ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #1843 from oywg11/new-ILP-parameters

Browse Source 
New ILP paramters  and pair style improvements
This commit is contained in:
Axel Kohlmeyer
2020-01-16 16:53:59 -05:00
committed by GitHub
parent f1c79fb914 96cc098dc1
commit 868df1f640
11 changed files with 69 additions and 353 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
doc/src/Commands_fix.rst
View File

@ -239,3 +239,8 @@ OPT.
* :doc:`wall/region <fix_wall_region>`
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`
*
*
*
*
*

20
doc/src/pair_ilp_graphene_hbn.rst
View File

@ -82,15 +82,15 @@ list for calculating the normals for each atom pair.
.. note::
Two new sets of parameters of ILP for two-dimensional hexagonal
Materials are presented in :ref:`(Ouyang) <Ouyang>`. These parameters provide
a good description in both short- and long-range interaction regimes.
Four new sets of parameters of ILP for 2D layered Materials with bilayer and
bulk configurations are presented in :ref:`(Ouyang1) <Ouyang1>` and :ref:`(Ouyang2) <Ouyang2>`, respectively.
These parameters provide a good description in both short- and long-range interaction regimes.
While the old ILP parameters published in :ref:`(Leven2) <Leven2>` and
:ref:`(Maaravi) <Maaravi2>` are only suitable for long-range interaction
regime. This feature is essential for simulations in high pressure
regime (i.e., the interlayer distance is smaller than the equilibrium
distance). The benchmark tests and comparison of these parameters can
be found in :ref:`(Ouyang) <Ouyang>`.
distance). The benchmark tests and comparison of these parameters can
be found in :ref:`(Ouyang1) <Ouyang1>` and :ref:`(Ouyang2) <Ouyang2>`.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair\_style *none*\ .
@ -185,11 +185,17 @@ Related commands
**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
.. _Ouyang:
.. _Ouyang1:
**(Ouyang)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
.. _Ouyang2:
**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
.. _lws: http://lammps.sandia.gov

14
doc/src/pair_kolmogorov_crespi_full.rst
View File

@ -70,7 +70,7 @@ list for calculating the normals for each atom pair.
Two new sets of parameters of KC potential for hydrocarbons, CH.KC
(without the taper function) and CH\_taper.KC (with the taper function)
are presented in :ref:`(Ouyang) <Ouyang1>`. The energy for the KC potential
are presented in :ref:`(Ouyang1) <Ouyang3>`. The energy for the KC potential
with the taper function goes continuously to zero at the cutoff. The
parameters in both CH.KC and CH\_taper.KC provide a good description in
both short- and long-range interaction regimes. While the original
@ -78,7 +78,7 @@ list for calculating the normals for each atom pair.
suitable for long-range interaction regime. This feature is essential
for simulations in high pressure regime (i.e., the interlayer distance
is smaller than the equilibrium distance). The benchmark tests and
comparison of these parameters can be found in :ref:`(Ouyang) <Ouyang1>`.
comparison of these parameters can be found in :ref:`(Ouyang1) <Ouyang3>` and :ref:`(Ouyang2) <Ouyang4>`.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair\_style *none*\ .
@ -154,11 +154,17 @@ Related commands
**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
.. _Ouyang1:
.. _Ouyang3:
**(Ouyang)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
.. _Ouyang4:
**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
.. _lws: http://lammps.sandia.gov

