 0.2 | 2.61
Comm | 0.004915 | 0.005528 | 0.006044 | 0.7 | 13.51
Output | 0.000129 | 0.0001535 | 0.000226 | 0.0 | 0.38
Modify | 0.000564 | 0.0005885 | 0.000604 | 0.0 | 1.44
Other | | 0.0002483 | | | 0.61
Nlocal: 128.000 ave 133 max 123 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 535.250 ave 542 max 531 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3669.00 ave 3822 max 3522 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 14676
Ave neighs/atom = 28.664062
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:00:00

34
examples/threebody/in.threebody
View File

@ -46,7 +46,7 @@ create_atoms 1 region myreg &
mass * 28.06
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create $t 5287287 loop geom
# Equilibrate using Stillinger-Weber model for silicon
@ -114,35 +114,3 @@ neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
# Test Tersoff/Mod model for Si
clear
read_restart restart.equil
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
# Test Tersoff/Mod/C model for Si
clear
read_restart restart.equil
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100

547
examples/threebody/log.13Jan21.threebody.g++.1 Normal file
View File

@ -0,0 +1,547 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
create_atoms CPU = 0.000 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading sw potential file Si.sw with DATE: 2007-06-11
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2220.3392 0 -2101.4457 12358.626
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
20 588.26396 -2139.7132 0 -2101.3117 11295.566
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
80 800.80221 -2146.1371 0 -2101.313 11995.66
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
Loop time of 0.092666 on 1 procs for 100 steps with 512 atoms
Performance: 93.238 ns/day, 0.257 hours/ns, 1079.144 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.089633 | 0.089633 | 0.089633 | 0.0 | 96.73
Neigh | 0.001474 | 0.001474 | 0.001474 | 0.0 | 1.59
Comm | 0.00041 | 0.00041 | 0.00041 | 0.0 | 0.44
Output | 0.000153 | 0.000153 | 0.000153 | 0.0 | 0.17
Modify | 0.000782 | 0.000782 | 0.000782 | 0.0 | 0.84
Other | | 0.000214 | | | 0.23
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017.00 ave 1017 max 1017 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: 13988.0 ave 13988 max 13988 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13988
Ave neighs/atom = 27.320312
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.002 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.6320004
ghost atom cutoff = 5.6320004
binsize = 2.8160002, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -625.76163 0 -564.38354 462129.66
110 1502.8461 -649.55768 0 -564.45814 463413.45
120 1926.4523 -674.71265 0 -564.53612 486338.88
130 1152.6663 -621.47264 0 -564.37203 514892.2
140 1762.244 -659.86941 0 -564.4985 488159.88
150 1767.8665 -657.67178 0 -564.48386 466721.31
160 1075.2874 -610.12809 0 -564.36709 470151.9
170 1697.9313 -649.3684 0 -564.47207 467953.71
180 1856.1197 -657.14338 0 -564.48754 488372.27
190 1346.1107 -621.42431 0 -564.38065 511750.04
200 1919.5266 -657.26587 0 -564.47797 488684.56
Loop time of 0.289193 on 1 procs for 100 steps with 512 atoms
Performance: 29.876 ns/day, 0.803 hours/ns, 345.790 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.28463 | 0.28463 | 0.28463 | 0.0 | 98.42
Neigh | 0.002821 | 0.002821 | 0.002821 | 0.0 | 0.98
Comm | 0.000605 | 0.000605 | 0.000605 | 0.0 | 0.21
Output | 0.000176 | 0.000176 | 0.000176 | 0.0 | 0.06
Modify | 0.000769 | 0.000769 | 0.000769 | 0.0 | 0.27
Other | | 0.000188 | | | 0.07
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1428.00 ave 1428 max 1428 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: 17344.0 ave 17344 max 17344 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17344
Ave neighs/atom = 33.875000
Neighbor list builds = 3
Dangerous builds = 0
# Test Vashishta model for In/P
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
110 1250.545 -1504.5795 0 -1435.9786 345188.52
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
140 1481.0477 -1513.0511 0 -1435.988 308725.1
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
Loop time of 0.126684 on 1 procs for 100 steps with 512 atoms
Performance: 68.201 ns/day, 0.352 hours/ns, 789.366 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11981 | 0.11981 | 0.11981 | 0.0 | 94.57
Neigh | 0.004903 | 0.004903 | 0.004903 | 0.0 | 3.87
Comm | 0.000846 | 0.000846 | 0.000846 | 0.0 | 0.67
Output | 0.000145 | 0.000145 | 0.000145 | 0.0 | 0.11
Modify | 0.000772 | 0.000772 | 0.000772 | 0.0 | 0.61
Other | | 0.000207 | | | 0.16
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1838.00 ave 1838 max 1838 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: 36482.0 ave 36482 max 36482 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36482
Ave neighs/atom = 71.253906
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
140 1486.0361 -3274.951 0 -3197.776 1871927.6
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
Loop time of 0.114312 on 1 procs for 100 steps with 512 atoms
Performance: 75.583 ns/day, 0.318 hours/ns, 874.799 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1121 | 0.1121 | 0.1121 | 0.0 | 98.06
Neigh | 0.000773 | 0.000773 | 0.000773 | 0.0 | 0.68
Comm | 0.000415 | 0.000415 | 0.000415 | 0.0 | 0.36
Output | 0.000136 | 0.000136 | 0.000136 | 0.0 | 0.12
Modify | 0.000703 | 0.000703 | 0.000703 | 0.0 | 0.61
Other | | 0.000186 | | | 0.16
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1028.00 ave 1028 max 1028 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: 14604.0 ave 14604 max 14604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14604
Ave neighs/atom = 28.523438
Neighbor list builds = 1
Dangerous builds = 0
# Test Tersoff/Mod model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.986 | 2.986 | 2.986 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
110 835.77436 -2289.6119 0 -2248.1918 19964.211
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
130 957.60664 -2293.7047 0 -2248.2139 14850.338
140 865.12471 -2285.7774 0 -2248.1971 17101.553
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
170 843.8591 -2277.9713 0 -2248.1911 18966.532
180 1008.7412 -2286.922 0 -2248.2075 17275.649
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
Loop time of 0.12412 on 1 procs for 100 steps with 512 atoms
Performance: 69.610 ns/day, 0.345 hours/ns, 805.672 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12079 | 0.12079 | 0.12079 | 0.0 | 97.32
Neigh | 0.001821 | 0.001821 | 0.001821 | 0.0 | 1.47
Comm | 0.000407 | 0.000407 | 0.000407 | 0.0 | 0.33
Output | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.13
Modify | 0.000736 | 0.000736 | 0.000736 | 0.0 | 0.59
Other | | 0.000203 | | | 0.16
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1007.00 ave 1007 max 1007 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: 8884.00 ave 8884 max 8884 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8884
Ave neighs/atom = 17.351562
Neighbor list builds = 3
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.205694
ghost atom cutoff = 4.205694
binsize = 2.102847, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.980 | 2.980 | 2.980 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -2309.1331 0 -2247.755 20346.718
110 831.93715 -2288.8853 0 -2247.7187 21758.195
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
130 972.43247 -2294.1847 0 -2247.7467 16614.835
140 815.76148 -2282.0495 0 -2247.7194 18310.116
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
170 787.17244 -2273.8946 0 -2247.7175 18586.606
180 932.5662 -2281.6828 0 -2247.7315 18154.167
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
Loop time of 0.12973 on 1 procs for 100 steps with 512 atoms
Performance: 66.600 ns/day, 0.360 hours/ns, 770.832 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12643 | 0.12643 | 0.12643 | 0.0 | 97.45
Neigh | 0.001798 | 0.001798 | 0.001798 | 0.0 | 1.39
Comm | 0.000421 | 0.000421 | 0.000421 | 0.0 | 0.32
Output | 0.00016 | 0.00016 | 0.00016 | 0.0 | 0.12
Modify | 0.000733 | 0.000733 | 0.000733 | 0.0 | 0.57
Other | | 0.000192 | | | 0.15
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 958.000 ave 958 max 958 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: 8416.00 ave 8416 max 8416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8416
Ave neighs/atom = 16.437500
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

547
examples/threebody/log.13Jan21.threebody.g++.4 Normal file
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@ -0,0 +1,547 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
create_atoms CPU = 0.001 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading sw potential file Si.sw with DATE: 2007-06-11
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.958 | 2.958 | 2.958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2220.3392 0 -2101.4457 12358.626
10 1006.0192 -2167.7053 0 -2101.3286 13892.426
20 588.26396 -2139.7132 0 -2101.3117 11295.566
30 990.55956 -2165.2164 0 -2101.3931 6279.0239
40 700.12917 -2144.4279 0 -2101.3427 5594.2388
50 523.64239 -2131.7796 0 -2101.3122 6013.0994
60 989.47092 -2161.3716 0 -2101.3839 5819.2688
70 877.27433 -2152.4432 0 -2101.3461 9116.6569
80 800.80221 -2146.1371 0 -2101.313 11995.66
90 1293.9689 -2176.9021 0 -2101.3848 11692.45
100 1112.9699 -2162.7259 0 -2101.3478 12263.758
Loop time of 0.0284905 on 4 procs for 100 steps with 512 atoms
Performance: 303.259 ns/day, 0.079 hours/ns, 3509.942 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022257 | 0.023383 | 0.025192 | 0.7 | 82.07
Neigh | 0.00036 | 0.00037475 | 0.000387 | 0.0 | 1.32
Comm | 0.002084 | 0.0039075 | 0.005034 | 1.8 | 13.72
Output | 9.9e-05 | 0.00011525 | 0.00016 | 0.0 | 0.40
Modify | 0.000428 | 0.00043675 | 0.000443 | 0.0 | 1.53
Other | | 0.0002728 | | | 0.96
Nlocal: 128.000 ave 132 max 125 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 525.000 ave 528 max 521 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3497.00 ave 3619 max 3397 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 13988
Ave neighs/atom = 27.320312
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.000 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.6320004
ghost atom cutoff = 5.6320004
binsize = 2.8160002, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.967 | 2.967 | 2.968 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -625.76163 0 -564.38354 462129.66
110 1502.8461 -649.55768 0 -564.45814 463413.45
120 1926.4523 -674.71265 0 -564.53613 486338.88
130 1152.6663 -621.47265 0 -564.37203 514892.19
140 1762.244 -659.86941 0 -564.4985 488159.88
150 1767.8665 -657.67179 0 -564.48386 466721.31
160 1075.2874 -610.1281 0 -564.36709 470151.9
170 1697.9313 -649.3684 0 -564.47208 467953.7
180 1856.1197 -657.14338 0 -564.48754 488372.26
190 1346.1107 -621.42432 0 -564.38065 511750.03
200 1919.5266 -657.26587 0 -564.47797 488684.56
Loop time of 0.084576 on 4 procs for 100 steps with 512 atoms
Performance: 102.157 ns/day, 0.235 hours/ns, 1182.369 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.072089 | 0.074912 | 0.076672 | 0.7 | 88.57
Neigh | 0.000745 | 0.0008125 | 0.000883 | 0.0 | 0.96
Comm | 0.006054 | 0.0077975 | 0.010598 | 2.1 | 9.22
Output | 0.000129 | 0.00015525 | 0.000219 | 0.0 | 0.18
Modify | 0.000523 | 0.000578 | 0.000641 | 0.0 | 0.68
Other | | 0.0003213 | | | 0.38
Nlocal: 128.000 ave 135 max 122 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 759.750 ave 770 max 751 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4336.00 ave 4563 max 4128 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 17344
Ave neighs/atom = 33.875000
Neighbor list builds = 3
Dangerous builds = 0
# Test Vashishta model for In/P
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.988 | 2.988 | 2.988 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -1497.2988 0 -1435.9207 355619.19
110 1250.545 -1504.5795 0 -1435.9786 345188.52
120 1360.2275 -1509.3443 0 -1435.9801 333306.3
130 1066.4516 -1487.9076 0 -1435.9076 334465.11
140 1481.0477 -1513.0511 0 -1435.988 308725.1
150 1216.1167 -1493.0774 0 -1435.9217 304249.09
160 1211.4398 -1490.7459 0 -1435.9164 288897.09
170 1542.2025 -1510.0774 0 -1435.9608 260104.14
180 1302.9041 -1491.7765 0 -1435.8971 249514.04
190 1332.3326 -1491.5271 0 -1435.9213 227537.99
200 1352.1813 -1490.4513 0 -1435.9049 207626.42
Loop time of 0.0404882 on 4 procs for 100 steps with 512 atoms
Performance: 213.395 ns/day, 0.112 hours/ns, 2469.852 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.032713 | 0.033094 | 0.033544 | 0.2 | 81.74
Neigh | 0.001251 | 0.0012875 | 0.001308 | 0.1 | 3.18
Comm | 0.004788 | 0.005204 | 0.00557 | 0.4 | 12.85
Output | 0.000123 | 0.0001385 | 0.000182 | 0.0 | 0.34
Modify | 0.000492 | 0.00050725 | 0.000533 | 0.0 | 1.25
Other | | 0.0002565 | | | 0.63
Nlocal: 128.000 ave 131 max 124 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 1013.25 ave 1025 max 1002 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 9120.50 ave 9356 max 8868 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 36482
Ave neighs/atom = 71.253906
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.948 | 2.948 | 2.948 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -3259.7676 0 -3198.3895 1912461.3
110 1772.8268 -3301.5479 0 -3198.8218 1885295.6
120 1169.7287 -3258.74 0 -3197.9294 1898705.2
130 1308.5623 -3265.1338 0 -3197.5922 1894187.5
140 1486.0361 -3274.951 0 -3197.776 1871927.6
150 1419.0362 -3267.7302 0 -3197.2296 1925234.6
160 1196.6689 -3250.1492 0 -3196.7078 1902235.1
170 1707.5846 -3281.7658 0 -3196.9721 1863047.3
180 1337.4358 -3254.9844 0 -3196.8222 1880420.9
190 1441.8052 -3259.0364 0 -3196.3556 1904512.1
200 1569.0317 -3265.0089 0 -3196.3328 1899462.7
Loop time of 0.03452 on 4 procs for 100 steps with 512 atoms
Performance: 250.290 ns/day, 0.096 hours/ns, 2896.871 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.029269 | 0.029729 | 0.030688 | 0.3 | 86.12
Neigh | 0.000203 | 0.00023375 | 0.000271 | 0.0 | 0.68
Comm | 0.00275 | 0.0036492 | 0.004132 | 0.9 | 10.57
Output | 0.000104 | 0.000121 | 0.000165 | 0.0 | 0.35
Modify | 0.000456 | 0.0004605 | 0.000463 | 0.0 | 1.33
Other | | 0.000326 | | | 0.94
Nlocal: 128.000 ave 132 max 123 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 529.500 ave 533 max 524 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3651.00 ave 3783 max 3494 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 14604
Ave neighs/atom = 28.523438
Neighbor list builds = 1
Dangerous builds = 0
# Test Tersoff/Mod model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading tersoff/mod potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -2309.6047 0 -2248.2266 17662.891
110 835.77436 -2289.6119 0 -2248.1918 19964.211
120 1067.0735 -2303.0587 0 -2248.2414 13767.101
130 957.60664 -2293.7047 0 -2248.2139 14850.338
140 865.12471 -2285.7774 0 -2248.1971 17101.553
150 1104.7368 -2299.5468 0 -2248.2286 13031.988
160 1077.1682 -2295.3841 0 -2248.2227 13615.019
170 843.8591 -2277.9713 0 -2248.1911 18966.532
180 1008.7412 -2286.922 0 -2248.2075 17275.649
190 1237.9346 -2299.5487 0 -2248.2305 14334.006
200 1060.2161 -2285.3352 0 -2248.1952 18999.834
Loop time of 0.043388 on 4 procs for 100 steps with 512 atoms
Performance: 199.133 ns/day, 0.121 hours/ns, 2304.785 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.033874 | 0.036197 | 0.037433 | 0.7 | 83.43
Neigh | 0.000538 | 0.00055575 | 0.000575 | 0.0 | 1.28
Comm | 0.004381 | 0.0055505 | 0.007783 | 1.8 | 12.79
Output | 0.000141 | 0.0001635 | 0.000228 | 0.0 | 0.38
Modify | 0.000532 | 0.000615 | 0.000692 | 0.0 | 1.42
Other | | 0.000306 | | | 0.71
Nlocal: 128.000 ave 135 max 121 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 515.000 ave 518 max 508 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2221.00 ave 2328 max 2103 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 8884
Ave neighs/atom = 17.351562
Neighbor list builds = 3
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 30 Nov 2020, LAMMPS = 30 Nov 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading tersoff/mod/c potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.205694
ghost atom cutoff = 4.205694
binsize = 2.102847, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.950 | 2.950 | 2.950 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1112.9699 -2309.1331 0 -2247.755 20346.718
110 831.93715 -2288.8853 0 -2247.7187 21758.195
120 1077.6698 -2303.2846 0 -2247.7693 16036.053
130 972.43247 -2294.1847 0 -2247.7467 16614.835
140 815.76148 -2282.0495 0 -2247.7194 18310.116
150 1072.7096 -2297.0491 0 -2247.7574 13896.767
160 1061.8824 -2294.0028 0 -2247.7522 13663.179
170 787.17244 -2273.8946 0 -2247.7175 18586.606
180 932.5662 -2281.6828 0 -2247.7315 18154.167
190 1205.7299 -2297.2769 0 -2247.7608 14504.136
200 1022.5285 -2282.7039 0 -2247.7245 18710.495
Loop time of 0.0526065 on 4 procs for 100 steps with 512 atoms
Performance: 164.238 ns/day, 0.146 hours/ns, 1900.906 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.044962 | 0.045875 | 0.046737 | 0.3 | 87.20
Neigh | 0.000603 | 0.00062075 | 0.000646 | 0.0 | 1.18
Comm | 0.003882 | 0.0047085 | 0.005598 | 1.0 | 8.95
Output | 0.000159 | 0.0001995 | 0.000321 | 0.0 | 0.38
Modify | 0.000767 | 0.0007775 | 0.000792 | 0.0 | 1.48
Other | | 0.0004255 | | | 0.81
Nlocal: 128.000 ave 131 max 122 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 483.000 ave 485 max 479 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2104.00 ave 2169 max 2008 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 8416
Ave neighs/atom = 16.437500
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