159
doc/txt/pair_ilp_graphene_hbn.txt
View File

@ -1,159 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style ilp/graphene/hbn command :h3
[Syntax:]
pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function :ul
[Examples:]
pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
pair_style hybrid/overlay rebo tersoff 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 :pre
[Description:]
The {ilp/graphene/hbn} style computes the registry-dependent interlayer
potential (ILP) potential as described in "(Leven1)"_#Leven1,
"(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2.
The normals are calculated in the way as described
in "(Kolmogorov)"_#Kolmogorov2.
:c,image(Eqs/pair_ilp_graphene_hbn.jpg)
Where Tap(r_ij) is the taper function which provides a continuous
cutoff (up to third derivative) for interatomic separations larger than
r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above
equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2.
It is important to include all the pairs to build the neighbor list for
calculating the normals.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.
To perform a realistic simulation, this potential must be used in combination with
intralayer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intralayer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intralayer potential and atoms residing on different layers
interact via the ILP. Here, the molecule id is chosen as the layer identifier,
thus a data file with the "full" atom style is required to use this potential.
The parameter file (e.g. BNCH.ILP), is intended for use with {metal}
"units"_units.html, with energies in meV. Two additional parameters,
{S}, and {rcut} are included in the parameter file. {S} is designed to
facilitate scaling of energies. {rcut} is designed to build the neighbor
list for calculating the normals for each atom pair.
NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful.
The parameters for atoms pairs between Boron and Nitrogen are fitted with
a screened Coulomb interaction "coul/shield"_pair_coul_shield.html. Therefore,
to simulated the properties of h-BN correctly, this potential must be used in
combination with the pair style "coul/shield"_pair_coul_shield.html.
NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal
Materials are presented in "(Ouyang)"_#Ouyang. These parameters provide
a good description in both short- and long-range interaction regimes.
While the old ILP parameters published in "(Leven2)"_#Leven2 and
"(Maaravi)"_#Maaravi2 are only suitable for long-range interaction
regime. This feature is essential for simulations in high pressure
regime (i.e., the interlayer distance is smaller than the equilibrium
distance). The benchmark tests and comparison of these parameters can
be found in "(Ouyang)"_#Ouyang.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html command as a vector of values of length 2.
The 2 values correspond to the following sub-categories:
{E_vdW} = vdW (attractive) energy
{E_Rep} = Repulsive energy :ol
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
compute 0 all pair ilp/graphene/hbn
variable Evdw equal c_0\[1\]
variable Erep equal c_0\[2\]
thermo_style custom step temp epair v_Erep v_Evdw :pre
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support the pair_modify mix, shift, table, and
tail options.
This pair style does not write their information to binary restart
files, since it is stored in potential files. Thus, you need to
re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
The BNCH.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for {metal} units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use {metal} units.
[Related commands:]
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
"pair_style pair_coul_shield"_pair_coul_shield.html.
[Default:] tap_flag = 1
:line
:link(Leven1)
[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
:link(Leven2)
[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
:link(Maaravi2)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
:link(Kolmogorov2)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
:link(Ouyang)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

138
doc/txt/pair_kolmogorov_crespi_full.txt
View File

@ -1,138 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style kolmogorov/crespi/full command :h3
[Syntax:]
pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function :ul
[Examples:]
pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
pair_coeff * * none
pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
pair_coeff * * rebo CH.rebo C H
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre
[Description:]
The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi (KC)
interaction potential as described in "(Kolmogorov)"_#Kolmogorov1.
No simplification is made,
:c,image(Eqs/pair_kolmogorov_crespi_full.jpg)
It is important to have a sufficiently large cutoff to ensure smooth
forces and to include all the pairs to build the neighbor list for
calculating the normals. Energies are shifted so that they go
continuously to zero at the cutoff assuming that the exponential part of
{Vij} (first term) decays sufficiently fast. This shift is achieved by
the last term in the equation for {Vij} above. This is essential only
when the tapper function is turned off. The formula of taper function
can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene. To perform a realistic simulation, this potential
must be used in combination with intralayer potential, such as
"AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intralayer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intralayer potential and atoms residing on different layers
interact via the ILP. Here, the molecule id is chosen as the layer identifier,
thus a data file with the "full" atom style is required to use this potential.
The parameter file (e.g. CH.KC), is intended for use with {metal}
"units"_units.html, with energies in meV. Two additional parameters, {S},
and {rcut} are included in the parameter file. {S} is designed to
facilitate scaling of energies. {rcut} is designed to build the neighbor
list for calculating the normals for each atom pair.
NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC
(without the taper function) and CH_taper.KC (with the taper function)
are presented in "(Ouyang)"_#Ouyang1. The energy for the KC potential
with the taper function goes continuously to zero at the cutoff. The
parameters in both CH.KC and CH_taper.KC provide a good description in
both short- and long-range interaction regimes. While the original
parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 are only
suitable for long-range interaction regime. This feature is essential
for simulations in high pressure regime (i.e., the interlayer distance
is smaller than the equilibrium distance). The benchmark tests and
comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html command as a vector of values of length 2.
The 2 values correspond to the following sub-categories:
{E_vdW} = vdW (attractive) energy
{E_Rep} = Repulsive energy :ol
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
compute 0 all pair kolmogorov/crespi/full
variable Evdw equal c_0\[1\]
variable Erep equal c_0\[2\]
thermo_style custom step temp epair v_Erep v_Evdw :pre
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support the pair_modify mix, shift, table,
and tail options.
This pair style does not write their information to binary restart
files, since it is stored in potential files. Thus, you need to
re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
The CH.KC potential file provided with LAMMPS (see the potentials
folder) are parameterized for metal units. You can use this potential
with any LAMMPS units, but you would need to create your own custom
CC.KC potential file with all coefficients converted to the appropriate
units.
[Related commands:]
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style drip"_pair_drip.html,
"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
[Default:] tap_flag = 0
:line
:link(Kolmogorov1)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
:link(Ouyang1)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