524
examples/threebody/log.27Nov18.threebody.g++.1
View File

@ -1,524 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
Time spent = 0.000483751 secs
mass * 28.06
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading potential file Si.sw with DATE: 2007-06-11
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2220.3392 0 -2101.4457 12358.626
10 993.48824 -2166.8749 0 -2101.3265 14121.853
20 587.90768 -2139.6876 0 -2101.3093 11864.886
30 1030.8616 -2167.8446 0 -2101.3947 6649.2566
40 724.62874 -2145.9637 0 -2101.3436 5859.6447
50 490.9053 -2129.5491 0 -2101.3077 6326.5434
60 960.24533 -2159.427 0 -2101.3794 5733.9889
70 906.76518 -2154.3675 0 -2101.3496 8380.4834
80 800.7253 -2146.0714 0 -2101.3113 11515.737
90 1249.2719 -2173.9445 0 -2101.3818 11593.728
100 1080.3797 -2160.6174 0 -2101.3445 12414.602
Loop time of 0.129171 on 1 procs for 100 steps with 512 atoms
Performance: 66.888 ns/day, 0.359 hours/ns, 774.165 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12468 | 0.12468 | 0.12468 | 0.0 | 96.52
Neigh | 0.0017159 | 0.0017159 | 0.0017159 | 0.0 | 1.33
Comm | 0.00088573 | 0.00088573 | 0.00088573 | 0.0 | 0.69
Output | 0.00011206 | 0.00011206 | 0.00011206 | 0.0 | 0.09
Modify | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 1.11
Other | | 0.0003417 | | | 0.26
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 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: 14044 ave 14044 max 14044 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14044
Ave neighs/atom = 27.4297
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.632
ghost atom cutoff = 5.632
binsize = 2.816, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.758 | 2.758 | 2.758 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -621.93681 0 -562.66385 464005.01
110 1512.4547 -648.51133 0 -562.74194 463733.24
120 1959.7565 -675.18668 0 -562.8255 486580.33
130 1138.5498 -618.80419 0 -562.6427 515406.41
140 1827.3403 -662.43867 0 -562.78985 485719
150 1822.9803 -659.56725 0 -562.76627 465652.59
160 1128.3444 -611.92808 0 -562.65512 469836.33
170 1699.6402 -647.82381 0 -562.75353 467977.54
180 1840.047 -654.5552 0 -562.77005 488397.41
190 1312.0974 -617.70228 0 -562.6629 510856.48
200 1809.8409 -648.6173 0 -562.75377 490822.97
Loop time of 0.399255 on 1 procs for 100 steps with 512 atoms
Performance: 21.640 ns/day, 1.109 hours/ns, 250.467 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38979 | 0.38979 | 0.38979 | 0.0 | 97.63
Neigh | 0.0061283 | 0.0061283 | 0.0061283 | 0.0 | 1.53
Comm | 0.0013483 | 0.0013483 | 0.0013483 | 0.0 | 0.34
Output | 0.00016642 | 0.00016642 | 0.00016642 | 0.0 | 0.04
Modify | 0.0014937 | 0.0014937 | 0.0014937 | 0.0 | 0.37
Other | | 0.0003231 | | | 0.08
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1386 ave 1386 max 1386 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: 17388 ave 17388 max 17388 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17388
Ave neighs/atom = 33.9609
Neighbor list builds = 5
Dangerous builds = 0
# Test Vashishta model for In/P
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading potential file InP.vashishta with DATE: 2015-10-14
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.783 | 2.783 | 2.783 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -1491.8652 0 -1432.5922 358930.65
110 1299.3069 -1504.494 0 -1432.6803 347566.41
120 1396.3035 -1508.3817 0 -1432.672 336798.42
130 1055.9254 -1483.8342 0 -1432.5849 341035.18
140 1543.9033 -1513.8559 0 -1432.6931 314268.54
150 1242.5383 -1491.417 0 -1432.6036 311068.53
160 1240.1733 -1489.2495 0 -1432.6033 295776.98
170 1559.5037 -1507.824 0 -1432.6417 266170.25
180 1379.0358 -1493.4092 0 -1432.5869 251410.63
190 1465.8073 -1496.8564 0 -1432.6105 226461.31
200 1456.6383 -1493.8133 0 -1432.5852 208188.34
Loop time of 0.198058 on 1 procs for 100 steps with 512 atoms
Performance: 43.624 ns/day, 0.550 hours/ns, 504.903 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.18746 | 0.18746 | 0.18746 | 0.0 | 94.65
Neigh | 0.00688 | 0.00688 | 0.00688 | 0.0 | 3.47
Comm | 0.001718 | 0.001718 | 0.001718 | 0.0 | 0.87
Output | 0.00013351 | 0.00013351 | 0.00013351 | 0.0 | 0.07
Modify | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.76
Other | | 0.0003531 | | | 0.18
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1810 ave 1810 max 1810 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: 36480 ave 36480 max 36480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36480
Ave neighs/atom = 71.25
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724)
orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724)
orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.74 | 2.74 | 2.74 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -3249.8451 0 -3190.5722 1925371.8
110 1878.2843 -3300.7205 0 -3191.0964 1893058.6
120 1153.8494 -3250.2114 0 -3190.5436 1932141.4
130 1363.8664 -3261.6889 0 -3190.6116 1902268.1
140 1565.5505 -3273.0405 0 -3190.6982 1878817
150 1416.9458 -3261.1805 0 -3190.865 1916554.4
160 1288.6997 -3249.8279 0 -3190.4141 1933227.4
170 1768.3043 -3279.2164 0 -3190.4535 1898123.4
180 1375.1942 -3251.0929 0 -3190.3781 1896205.1
190 1527.0671 -3258.7679 0 -3190.4344 1900673.6
200 1586.8691 -3260.4713 0 -3190.434 1912454.8
Loop time of 0.210082 on 1 procs for 100 steps with 512 atoms
Performance: 41.127 ns/day, 0.584 hours/ns, 476.006 timesteps/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20628 | 0.20628 | 0.20628 | 0.0 | 98.19
Neigh | 0.00099182 | 0.00099182 | 0.00099182 | 0.0 | 0.47
Comm | 0.00085139 | 0.00085139 | 0.00085139 | 0.0 | 0.41
Output | 0.00013494 | 0.00013494 | 0.00013494 | 0.0 | 0.06
Modify | 0.0014665 | 0.0014665 | 0.0014665 | 0.0 | 0.70
Other | | 0.0003612 | | | 0.17
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1027 ave 1027 max 1027 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: 14602 ave 14602 max 14602 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14602
Ave neighs/atom = 28.5195
Neighbor list builds = 1
Dangerous builds = 0
# Test Tersoff/Mod model for Si
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.744 | 2.744 | 2.744 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -2307.5808 0 -2248.3078 18624.75
110 851.21757 -2290.7529 0 -2248.2817 21041.97
120 1074.6349 -2303.6437 0 -2248.321 15244.809
130 1006.5662 -2296.9866 0 -2248.3057 15954.09
140 855.64354 -2285.1581 0 -2248.2781 19346.662
150 1111.1546 -2300.024 0 -2248.314 14698.998
160 1114.7933 -2297.8629 0 -2248.3098 14414.14
170 853.9568 -2278.6047 0 -2248.2716 20120.632
180 1031.0925 -2288.3481 0 -2248.2949 18332.008
190 1230.3458 -2298.9946 0 -2248.3111 15520.302
200 1053.8799 -2284.8931 0 -2248.2816 20033.536
Loop time of 0.158428 on 1 procs for 100 steps with 512 atoms
Performance: 54.536 ns/day, 0.440 hours/ns, 631.200 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15318 | 0.15318 | 0.15318 | 0.0 | 96.69
Neigh | 0.0022631 | 0.0022631 | 0.0022631 | 0.0 | 1.43
Comm | 0.00093651 | 0.00093651 | 0.00093651 | 0.0 | 0.59
Output | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.12
Modify | 0.0015035 | 0.0015035 | 0.0015035 | 0.0 | 0.95
Other | | 0.0003462 | | | 0.22
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1001 ave 1001 max 1001 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: 8872 ave 8872 max 8872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8872
Ave neighs/atom = 17.3281
Neighbor list builds = 3
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.20569
ghost atom cutoff = 4.20569
binsize = 2.10285, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -2307.5509 0 -2248.2779 21368.36
110 846.70637 -2290.4239 0 -2248.2488 22856.37
120 1083.0906 -2304.1686 0 -2248.2895 17530.457
130 1008.7015 -2297.0835 0 -2248.2781 17698.498
140 811.71413 -2282.2528 0 -2248.2417 19986.737
150 1094.4969 -2298.9718 0 -2248.2836 15822.967
160 1100.1109 -2296.9461 0 -2248.2804 15213.75
170 801.20165 -2275.2175 0 -2248.2372 20153.957
180 994.63485 -2286.1145 0 -2248.2621 19167.021
190 1215.6425 -2298.2082 0 -2248.284 15895.654
200 992.20385 -2281.0372 0 -2248.2425 19643.792
Loop time of 0.282035 on 1 procs for 100 steps with 512 atoms
Performance: 30.634 ns/day, 0.783 hours/ns, 354.565 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.27701 | 0.27701 | 0.27701 | 0.0 | 98.22
Neigh | 0.0021927 | 0.0021927 | 0.0021927 | 0.0 | 0.78
Comm | 0.00089169 | 0.00089169 | 0.00089169 | 0.0 | 0.32
Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.05
Modify | 0.0014682 | 0.0014682 | 0.0014682 | 0.0 | 0.52
Other | | 0.0003295 | | | 0.12
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 972 ave 972 max 972 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: 8390 ave 8390 max 8390 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8390
Ave neighs/atom = 16.3867
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:01