6
potentials/BNCH-old.ILP
View File

@ -1,8 +1,8 @@
# Interlayer Potential for graphitic and boron nitride systems
#
# Interlayer Potential (ILP) for bilayer graphene/graphene, graphene/hBN and hBN/hBN junctions
# The parameters below are fitted against the HSE + MBD DFT referece data from 3.1 A to 15 A.
# Cite J. Chem.Theory Comput. 2016, 12, 2896-905 and J. Phys. Chem. C 2017, 121, 22826-22835.
# beta alpha delta epsilon C d sR reff C6 S rcut
# beta alpha delta epsilon C d sR reff C6 S rcut
C C 3.22 9.200 1.20 0.010 0.800 15.0 0.704 3.586 522.915 43.363442016573508 2.0
B B 3.10 8.000 1.60 0.460 0.450 15.0 0.800 3.786 1037.322 43.363442016573508 2.0
N N 3.34 8.000 1.20 0.210 0.680 15.0 0.800 3.365 310.433 43.363442016573508 2.0

4
potentials/BNCH.ILP
View File

@ -1,5 +1,5 @@
# Interlayer Potential (ILP) for graphene/graphene, graphene/hBN and hBN/hBN junctions
#
# Interlayer Potential (ILP) for bilayer graphene/graphene, graphene/hBN and hBN/hBN junctions
# The parameters below are fitted against the HSE + MBD DFT referece data from 2.5 A to 15 A.
# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
#
# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************

16
potentials/BNC_MBD_bulk.ILP Normal file
View File

@ -0,0 +1,16 @@
# Interlayer Potential (ILP) for graphite, bulk-hBN and their heterojunctions
# The parameters below are fitted against the HSE + MBD DFT referece data from 2 A to 10 A.
# Cite as W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
#
# ------------------------------ Repulsion Potential --------------------++++++++++++++ Vdw Potential ++++++++++++++++************
# MBD-HSE beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
C C 3.1894274136 8.2113165501 1.2600313066 0.0106237125 38.9820878926 10.9736146687 0.7869029010 3.4578620004 25249.6185284695 1.0000 2.0
B B 3.2146562020 7.1651845022 1.7458546494 11.0735774589 15.4819142891 15.4815063183 0.8550308760 3.4423900567 49498.4383474008 1.0000 2.0
N N 3.3006476373 6.9225730132 1.4844871606 7.9907993147 46.6114968784 16.9081462104 0.7584806746 3.3265576243 14810.6448568309 1.0000 2.0
B N 3.1708595336 8.5168240743 2.8657479230 5.4561495348 2.5548134497 13.5321053144 0.8863432069 3.4553049811 24670.8164462408 1.0000 2.0
C B 3.1007371653 5.1145801996 3.8386588076 18.2345048230 1.1901887968 10.2155326647 0.7686152602 3.5030009241 39262.8518949659 1.0000 2.0
C N 3.3172548125 10.3496923621 1.3792655319 16.3162761182 19.5690538017 15.7748377566 0.5645056777 3.2659337344 19963.0795570299 1.0000 2.0
# Symmetric part
B C 3.1007371653 5.1145801996 3.8386588076 18.2345048230 1.1901887968 10.2155326647 0.7686152602 3.5030009241 39262.8518949659 1.0000 2.0
N C 3.3172548125 10.3496923621 1.3792655319 16.3162761182 19.5690538017 15.7748377566 0.5645056777 3.2659337344 19963.0795570299 1.0000 2.0
N B 3.1708595336 8.5168240743 2.8657479230 5.4561495348 2.5548134497 13.5321053144 0.8863432069 3.4553049811 24670.8164462408 1.0000 2.0

16
potentials/BNC_TS_bulk.ILP Normal file
View File

@ -0,0 +1,16 @@
# Interlayer Potential (ILP) for graphite, bulk-hBN and their heterojunctions
# The parameters below are fitted against the HSE + TS DFT referece data from 2 A to 10 A.
# Cite as W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
#
# ------------------------------ Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
# TS-HSE beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
C C 3.1911991861 8.8422960372 1.1312263335 0.0863236828 33.4354373112 10.0195636456 0.9251350921 3.4842048950 32402.5447674022 1.0000 2.0
B B 3.5386170858 5.1268088040 2.2006291426 12.8752511690 27.5894275824 13.3599605541 0.8414408912 3.6431051884 99513.2942026427 1.0000 2.0
N N 3.5915052274 3.2218485106 1.4354352315 6.6765695916 73.1025964821 13.0709665964 0.7465905646 3.3082847788 74823.5568235260 1.0000 2.0
B N 3.9928670174 7.8553264966 2.5853334572 4.5784769626 2.3283590129 16.2664653527 0.8669270315 3.9824166141 84699.9699356515 1.0000 2.0
C B 3.0183281153 9.8126192181 3.6974442648 22.1591263112 0.8264956969 11.1782507988 0.9510337752 3.8465295183 40165.3497011995 1.0000 2.0
C N 3.4895869665 10.1614317973 1.1614801250 4.2614500372 11.1810783861 11.0390855050 0.9257256781 3.2512446017 29066.8955087607 1.0000 2.0
# Symmetric part
B C 3.0183281153 9.8126192181 3.6974442648 22.1591263112 0.8264956969 11.1782507988 0.9510337752 3.8465295183 40165.3497011995 1.0000 2.0
N C 3.4895869665 10.1614317973 1.1614801250 4.2614500372 11.1810783861 11.0390855050 0.9257256781 3.2512446017 29066.8955087607 1.0000 2.0
N B 3.9928670174 7.8553264966 2.5853334572 4.5784769626 2.3283590129 16.2664653527 0.8669270315 3.9824166141 84699.9699356515 1.0000 2.0

22
src/USER-MISC/pair_ilp_graphene_hbn.cpp
View File

@ -576,9 +576,6 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
// loop over neighbors of owned atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (ILP_numneigh[i] == -1) {
continue;
}
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
@ -589,9 +586,6 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (ILP_numneigh[j] == -1) {
continue;
}
jtype = type[j];
delx = xtmp - x[j][0];
@ -741,17 +735,8 @@ void PairILPGrapheneHBN::ILP_neigh()
} // loop over jj
ILP_firstneigh[i] = neighptr;
if (n == 3) {
ILP_numneigh[i] = n;
}
else if (n < 3) {
if (i < inum) {
ILP_numneigh[i] = n;
} else {
ILP_numneigh[i] = -1;
}
}
else if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration");
ILP_numneigh[i] = n;
if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration");
ipage->vgot(n);
if (ipage->status())
@ -814,9 +799,6 @@ void PairILPGrapheneHBN::calc_normal()
}
}
if (ILP_numneigh[i] == -1) {
continue;
}
xtp = x[i][0];
ytp = x[i][1];
ztp = x[i][2];

22
src/USER-MISC/pair_kolmogorov_crespi_full.cpp
View File

@ -576,9 +576,6 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */)
// loop over neighbors of owned atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (KC_numneigh[i] == -1) {
continue;
}
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
@ -589,9 +586,6 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
if (KC_numneigh[j] == -1) {
continue;
}
jtype = type[j];
delx = xtmp - x[j][0];
@ -746,17 +740,8 @@ void PairKolmogorovCrespiFull::KC_neigh()
}
KC_firstneigh[i] = neighptr;
if (n == 3) {
KC_numneigh[i] = n;
}
else if (n < 3) {
if (i < inum) {
KC_numneigh[i] = n;
} else {
KC_numneigh[i] = -1;
}
}
else if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration");
KC_numneigh[i] = n;
if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration");
ipage->vgot(n);
if (ipage->status())
@ -819,9 +804,6 @@ void PairKolmogorovCrespiFull::calc_normal()
}
}
if (KC_numneigh[i] == -1) {
continue;
}
xtp = x[i][0];
ytp = x[i][1];
ztp = x[i][2];