524
examples/threebody/log.27Nov18.threebody.g++.4
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@ -1,524 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
Time spent = 0.000348091 secs
mass * 28.06
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading potential file Si.sw with DATE: 2007-06-11
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.957 | 2.957 | 2.957 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2220.3392 0 -2101.4457 12358.626
10 979.93888 -2165.9769 0 -2101.3242 14172.134
20 579.6159 -2139.1412 0 -2101.3085 11866.038
30 1027.5223 -2167.6187 0 -2101.3942 6885.6751
40 711.03138 -2145.0665 0 -2101.3405 6357.0866
50 497.18304 -2129.9748 0 -2101.3052 7137.6093
60 1008.411 -2162.5834 0 -2101.3804 6745.1775
70 947.58674 -2156.9872 0 -2101.3508 9678.1622
80 798.43683 -2145.8382 0 -2101.3074 12728.694
90 1259.2065 -2174.5324 0 -2101.3799 12033.395
100 1100.5203 -2161.8599 0 -2101.3468 12356.137
Loop time of 0.0414283 on 4 procs for 100 steps with 512 atoms
Performance: 208.553 ns/day, 0.115 hours/ns, 2413.811 timesteps/s
95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.030011 | 0.032047 | 0.034036 | 0.8 | 77.36
Neigh | 0.00043392 | 0.00045151 | 0.0004642 | 0.0 | 1.09
Comm | 0.0050831 | 0.0067263 | 0.0091536 | 1.8 | 16.24
Output | 0.00018191 | 0.00018775 | 0.00020432 | 0.0 | 0.45
Modify | 0.00068116 | 0.0010136 | 0.001817 | 1.5 | 2.45
Other | | 0.001002 | | | 2.42
Nlocal: 128 ave 132 max 126 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 525 ave 527 max 521 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3507 ave 3596 max 3470 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 14028
Ave neighs/atom = 27.3984
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.632
ghost atom cutoff = 5.632
binsize = 2.816, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.718 | 2.718 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -621.61663 0 -561.10352 462716.2
110 1478.2708 -644.61282 0 -561.16927 464567.29
120 1989.4577 -675.5312 0 -561.25985 486476.63
130 1185.4652 -620.23829 0 -561.09359 514103.86
140 1726.9774 -654.21952 0 -561.20676 488915.22
150 1863.2061 -660.66167 0 -561.21416 466985.15
160 1119.0313 -609.68409 0 -561.08624 471511.61
170 1708.2653 -646.79823 0 -561.18829 468697.42
180 1891.8451 -656.32585 0 -561.2042 489912.65
190 1345.7703 -618.29258 0 -561.09909 512364.68
200 1865.9507 -650.72167 0 -561.19281 491531.23
Loop time of 0.117532 on 4 procs for 100 steps with 512 atoms
Performance: 73.512 ns/day, 0.326 hours/ns, 850.834 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.096347 | 0.10005 | 0.10244 | 0.8 | 85.13
Neigh | 0.000947 | 0.0010053 | 0.0011535 | 0.3 | 0.86
Comm | 0.0098422 | 0.012949 | 0.016335 | 2.2 | 11.02
Output | 0.00017452 | 0.00022596 | 0.00037885 | 0.0 | 0.19
Modify | 0.00078702 | 0.0013881 | 0.0021975 | 1.6 | 1.18
Other | | 0.001909 | | | 1.62
Nlocal: 128 ave 133 max 125 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 754.5 ave 759 max 748 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4353 ave 4512 max 4252 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 17412
Ave neighs/atom = 34.0078
Neighbor list builds = 3
Dangerous builds = 0
# Test Vashishta model for In/P
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading potential file InP.vashishta with DATE: 2015-10-14
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -1495.2135 0 -1434.7004 357102.51
110 1238.7371 -1502.5372 0 -1434.7528 348870.19
120 1409.575 -1511.3137 0 -1434.7612 336831.6
130 1081.541 -1487.5554 0 -1434.6881 339244.71
140 1484.7455 -1512.0076 0 -1434.7646 313026.51
150 1263.0321 -1494.834 0 -1434.7018 306496.02
160 1253.4363 -1492.1804 0 -1434.7025 290683.01
170 1536.7348 -1508.3735 0 -1434.7312 261755.69
180 1342.0478 -1493.0615 0 -1434.6754 248519.54
190 1457.921 -1498.4355 0 -1434.6991 223607.39
200 1499.5384 -1498.7005 0 -1434.6898 204647.17
Loop time of 0.060006 on 4 procs for 100 steps with 512 atoms
Performance: 143.986 ns/day, 0.167 hours/ns, 1666.501 timesteps/s
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.043862 | 0.047754 | 0.04964 | 1.0 | 79.58
Neigh | 0.0018079 | 0.0018883 | 0.0019724 | 0.1 | 3.15
Comm | 0.0067413 | 0.0083464 | 0.011978 | 2.3 | 13.91
Output | 0.00018859 | 0.00029892 | 0.00062919 | 0.0 | 0.50
Modify | 0.00088429 | 0.0011829 | 0.0014911 | 0.8 | 1.97
Other | | 0.0005357 | | | 0.89
Nlocal: 128 ave 129 max 127 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 992.75 ave 1001 max 987 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 9116 ave 9213 max 9051 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 36464
Ave neighs/atom = 71.2188
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724)
orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724)
orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.699 | 2.699 | 2.699 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -3252.8699 0 -3192.3567 1930742.5
110 1858.7735 -3301.1227 0 -3192.8403 1901753.1
120 1107.7693 -3248.8236 0 -3192.2522 1953649.4
130 1315.4397 -3260.1471 0 -3192.2616 1898713.9
140 1541.4371 -3273.1832 0 -3192.41 1887352.3
150 1424.7104 -3262.9648 0 -3192.216 1960688.1
160 1291.2932 -3251.5548 0 -3192.0201 1914541.2
170 1719.1133 -3277.7936 0 -3192.33 1893926
180 1312.8066 -3248.6914 0 -3192.1477 1921417.4
190 1481.3472 -3257.1585 0 -3191.8991 1927045.6
200 1615.282 -3263.8377 0 -3192.055 1920616.3
Loop time of 0.0635643 on 4 procs for 100 steps with 512 atoms
Performance: 135.925 ns/day, 0.177 hours/ns, 1573.210 timesteps/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.051391 | 0.053262 | 0.05459 | 0.6 | 83.79
Neigh | 0.00052404 | 0.00052798 | 0.00053144 | 0.0 | 0.83
Comm | 0.0063059 | 0.0079132 | 0.0095143 | 1.5 | 12.45
Output | 0.00017905 | 0.00029147 | 0.00062609 | 0.0 | 0.46
Modify | 0.00064421 | 0.00096625 | 0.0012674 | 0.0 | 1.52
Other | | 0.0006039 | | | 0.95
Nlocal: 128 ave 131 max 125 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 526.75 ave 532 max 523 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3646.5 ave 3722 max 3567 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 14586
Ave neighs/atom = 28.4883
Neighbor list builds = 2
Dangerous builds = 0
# Test Tersoff/Mod model for Si
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.701 | 2.701 | 2.701 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -2308.936 0 -2248.4229 18087.231
110 821.82813 -2288.8477 0 -2248.3856 21245.995
120 1082.3774 -2304.2287 0 -2248.4366 15467.483
130 995.26561 -2296.2957 0 -2248.4145 16341.517
140 826.97009 -2283.3692 0 -2248.3897 19123.5
150 1048.4178 -2296.0496 0 -2248.4172 15060.312
160 1101.7884 -2297.2417 0 -2248.426 15070.879
170 859.48562 -2279.1747 0 -2248.383 21416.479
180 1041.679 -2289.2303 0 -2248.4038 19572.707
190 1278.0514 -2302.2822 0 -2248.4257 16006.173
200 1097.0682 -2287.8121 0 -2248.3929 20906.774
Loop time of 0.046846 on 4 procs for 100 steps with 512 atoms
Performance: 184.434 ns/day, 0.130 hours/ns, 2134.653 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037434 | 0.039142 | 0.041109 | 0.7 | 83.55
Neigh | 0.0005877 | 0.00059921 | 0.00061464 | 0.0 | 1.28
Comm | 0.0036416 | 0.0055436 | 0.0073476 | 1.8 | 11.83
Output | 0.00016212 | 0.00027066 | 0.00059533 | 0.0 | 0.58
Modify | 0.00063038 | 0.00065678 | 0.00067234 | 0.0 | 1.40
Other | | 0.0006335 | | | 1.35
Nlocal: 128 ave 131 max 126 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 518 ave 525 max 513 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2202 ave 2257 max 2175 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 8808
Ave neighs/atom = 17.2031
Neighbor list builds = 3
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.20569
ghost atom cutoff = 4.20569
binsize = 2.10285, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.701 | 2.701 | 2.701 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -2308.5955 0 -2248.0824 20775.991
110 813.33618 -2287.9469 0 -2248.04 22564.16
120 1100.0902 -2305.051 0 -2248.092 17540.971
130 1022.9471 -2297.7384 0 -2248.0801 17985.336
140 761.99242 -2278.7251 0 -2248.0345 20462.975
150 1053.3973 -2296.1039 0 -2248.081 16130.559
160 1089.2622 -2296.1059 0 -2248.0833 15434.234
170 776.25788 -2273.4496 0 -2248.0321 20642.702
180 1016.1885 -2287.4305 0 -2248.0641 19276.936
190 1266.3943 -2301.3675 0 -2248.0865 16199.281
200 1012.4185 -2282.134 0 -2248.0423 20795.113
Loop time of 0.0840016 on 4 procs for 100 steps with 512 atoms
Performance: 102.855 ns/day, 0.233 hours/ns, 1190.454 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.068133 | 0.071658 | 0.075315 | 1.0 | 85.31
Neigh | 0.00057864 | 0.00058872 | 0.00060058 | 0.0 | 0.70
Comm | 0.0049844 | 0.008617 | 0.012086 | 2.8 | 10.26
Output | 0.0001626 | 0.00027418 | 0.00060463 | 0.0 | 0.33
Modify | 0.00070477 | 0.0011689 | 0.0022428 | 1.8 | 1.39
Other | | 0.001694 | | | 2.02
Nlocal: 128 ave 129 max 127 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 489.75 ave 501 max 481 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2094.5 ave 2121 max 2060 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8378
Ave neighs/atom = 16.3633
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

2
src/KOKKOS/pair_tersoff_kokkos.cpp
View File

@ -28,6 +28,7 @@
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -41,6 +42,7 @@ template<class DeviceType>
PairTersoffKokkos<DeviceType>::PairTersoffKokkos(LAMMPS *lmp) : PairTersoff(lmp)
{
respa_enable = 0;
suffix_flag |= Suffix::KOKKOS;
kokkosable = 1;
atomKK = (AtomKokkos *) atom;

2
src/KOKKOS/pair_tersoff_mod_kokkos.cpp
View File

@ -28,6 +28,7 @@
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -41,6 +42,7 @@ template<class DeviceType>
PairTersoffMODKokkos<DeviceType>::PairTersoffMODKokkos(LAMMPS *lmp) : PairTersoffMOD(lmp)
{
respa_enable = 0;
suffix_flag |= Suffix::KOKKOS;
kokkosable = 1;
atomKK = (AtomKokkos *) atom;

150
src/MANYBODY/pair_tersoff.cpp
View File

@ -12,7 +12,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (SNL)
Contributing author: Aidan Thompson (SNL) - original Tersoff implementation
Wengen Ouyang (TAU) - Shift addition
------------------------------------------------------------------------- */
#include "pair_tersoff.h"
@ -28,6 +29,7 @@
#include "neigh_request.h"
#include "neighbor.h"
#include "potential_file_reader.h"
#include "suffix.h"
#include "tokenizer.h"
#include <cmath>
@ -86,18 +88,50 @@ PairTersoff::~PairTersoff()
/* ---------------------------------------------------------------------- */
void PairTersoff::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
if (shift_flag) {
if (evflag) {
if (eflag) {
if (vflag_atom) eval<1,1,1,1>();
else eval<1,1,1,0>();
} else {
if (vflag_atom) eval<1,1,0,1>();
else eval<1,1,0,0>();
}
} else eval<1,0,0,0>();
} else {
if (evflag) {
if (eflag) {
if (vflag_atom) eval<0,1,1,1>();
else eval<0,1,1,0>();
} else {
if (vflag_atom) eval<0,1,0,1>();
else eval<0,1,0,0>();
}
} else eval<0,0,0,0>();
}
}
template <int SHIFT_FLAG, int EVFLAG, int EFLAG, int VFLAG_ATOM>
void PairTersoff::eval()
{
int i,j,k,ii,jj,kk,inum,jnum;
int itype,jtype,ktype,iparam_ij,iparam_ijk;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double fforce;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
double r1_hat[3],r2_hat[3];
double zeta_ij,prefactor;
double forceshiftfac;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **f = atom->f;
@ -140,6 +174,14 @@ void PairTersoff::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
// shift rsq and store correction for force
if (SHIFT_FLAG) {
double rsqtmp = rsq + shift*shift + 2*sqrt(rsq)*shift;
forceshiftfac = sqrt(rsqtmp/rsq);
rsq = rsqtmp;
}
if (rsq < cutshortsq) {
neighshort[numshort++] = j;
if (numshort >= maxshort) {
@ -163,7 +205,11 @@ void PairTersoff::compute(int eflag, int vflag)
iparam_ij = elem2param[itype][jtype][jtype];
if (rsq >= params[iparam_ij].cutsq) continue;
repulsive(&params[iparam_ij],rsq,fpair,eflag,evdwl);
repulsive(&params[iparam_ij],rsq,fpair,EFLAG,evdwl);
// correct force for shift in rsq
if (SHIFT_FLAG) fpair *= forceshiftfac;
fxtmp += delx*fpair;
fytmp += dely*fpair;
@ -172,7 +218,7 @@ void PairTersoff::compute(int eflag, int vflag)
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
if (EVFLAG) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
@ -189,8 +235,15 @@ void PairTersoff::compute(int eflag, int vflag)
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (SHIFT_FLAG)
rsq1 += shift*shift + 2*sqrt(rsq1)*shift;
if (rsq1 >= params[iparam_ij].cutsq) continue;
double r1inv = 1.0/sqrt(vec3_dot(delr1, delr1));
vec3_scale(r1inv, delr1, r1_hat);
// accumulate bondorder zeta for each i-j interaction via loop over k
fjxtmp = fjytmp = fjztmp = 0.0;
@ -206,14 +259,23 @@ void PairTersoff::compute(int eflag, int vflag)
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (SHIFT_FLAG)
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
if (rsq2 >= params[iparam_ijk].cutsq) continue;
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,delr1,delr2);
double r2inv = 1.0/sqrt(vec3_dot(delr2, delr2));
vec3_scale(r2inv, delr2, r2_hat);
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,r1_hat,r2_hat);
}
// pairwise force due to zeta
force_zeta(&params[iparam_ij],rsq1,zeta_ij,fpair,prefactor,eflag,evdwl);
force_zeta(&params[iparam_ij],rsq1,zeta_ij,fforce,prefactor,EFLAG,evdwl);
fpair = fforce*r1inv;
fxtmp += delr1[0]*fpair;
fytmp += delr1[1]*fpair;
@ -222,7 +284,7 @@ void PairTersoff::compute(int eflag, int vflag)
fjytmp -= delr1[1]*fpair;
fjztmp -= delr1[2]*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
if (EVFLAG) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
// attractive term via loop over k
@ -237,10 +299,17 @@ void PairTersoff::compute(int eflag, int vflag)
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (SHIFT_FLAG)
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
if (rsq2 >= params[iparam_ijk].cutsq) continue;
double r2inv = 1.0/sqrt(vec3_dot(delr2, delr2));
vec3_scale(r2inv, delr2, r2_hat);
attractive(&params[iparam_ijk],prefactor,
rsq1,rsq2,delr1,delr2,fi,fj,fk);
rsq1,rsq2,r1_hat,r2_hat,fi,fj,fk);
fxtmp += fi[0];
fytmp += fi[1];
@ -252,7 +321,7 @@ void PairTersoff::compute(int eflag, int vflag)
f[k][1] += fk[1];
f[k][2] += fk[2];
if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
if (VFLAG_ATOM) v_tally3(i,j,k,fj,fk,delr1,delr2);
}
f[j][0] += fjxtmp;
f[j][1] += fjytmp;
@ -283,9 +352,27 @@ void PairTersoff::allocate()
global settings
------------------------------------------------------------------------- */
void PairTersoff::settings(int narg, char **/*arg*/)
void PairTersoff::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
// default values
shift_flag = 0;
// process optional keywords
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"shift") == 0) {
if (suffix_flag & (Suffix::INTEL|Suffix::GPU|Suffix::KOKKOS))
error->all(FLERR,"Keyword 'shift' not supported for this style");
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style command");
shift = utils::numeric(FLERR,arg[iarg+1],false,lmp);
shift_flag = 1;
iarg += 2;
} else error->all(FLERR,"Illegal pair_style command");
}
}
/* ----------------------------------------------------------------------
@ -573,14 +660,13 @@ void PairTersoff::repulsive(Param *param, double rsq, double &fforce,
/* ---------------------------------------------------------------------- */
double PairTersoff::zeta(Param *param, double rsqij, double rsqik,
double *delrij, double *delrik)
double *rij_hat, double *rik_hat)
{
double rij,rik,costheta,arg,ex_delr;
rij = sqrt(rsqij);
rik = sqrt(rsqik);
costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
delrij[2]*delrik[2]) / (rij*rik);
costheta = vec3_dot(rij_hat,rik_hat);
if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
else arg = param->lam3 * (rij-rik);
@ -604,7 +690,7 @@ void PairTersoff::force_zeta(Param *param, double rsq, double zeta_ij,
fa = ters_fa(r,param);
fa_d = ters_fa_d(r,param);
bij = ters_bij(zeta_ij,param);
fforce = 0.5*bij*fa_d / r;
fforce = 0.5*bij*fa_d;
prefactor = -0.5*fa * ters_bij_d(zeta_ij,param);
if (eflag) eng = 0.5*bij*fa;
}
@ -617,21 +703,25 @@ void PairTersoff::force_zeta(Param *param, double rsq, double zeta_ij,
void PairTersoff::attractive(Param *param, double prefactor,
double rsqij, double rsqik,
double *delrij, double *delrik,
double *rij_hat, double *rik_hat,
double *fi, double *fj, double *fk)
{
double rij_hat[3],rik_hat[3];
double rij,rijinv,rik,rikinv;
rij = sqrt(rsqij);
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
rik = sqrt(rsqik);
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
ters_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,fi,fj,fk,param);
// correct 1/r for shift in rsq
if (shift_flag == 1) {
rijinv = 1.0/(rij - shift);
rikinv = 1.0/(rik - shift);
} else {
rijinv = 1.0/rij;
rikinv = 1.0/rik;
}
ters_zetaterm_d(prefactor,rij_hat,rij,rijinv,rik_hat,rik,rikinv,fi,fj,fk,param);
}
/* ---------------------------------------------------------------------- */
@ -712,8 +802,8 @@ double PairTersoff::ters_bij_d(double zeta, Param *param)
/* ---------------------------------------------------------------------- */
void PairTersoff::ters_zetaterm_d(double prefactor,
double *rij_hat, double rij,
double *rik_hat, double rik,
double *rij_hat, double rij, double rijinv,
double *rik_hat, double rik, double rikinv,
double *dri, double *drj, double *drk,
Param *param)
{
@ -736,7 +826,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
cos_theta = vec3_dot(rij_hat,rik_hat);
gijk = ters_gijk(cos_theta,param);
gijk_d = ters_gijk_d(cos_theta,param);
costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
costheta_d(rij_hat,rijinv,rik_hat,rikinv,dcosdri,dcosdrj,dcosdrk);
// compute the derivative wrt Ri
// dri = -dfc*gijk*ex_delr*rik_hat;
@ -770,8 +860,8 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
/* ---------------------------------------------------------------------- */
void PairTersoff::costheta_d(double *rij_hat, double rij,
double *rik_hat, double rik,
void PairTersoff::costheta_d(double *rij_hat, double rijinv,
double *rik_hat, double rikinv,
double *dri, double *drj, double *drk)
{
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
@ -779,9 +869,9 @@ void PairTersoff::costheta_d(double *rij_hat, double rij,
double cos_theta = vec3_dot(rij_hat,rik_hat);
vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
vec3_scale(1.0/rij,drj,drj);
vec3_scale(rijinv,drj,drj);
vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
vec3_scale(1.0/rik,drk,drk);
vec3_scale(rikinv,drk,drk);
vec3_add(drj,drk,dri);
vec3_scale(-1.0,dri,dri);
}

10
src/MANYBODY/pair_tersoff.h
View File

@ -34,6 +34,9 @@ class PairTersoff : public Pair {
virtual void init_style();
double init_one(int, int);
template <int SHIFT_FLAG, int EVFLAG, int EFLAG, int VFLAG_ATOM>
void eval();
static constexpr int NPARAMS_PER_LINE = 17;
protected:
@ -66,6 +69,9 @@ class PairTersoff : public Pair {
int maxshort; // size of short neighbor list array
int *neighshort; // short neighbor list array
int shift_flag; // flag to turn on/off shift
double shift; // negative change in equilibrium bond length
virtual void allocate();
virtual void read_file(char *);
virtual void setup_params();
@ -83,7 +89,8 @@ class PairTersoff : public Pair {
virtual double ters_bij(double, Param *);
virtual double ters_bij_d(double, Param *);
virtual void ters_zetaterm_d(double, double *, double, double *, double,
virtual void ters_zetaterm_d(double, double *, double, double,
double *, double, double,
double *, double *, double *, Param *);
void costheta_d(double *, double, double *, double,
double *, double *, double *);
@ -129,6 +136,7 @@ class PairTersoff : public Pair {
z[1] = k*x[1]+y[1];
z[2] = k*x[2]+y[2];
}
};
}

11
src/MANYBODY/pair_tersoff_mod.cpp
View File

@ -206,14 +206,13 @@ void PairTersoffMOD::setup_params()
/* ---------------------------------------------------------------------- */
double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
double *delrij, double *delrik)
double *rij_hat, double *rik_hat)
{
double rij,rik,costheta,arg,ex_delr;
rij = sqrt(rsqij);
rik = sqrt(rsqik);
costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
delrij[2]*delrik[2]) / (rij*rik);
costheta = vec3_dot(rij_hat,rik_hat);
if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
else arg = param->lam3 * (rij-rik);
@ -278,8 +277,8 @@ double PairTersoffMOD::ters_bij_d(double zeta, Param *param)
/* ---------------------------------------------------------------------- */
void PairTersoffMOD::ters_zetaterm_d(double prefactor,
double *rij_hat, double rij,
double *rik_hat, double rik,
double *rij_hat, double rij, double rijinv,
double *rik_hat, double rik, double rikinv,
double *dri, double *drj, double *drk,
Param *param)
{
@ -302,7 +301,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor,
cos_theta = vec3_dot(rij_hat,rik_hat);
gijk = ters_gijk_mod(cos_theta,param);
gijk_d = ters_gijk_d_mod(cos_theta,param);
costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
costheta_d(rij_hat,rijinv,rik_hat,rikinv,dcosdri,dcosdrj,dcosdrk);
// compute the derivative wrt Ri
// dri = -dfc*gijk*ex_delr*rik_hat;

3
src/MANYBODY/pair_tersoff_mod.h
View File

@ -41,7 +41,8 @@ class PairTersoffMOD : public PairTersoff {
double ters_fc_d(double, Param *);
double ters_bij(double, Param *);
double ters_bij_d(double, Param *);
void ters_zetaterm_d(double, double *, double, double *, double,
void ters_zetaterm_d(double, double *, double, double,
double *, double, double,
double *, double *, double *, Param *);
// inlined functions for efficiency

13
src/USER-MISC/pair_ilp_graphene_hbn.cpp
View File

@ -34,6 +34,7 @@
#include "my_page.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"
using namespace LAMMPS_NS;
@ -42,6 +43,16 @@ using namespace LAMMPS_NS;
#define DELTA 4
#define PGDELTA 1
static const char cite_ilp[] =
"@Article{Ouyang2018\n"
" author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
" title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
" journal = {Nano Letters},\n"
" volume = 18,\n"
" pages = {6009}\n"
" year = 2018,\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp)
@ -49,6 +60,8 @@ PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp)
restartinfo = 0;
one_coeff = 1;
if (lmp->citeme) lmp->citeme->add(cite_ilp);
nextra = 2;
pvector = new double[nextra];

13
src/USER-MISC/pair_kolmogorov_crespi_full.cpp
View File

@ -34,6 +34,7 @@
#include "my_page.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"
using namespace LAMMPS_NS;
@ -42,6 +43,16 @@ using namespace LAMMPS_NS;
#define DELTA 4
#define PGDELTA 1
static const char cite_kc[] =
"@Article{Ouyang2018\n"
" author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
" title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
" journal = {Nano Letters},\n"
" volume = 18,\n"
" pages = {6009}\n"
" year = 2018,\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp)
@ -49,6 +60,8 @@ PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp)
restartinfo = 0;
one_coeff = 1;
if (lmp->citeme) lmp->citeme->add(cite_kc);
nextra = 2;
pvector = new double[nextra];

47
src/USER-OMP/pair_tersoff_mod_c_omp.cpp
View File

@ -74,9 +74,12 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr)
tagint itag,jtag;
int itype,jtype,ktype,iparam_ij,iparam_ijk;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double fforce;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
double r1_hat[3],r2_hat[3];
double zeta_ij,prefactor;
double forceshiftfac;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
@ -132,11 +135,26 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr)
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
// shift rsq and store correction for force
if (shift_flag) {
double rsqtmp = rsq + shift*shift + 2*sqrt(rsq)*shift;
forceshiftfac = sqrt(rsqtmp/rsq);
rsq = rsqtmp;
}
iparam_ij = elem2param[itype][jtype][jtype];
if (rsq > params[iparam_ij].cutsq) continue;
double r1inv = 1.0/sqrt(vec3_dot(delr1, delr1));
vec3_scale(r1inv, delr1, r1_hat);
repulsive(&params[iparam_ij],rsq,fpair,EFLAG,evdwl);
// correct force for shift in rsq
if (shift_flag) fpair *= forceshiftfac;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
@ -162,8 +180,15 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr)
delr1[1] = x[j].y - ytmp;
delr1[2] = x[j].z - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (shift_flag)
rsq1 += shift*shift + 2*sqrt(rsq1)*shift;
if (rsq1 > params[iparam_ij].cutsq) continue;
double r1inv = 1.0/sqrt(vec3_dot(delr1, delr1));
vec3_scale(r1inv, delr1, r1_hat);
// accumulate bondorder zeta for each i-j interaction via loop over k
fjxtmp = fjytmp = fjztmp = 0.0;
@ -180,14 +205,23 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr)
delr2[1] = x[k].y - ytmp;
delr2[2] = x[k].z - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (shift_flag)
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
if (rsq2 > params[iparam_ijk].cutsq) continue;
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,delr1,delr2);
double r2inv = 1.0/sqrt(vec3_dot(delr2, delr2));
vec3_scale(r2inv, delr2, r2_hat);
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,r1_hat,r2_hat);
}
// pairwise force due to zeta
force_zeta(&params[iparam_ij],rsq1,zeta_ij,fpair,prefactor,EFLAG,evdwl);
force_zeta(&params[iparam_ij],rsq1,zeta_ij,fforce,prefactor,EFLAG,evdwl);
fpair = fforce*r1inv;
fxtmp += delr1[0]*fpair;
fytmp += delr1[1]*fpair;
@ -212,10 +246,17 @@ void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr)
delr2[1] = x[k].y - ytmp;
delr2[2] = x[k].z - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (shift_flag)
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
if (rsq2 > params[iparam_ijk].cutsq) continue;
double r2inv = 1.0/sqrt(vec3_dot(delr2, delr2));
vec3_scale(r2inv, delr2, r2_hat);
attractive(&params[iparam_ijk],prefactor,
rsq1,rsq2,delr1,delr2,fi,fj,fk);
rsq1,rsq2,r1_hat,r2_hat,fi,fj,fk);
fxtmp += fi[0];
fytmp += fi[1];

47
src/USER-OMP/pair_tersoff_mod_omp.cpp
View File

@ -76,9 +76,12 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr)
tagint itag,jtag;
int itype,jtype,ktype,iparam_ij,iparam_ijk;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double fforce;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
double r1_hat[3],r2_hat[3];
double zeta_ij,prefactor;
double forceshiftfac;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
@ -134,11 +137,26 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr)
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
// shift rsq and store correction for force
if (shift_flag) {
double rsqtmp = rsq + shift*shift + 2*sqrt(rsq)*shift;
forceshiftfac = sqrt(rsqtmp/rsq);
rsq = rsqtmp;
}
iparam_ij = elem2param[itype][jtype][jtype];
if (rsq > params[iparam_ij].cutsq) continue;
double r1inv = 1.0/sqrt(vec3_dot(delr1, delr1));
vec3_scale(r1inv, delr1, r1_hat);
repulsive(&params[iparam_ij],rsq,fpair,EFLAG,evdwl);
// correct force for shift in rsq
if (shift_flag) fpair *= forceshiftfac;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
@ -164,8 +182,15 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr)
delr1[1] = x[j].y - ytmp;
delr1[2] = x[j].z - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (shift_flag)
rsq1 += shift*shift + 2*sqrt(rsq1)*shift;
if (rsq1 > params[iparam_ij].cutsq) continue;
double r1inv = 1.0/sqrt(vec3_dot(delr1, delr1));
vec3_scale(r1inv, delr1, r1_hat);
// accumulate bondorder zeta for each i-j interaction via loop over k
fjxtmp = fjytmp = fjztmp = 0.0;
@ -182,14 +207,23 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr)
delr2[1] = x[k].y - ytmp;
delr2[2] = x[k].z - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (shift_flag)
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
if (rsq2 > params[iparam_ijk].cutsq) continue;
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,delr1,delr2);
double r2inv = 1.0/sqrt(vec3_dot(delr2, delr2));
vec3_scale(r2inv, delr2, r2_hat);
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,r1_hat,r2_hat);
}
// pairwise force due to zeta
force_zeta(&params[iparam_ij],rsq1,zeta_ij,fpair,prefactor,EFLAG,evdwl);
force_zeta(&params[iparam_ij],rsq1,zeta_ij,fforce,prefactor,EFLAG,evdwl);
fpair = fforce*r1inv;
fxtmp += delr1[0]*fpair;
fytmp += delr1[1]*fpair;
@ -214,10 +248,17 @@ void PairTersoffMODOMP::eval(int iifrom, int iito, ThrData * const thr)
delr2[1] = x[k].y - ytmp;
delr2[2] = x[k].z - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (shift_flag)
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
if (rsq2 > params[iparam_ijk].cutsq) continue;
double r2inv = 1.0/sqrt(vec3_dot(delr2, delr2));
vec3_scale(r2inv, delr2, r2_hat);
attractive(&params[iparam_ijk],prefactor,
rsq1,rsq2,delr1,delr2,fi,fj,fk);
rsq1,rsq2,r1_hat,r2_hat,fi,fj,fk);
fxtmp += fi[0];
fytmp += fi[1];

78
src/USER-OMP/pair_tersoff_omp.cpp
View File

@ -55,31 +55,48 @@ void PairTersoffOMP::compute(int eflag, int vflag)
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
if (evflag) {
if (eflag) {
if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else eval<0,0,0>(ifrom, ito, thr);
if (shift_flag) {
if (evflag) {
if (eflag) {
if (vflag_atom) eval<1,1,1,1>(ifrom, ito, thr);
else eval<1,1,1,0>(ifrom, ito, thr);
} else {
if (vflag_atom) eval<1,1,0,1>(ifrom, ito, thr);
else eval<1,1,0,0>(ifrom, ito, thr);
}
} else eval<1,0,0,0>(ifrom, ito, thr);
} else {
if (evflag) {
if (eflag) {
if (vflag_atom) eval<0,1,1,1>(ifrom, ito, thr);
else eval<0,1,1,0>(ifrom, ito, thr);
} else {
if (vflag_atom) eval<0,1,0,1>(ifrom, ito, thr);
else eval<0,1,0,0>(ifrom, ito, thr);
}
} else eval<0,0,0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int VFLAG_ATOM>
template <int SHIFT_FLAG, int EVFLAG, int EFLAG, int VFLAG_ATOM>
void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,k,ii,jj,kk,jnum,maxshort_thr;
tagint itag,jtag;
int itype,jtype,ktype,iparam_ij,iparam_ijk;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double fforce;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
double r1_hat[3],r2_hat[3];
double zeta_ij,prefactor;
double forceshiftfac;
int *ilist,*jlist,*numneigh,**firstneigh,*neighshort_thr;
evdwl = 0.0;
@ -126,6 +143,14 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
// shift rsq and store correction for force
if (SHIFT_FLAG) {
double rsqtmp = rsq + shift*shift + 2*sqrt(rsq)*shift;
forceshiftfac = sqrt(rsqtmp/rsq);
rsq = rsqtmp;
}
if (rsq < cutshortsq) {
neighshort_thr[numshort++] = j;
if (numshort >= maxshort_thr) {
@ -151,6 +176,10 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
repulsive(&params[iparam_ij],rsq,fpair,EFLAG,evdwl);
// correct force for shift in rsq
if (SHIFT_FLAG) fpair *= forceshiftfac;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
@ -175,8 +204,15 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
delr1[1] = x[j].y - ytmp;
delr1[2] = x[j].z - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (SHIFT_FLAG)
rsq1 += shift*shift + 2*sqrt(rsq1)*shift;
if (rsq1 >= params[iparam_ij].cutsq) continue;
double r1inv = 1.0/sqrt(vec3_dot(delr1, delr1));
vec3_scale(r1inv, delr1, r1_hat);
// accumulate bondorder zeta for each i-j interaction via loop over k
fjxtmp = fjytmp = fjztmp = 0.0;
@ -192,14 +228,23 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
delr2[1] = x[k].y - ytmp;
delr2[2] = x[k].z - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (SHIFT_FLAG)
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
if (rsq2 >= params[iparam_ijk].cutsq) continue;
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,delr1,delr2);
double r2inv = 1.0/sqrt(vec3_dot(delr2, delr2));
vec3_scale(r2inv, delr2, r2_hat);
zeta_ij += zeta(&params[iparam_ijk],rsq1,rsq2,r1_hat,r2_hat);
}
// pairwise force due to zeta
force_zeta(&params[iparam_ij],rsq1,zeta_ij,fpair,prefactor,EFLAG,evdwl);
force_zeta(&params[iparam_ij],rsq1,zeta_ij,fforce,prefactor,EFLAG,evdwl);
fpair = fforce*r1inv;
fxtmp += delr1[0]*fpair;
fytmp += delr1[1]*fpair;
@ -223,10 +268,17 @@ void PairTersoffOMP::eval(int iifrom, int iito, ThrData * const thr)
delr2[1] = x[k].y - ytmp;
delr2[2] = x[k].z - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (SHIFT_FLAG)
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
if (rsq2 >= params[iparam_ijk].cutsq) continue;
double r2inv = 1.0/sqrt(vec3_dot(delr2, delr2));
vec3_scale(r2inv, delr2, r2_hat);
attractive(&params[iparam_ijk],prefactor,
rsq1,rsq2,delr1,delr2,fi,fj,fk);
rsq1,rsq2,r1_hat,r2_hat,fi,fj,fk);
fxtmp += fi[0];
fytmp += fi[1];

2
src/USER-OMP/pair_tersoff_omp.h
View File

@ -33,7 +33,7 @@ class PairTersoffOMP : public PairTersoff, public ThrOMP {
virtual double memory_usage();
private:
template <int EVFLAG, int EFLAG, int VFLAG_ATOM>
template <int SHIFT_FLAG, int EVFLAG, int EFLAG, int VFLAG_ATOM>
void eval(int ifrom, int ito, ThrData * const thr);
};

2
src/USER-OMP/pair_tersoff_zbl_omp.cpp
View File

@ -219,7 +219,7 @@ void PairTersoffZBLOMP::force_zeta(Param *param, double rsq, double zeta_ij,
- ters_fc(r,param) * F_fermi_d(r,param->ZBLexpscale,param->ZBLcut));
bij = ters_bij(zeta_ij,param);
fforce = 0.5*bij*fa_d / r;
fforce = 0.5*bij*fa_d;
prefactor = -0.5*fa * ters_bij_d(zeta_ij,param);
if (eflag) eng = 0.5*bij*fa;
}

4
unittest/force-styles/test_pair_style.cpp
View File

@ -831,7 +831,9 @@ TEST(PairStyle, intel)
GTEST_SKIP();
}
if ((test_config.pair_style == "rebo") || utils::strmatch(test_config.pair_style, "^dpd")) {
if ((test_config.pair_style == "rebo")
|| utils::strmatch(test_config.pair_style, "^dpd")
|| utils::strmatch(test_config.pair_style, "^tersoff.* shift ")) {
std::cerr << "Skipping pair style " << lmp->force->pair_style << "\n";
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);

155
unittest/force-styles/tests/manybody-pair-tersoff_mod_c_shift.yaml Normal file
View File

@ -0,0 +1,155 @@
---
lammps_version: 24 Dec 2020
date_generated: Mon Jan 11 03:57:49 202
epsilon: 1e-12
prerequisites: ! |
pair tersoff/mod/c
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
post_commands: ! ""
input_file: in.manybody
pair_style: tersoff/mod/c shift -0.001
pair_coeff: ! |
* * Si.tersoff.modc Si Si Si Si Si Si Si Si
extract: ! ""
natoms: 64
init_vdwl: -270.144069879548
init_coul: 0
init_stress: ! |2-
3.9009683820158699e+01 4.1712442670553941e+01 4.6810691626449191e+01 -4.8650488078636389e+00 4.8866660639888494e+01 1.1391803040419603e+01
init_forces: ! |2
1 -1.1173716272516789e+00 3.3109586327606744e+00 1.7302861475787994e+00
2 -2.6342753750130683e+00 -1.1403560562924286e+00 -2.3901186557684757e+00
3 1.2479875429864278e+00 -2.2663006997882817e-02 -8.9996700326808798e-01
4 -2.9211674286187548e+00 3.4983061991416058e+00 1.2669247300246793e+00
5 -2.1675011144850376e+00 -5.0217578461526347e-01 1.7105271274405709e-01
6 6.2824954938181765e-01 4.1217127031288783e+00 1.7204090495344515e+00
7 -7.2619625442116420e-01 -8.7964777297310381e-01 3.2018428144019415e+00
8 3.5206357823879997e-01 9.6381791420204954e-01 -1.2860305798339342e+00
9 -8.9678243104762689e-02 -3.7443401531769585e+00 -3.2223564420242132e+00
10 -3.1541401492154175e-02 -2.3464248918588106e+00 -3.0987275312413014e+00
11 4.2014256907318686e+00 -4.8637357805319041e+00 3.8406536624461323e+00
12 -9.6944024792053192e+00 -6.6352124723672885e+00 -4.6651918902499370e+00
13 1.8733910234257256e-01 8.0063627281481402e+00 -2.7365433765098626e+00
14 -2.7766558733653817e+00 5.6132867687761410e+00 -4.0624346392600319e-01
15 -7.2905272255153912e+00 8.3629972472941301e+00 -3.2621951682319246e+00
16 3.2905046878670277e+00 1.4733622272834496e-01 9.9930989568566400e+00
17 1.8234393526686401e+00 5.6303260914876159e+00 -6.6900775620274109e+00
18 -2.8962213997409370e-01 7.0700548977173261e-01 4.3799750053804019e+00
19 -1.7857871258441089e+00 -3.2851157595133302e+00 -8.1382343591280071e-01
20 -9.9695940614268874e+00 -4.3691669537165811e-01 2.9007948519739939e+00
21 4.0782998494290297e+00 2.5002152762636358e+00 -3.9369045552072901e+00
22 -8.5010243348339181e+00 6.8782066736408982e+00 -7.2310397022477400e+00
23 2.5213223345753955e+00 5.0922956471783847e+00 1.6208002764334704e+00
24 2.7580296681021066e+00 1.7386510263129471e+00 3.6679841712231784e+00
25 1.0252536574439250e+00 3.9244781228364167e-02 1.5588211261866818e+00
26 -6.9778754276018118e-01 -1.3570798101907440e+00 2.0564657828178792e+00
27 2.8986453721866456e+00 -2.5917236253556647e-01 1.7077037950475380e+00
28 7.8465782726392108e-01 2.2547202678110634e+00 5.6995473335322711e+00
29 -3.8015262677685686e+00 1.1989004955442599e+00 -1.8647113329774676e+00
30 -1.5715129394298437e+00 1.3842312628741091e+00 -1.0456701818034704e+00
31 -1.4897698702486464e+00 2.2007435905694872e+00 9.0398497947792644e-02
32 -3.3051289001463600e+00 6.2541690190316102e-01 -1.2919765628100222e+00
33 6.9295965162529853e+00 -4.6855709035720698e+00 4.5473389931983572e+00
34 5.9943580669732865e-01 5.0617068503431728e-02 2.1178136441259143e-01
35 1.3921291137974459e+00 2.2418896585084624e-01 3.1797777991155276e+00
36 -7.2428864271959037e-01 -2.9573659323803683e+00 1.5976210983613715e-01
37 -2.2234148634296855e+00 1.5860119120352065e+00 -2.5479898456769083e+00
38 -7.4823804393825977e-01 -7.1295876839157746e-01 6.9809508667929410e-01
39 5.0785547594244482e+00 -7.1930212714073338e-01 -5.9276817117501652e+00
40 5.1245358404288801e+00 -2.6680019748925852e+00 -3.0417700554546037e+00
41 -1.5518280827841124e-02 -1.0005121969962949e+00 -7.7867766182110909e-01
42 -5.8806209372013152e+00 -3.2273730282518116e+00 7.3578542562157712e-01
43 2.1124604022474096e+00 -7.5431014454569159e+00 -1.0811805712004026e+00
44 6.3287851826618340e+00 -6.7528471241890777e+00 1.1247477569599389e+00
45 -2.7299671204604028e+00 2.5692725743333424e+00 -3.7213565280111505e+00
46 8.1218821749530878e-02 -2.0252882869408646e+00 7.0485630693978720e+00
47 3.3380550458022347e+00 2.1589370003355057e+00 1.2514493030053107e+00
48 1.2640794226048300e+00 -5.5962707627217112e-02 -4.0272905054995661e-01
49 -3.4157571320376028e+00 -6.1295035666736855e+00 -3.5432651832916466e+00
50 -1.2234964912331092e+00 4.1973728786034270e+00 -2.5642859385774508e+00
51 -2.3823468455205550e+00 3.4306555183787362e+00 5.0803042140735073e+00
52 7.5203863161925986e+00 -8.0170421745756251e+00 7.3361098652956755e+00
53 4.8736993345086530e+00 4.5427918027068221e+00 2.4358795316149320e+00
54 3.4091438050901699e+00 -4.0344938491640754e+00 -2.4887755586549232e+00
55 2.0643852492223900e+00 -4.5150631679692914e+00 -5.8753746462775407e+00
56 -8.2187309607559600e-01 1.0691103354949494e-02 -2.5046624669464554e+00
57 1.9284684258335791e-01 -1.3992808180700229e+00 -1.8258079363547955e-01
58 2.7953327747251429e+00 -1.4805384976490406e+00 1.8748424393367924e+00
59 3.9433586018736104e+00 2.9233334663681720e+00 -3.6625177028423468e+00
60 -5.2228824961236668e+00 -8.3900954959495913e+00 -5.4196336011933104e+00
61 -8.8070206277929552e-01 2.1267386126438721e+00 -1.4693251720512399e+00
62 -4.7979190616865797e+00 4.3434102172669791e+00 -2.6756525986102213e+00
63 3.8865402117110119e+00 -6.6984406381466162e+00 6.8155291040779375e-01
64 5.1963330181467731e+00 6.0468262093154790e+00 1.0756287747499645e+01
run_vdwl: -270.147719451179
run_coul: 0
run_stress: ! |2-
3.8962163987527319e+01 4.1632267398787846e+01 4.6901025481128798e+01 -4.7107503318061195e+00 4.8780605963278717e+01 1.1878434080817474e+01
run_forces: ! |2
1 -1.1195037281603057e+00 3.3034434205914920e+00 1.7330179921283344e+00
2 -2.6261355780809836e+00 -1.1779211363483650e+00 -2.3788698683400558e+00
3 1.2113802651789900e+00 -8.5846198620282976e-03 -8.7116105473782901e-01
4 -2.8885951358444770e+00 3.5006501432344930e+00 1.2312123379860225e+00
5 -2.1831892475177512e+00 -5.1036758539283067e-01 1.8635786504929341e-01
6 6.8661399810394930e-01 4.1310963287496634e+00 1.7546746413906325e+00
7 -7.0198715858811056e-01 -8.4811017970678915e-01 3.1743158467327701e+00
8 3.3622176399366066e-01 9.5272926739276143e-01 -1.2814975762263769e+00
9 -1.2762830595653840e-01 -3.7790083764444735e+00 -3.2544275991463332e+00
10 -3.9514482476306192e-02 -2.3518523303990606e+00 -3.0442173239995549e+00
11 4.1429788769734284e+00 -4.8121901687300612e+00 3.8116323085857604e+00
12 -9.6850677239499277e+00 -6.6103785401971464e+00 -4.6150992561940702e+00
13 2.9145069827431891e-01 7.9986954019430465e+00 -2.6896746529264415e+00
14 -2.8145842522124624e+00 5.6198174361402682e+00 -4.3043355368744834e-01
15 -7.2777883159887438e+00 8.3401909614991165e+00 -3.2247080759197377e+00
16 3.2712587381653484e+00 1.7167944442984362e-01 9.9147308015175195e+00
17 1.8032743903561275e+00 5.6183321020364607e+00 -6.6441110771787946e+00
18 -3.3114136802713923e-01 7.3624686696541541e-01 4.3974842390969542e+00
19 -1.8266166165290070e+00 -3.3133522513570464e+00 -8.4975857709798830e-01
20 -9.9137551188949082e+00 -4.7673208245676602e-01 2.8505302828969090e+00
21 4.0763035034367210e+00 2.4342732269959337e+00 -3.9639654195103855e+00
22 -8.4722107478051925e+00 6.8743183611498484e+00 -7.2373252379598227e+00
23 2.5598965562113682e+00 5.1270156872713999e+00 1.6376733213763552e+00
24 2.8003576429477244e+00 1.7207767400904177e+00 3.6485255621239157e+00
25 1.0266241443572584e+00 4.7842258168785456e-02 1.5385828662233976e+00
26 -7.2161630733228976e-01 -1.3538766450428663e+00 2.0774583349947746e+00
27 2.9172211765053486e+00 -2.9283065512199297e-01 1.7199838302568207e+00
28 7.5500583919036357e-01 2.2998189870411343e+00 5.7160957003230921e+00
29 -3.8118579612327887e+00 1.2089386115853937e+00 -1.8717531605562789e+00
30 -1.5491992627748359e+00 1.3637804457345033e+00 -1.0510140288499303e+00
31 -1.4829752246906760e+00 2.2174421999021132e+00 9.3177962644967582e-02
32 -3.2866131991366019e+00 6.0651899337798243e-01 -1.3061439069096379e+00
33 6.8808318027892188e+00 -4.6659214567845400e+00 4.5373373537359614e+00
34 5.9255028757483941e-01 5.1639086392120781e-02 2.1554792215895313e-01
35 1.4003681186614290e+00 2.3875131357295976e-01 3.1835436962002115e+00
36 -7.6764735106380511e-01 -2.9438000295903510e+00 1.2084770661188927e-01
37 -2.2104945971260679e+00 1.5652695194240802e+00 -2.5549352049796985e+00
38 -7.3656255936035997e-01 -7.0714714971015491e-01 7.0472479499898655e-01
39 5.0236662692472009e+00 -7.1753463478173618e-01 -5.8887887679592126e+00
40 5.1850979003834325e+00 -2.6923807384431466e+00 -3.0694479624717319e+00
41 1.0821581971298677e-02 -9.7157383831061239e-01 -7.5618360110306648e-01
42 -5.8530161410211203e+00 -3.2303236763848266e+00 6.8678919083831114e-01
43 2.0846856267668881e+00 -7.5087401579467477e+00 -1.1012347548426082e+00
44 6.3518612233350735e+00 -6.7640518284681166e+00 1.1060450097787580e+00
45 -2.7465124895859225e+00 2.5279449066561503e+00 -3.7003815935159539e+00
46 7.4858987134390653e-02 -2.0238445024552023e+00 7.0813430489495595e+00
47 3.3461650608873414e+00 2.1445696167712001e+00 1.2587419040428063e+00
48 1.2667990698009335e+00 -2.4341430363435335e-02 -4.1167887931108327e-01
49 -3.4944023515728810e+00 -6.2299209783876552e+00 -3.6219570597062343e+00
50 -1.2284916356102240e+00 4.2052196550920913e+00 -2.6039269212215150e+00
51 -2.4430495020181269e+00 3.4818669367591002e+00 5.1066333217407553e+00
52 7.5165381894373207e+00 -7.9880007248651248e+00 7.3324833594869752e+00
53 4.9366266919828394e+00 4.6175050994962552e+00 2.5484353944014431e+00
54 3.3933981274505474e+00 -4.0312449714063359e+00 -2.4814211580014942e+00
55 2.0173646244855474e+00 -4.4826704573826550e+00 -5.8170530531309037e+00
56 -8.2773350734424855e-01 -3.4183501298294505e-02 -2.5003485880874341e+00
57 1.8814673223574310e-01 -1.4335987285737317e+00 -1.8662921315508882e-01
58 2.7970333676895960e+00 -1.4555529096442483e+00 1.8464051983238567e+00
59 3.9746969718749958e+00 2.9548867851808174e+00 -3.6651069099861551e+00
60 -5.3286587551296112e+00 -8.4827924229151499e+00 -5.5167561536702774e+00
61 -8.6221352727030132e-01 2.1435262658503302e+00 -1.4697646542540870e+00
62 -4.7849482113350135e+00 4.3211526727812579e+00 -2.6531595521322231e+00
63 3.8957390027738494e+00 -6.7363618973736177e+00 6.4318019416858729e-01
64 5.3278731334596312e+00 6.1332518638686553e+00 1.0855422408004880e+01
...

155
unittest/force-styles/tests/manybody-pair-tersoff_mod_shift.yaml Normal file
View File

@ -0,0 +1,155 @@
---
lammps_version: 24 Dec 2020
date_generated: Mon Jan 11 03:57:49 202
epsilon: 5e-11
prerequisites: ! |
pair tersoff/mod
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
post_commands: ! ""
input_file: in.manybody
pair_style: tersoff/mod shift -0.001
pair_coeff: ! |
* * Si.tersoff.mod Si Si Si Si Si Si Si Si
extract: ! ""
natoms: 64
init_vdwl: -271.644724447578
init_coul: 0
init_stress: ! |2-
4.6467578511150705e+01 4.9672630447521129e+01 5.1076156386253835e+01 -9.5884521777215621e+00 3.2774050937983333e+01 3.8044769072311828e+00
init_forces: ! |2
1 -1.1945327845016744e+00 3.4404347943712756e+00 1.7962743648862558e+00
2 -2.1071475352987754e+00 -1.7688444203665936e+00 -1.8620466055365370e+00
3 1.1899962745991819e+00 1.7437113666502135e-02 -9.0625021511005799e-01
4 -2.5304413212324115e+00 3.0648781519545678e+00 8.6022564695336801e-01
5 -2.2401753389024321e+00 -4.0336905351600261e-01 1.2406956659205726e-01
6 6.9650957270644254e-01 4.0905468831677085e+00 1.5325178170433358e+00
7 -8.6911675556130641e-01 -9.4735576249996667e-01 3.4885785686084727e+00
8 3.0074079056337677e-01 9.5669168244327940e-01 -1.3691402501040602e+00
9 -6.9338849568836602e-01 -2.8820619168445445e+00 -2.4856795964568192e+00
10 4.6638520371908854e-02 -2.2785527912364159e+00 -3.1821844995343413e+00
11 3.7221930078457590e+00 -4.4479312723103002e+00 3.5868933819134727e+00
12 -6.2450663880790014e+00 -4.2877677616135426e+00 -3.8805345552078281e+00
13 -1.0588589449879247e+00 5.9766828377143266e+00 -1.2578380123576507e+00
14 -1.9615356414615313e+00 4.9688993945891760e+00 7.6331845597450737e-02
15 -4.3834396738712638e+00 5.2217595464037094e+00 -3.9049543497684303e+00
16 2.0452533059859110e+00 4.2601532928650043e-02 7.3659239299753052e+00
17 2.5955719288406867e+00 3.3972007119179901e+00 -4.3707785213745058e+00
18 -2.0528492944347110e-01 1.1471639456647598e-01 4.0098987701532032e+00
19 -1.7237575351349257e+00 -3.3052557476877595e+00 -6.7652826999219351e-01
20 -6.7138568668931251e+00 6.5860974348566703e-01 8.5948993917890526e-01
21 1.9742114073881845e+00 5.8505490808742078e-01 -2.1525493396585862e+00
22 -6.5058811573652031e+00 5.2782453056661804e+00 -5.8675430701230553e+00
23 2.2023083360587870e+00 3.8802430704792332e+00 1.6261847563909013e+00
24 2.5226014816919888e+00 1.4689423245850439e+00 3.4535672253796781e+00
25 1.0550765980632510e+00 -5.3725947013416431e-02 1.5948717710546678e+00
26 5.8080754067770066e-02 -5.7564368537117383e-01 1.3164234920286564e+00
27 2.9182515510729137e+00 -5.2719126822087592e-01 1.7948235547117499e+00
28 8.9783882698739337e-01 2.0048959669364672e+00 4.7828622399508305e+00
29 -3.8046886336210015e+00 1.3518947542714881e+00 -1.9318483702658500e+00
30 -1.6196111626379648e+00 1.3938538157693876e+00 -1.0864768932321174e+00
31 -1.3214441563505464e+00 1.8918181985012741e+00 -2.7284909414037040e-01
32 -3.2854645445409112e+00 7.1270991044565513e-01 -1.2751668537430956e+00
33 5.3106047885833760e+00 -3.4116023667986290e+00 3.6673370068697690e+00
34 7.9570462198642677e-01 -1.0644951408487513e-01 1.3257555770959684e-01
35 1.4117929491838686e+00 2.4555833176987729e-02 3.3295422980603511e+00
36 -5.9274271412219603e-01 -3.0880957224444074e+00 7.4528435144694288e-02
37 -2.1955951970825303e+00 1.8425382007214959e+00 -2.6058340998466032e+00
38 -8.4045337400840647e-01 -5.1220996003306629e-01 7.5733931697378054e-01
39 3.2060404384981487e+00 -1.7982148830366791e+00 -3.8355125579045843e+00
40 5.0343863951967345e+00 -2.4475586408802559e+00 -2.8014822479801271e+00
41 -2.2950777077556328e-02 -9.5823298812488811e-01 -8.4366462899746586e-01
42 -3.7486997507888815e+00 -1.5032117300840788e+00 -6.6561054578331036e-01
43 8.2336674271162202e-01 -5.6775961548555118e+00 3.5051778727725813e-01
44 3.7235516362464245e+00 -4.0460873219480460e+00 2.4473727620865819e+00
45 -2.5462650466866013e+00 2.3633058120250174e+00 -3.3828495858745562e+00
46 -8.0735831619483456e-01 -1.8147929806890615e+00 5.9496202714573361e+00
47 3.2308721712834281e+00 2.1100733377780463e+00 1.1141268607872858e+00
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run_vdwl: -271.634962995706
run_coul: 0
run_stress: ! |2-
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run_forces: ! |2
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64 3.6027960550152676e+00 3.8649252631032383e+00 5.8903421688741702e+00
...

155
unittest/force-styles/tests/manybody-pair-tersoff_shift.yaml Normal file
View File

@ -0,0 +1,155 @@
---
lammps_version: 24 Dec 2020
date_generated: Mon Jan 11 03:57:49 202
epsilon: 5e-13
prerequisites: ! |
pair tersoff
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
post_commands: ! ""
input_file: in.manybody
pair_style: tersoff shift -0.001
pair_coeff: ! |
* * SiC.tersoff Si Si Si Si C C C C
extract: ! ""
natoms: 64
init_vdwl: -163.865146267879
init_coul: 0
init_stress: ! |-
-5.5024582031400666e+02 -5.4774409204093763e+02 -5.6246628126776079e+02 -1.4924154780208189e+01 -1.3705992344344143e+01 5.3802808177851460e+01
init_forces: ! |2
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63 -6.1744135275042584e+00 -4.9438000546782721e+00 -5.2824439552248172e+00
64 5.0707719795244213e+00 5.2903461624479675e+00 -8.6920086960823717e+00
run_vdwl: -163.941878707801
run_coul: 0
run_stress: ! |-
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run_forces: ! |2
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...

155
unittest/force-styles/tests/manybody-pair-tersoff_zbl_shift.yaml Normal file
View File

@ -0,0 +1,155 @@
---
lammps_version: 24 Dec 2020
date_generated: Mon Jan 11 03:57:49 202
epsilon: 5e-11
prerequisites: ! |
pair tersoff/zbl
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
post_commands: ! ""
input_file: in.manybody
pair_style: tersoff/zbl shift -0.001
pair_coeff: ! |
* * SiC.tersoff.zbl Si Si Si Si C C C C
extract: ! ""
natoms: 64
init_vdwl: -155.022688586515
init_coul: 0
init_stress: ! |-
-5.4681450061751207e+02 -5.4765383545405757e+02 -5.5958816472819717e+02 -1.7937919946334258e+01 -7.4255270557571622e+00 5.3848489658845857e+01
init_forces: ! |2
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63 -5.7748251912125133e+00 -5.8348082998315114e+00 -4.9427609042011902e+00
64 5.1516801198779412e+00 5.3652063468862412e+00 -7.4260492325704002e+00
run_vdwl: -155.089673421163
run_coul: 0
run_stress: ! |-
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run_forces: ! |2
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...