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Merge pull request #1122 from oywg11/master

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collecting small changes for potential #839
This commit is contained in:
Axel Kohlmeyer
2018-09-28 12:22:29 +02:00
committed by GitHub
parent e4d4f3a775 36c5fb2ec6
commit 1de76c33fd
8 changed files with 91 additions and 68 deletions
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9
doc/src/pair_coul_shield.txt
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@ -38,7 +38,8 @@ charge and molecule ID information is included.
Where Tap(r_ij) is the taper function which provides a continuous cutoff
(up to third derivative) for inter-atomic separations larger than r_c
"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1.
Here {lambda} is the shielding parameter that
eliminates the short-range singularity of the classical mono-polar
electrostatic interaction expression "(Maaravi)"_#Maaravi1.
@ -82,5 +83,11 @@ package"_Build_package.html doc page for more info.
:line
:link(Leven3)
[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
:link(Leven4)
[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
:link(Maaravi1)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

41
doc/src/pair_ilp_graphene_hbn.txt
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@ -25,22 +25,24 @@ pair_coeff * * rebo CH.airebo 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 0.69498201415576216335
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 "(Leven)"_#Leven and
"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
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 "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
r_c "(Maaravi)"_#Maaravi2. The definitons 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.
@ -61,13 +63,15 @@ 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.
NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials
are presented in "(Ouyang)"_#Ouyang1. These parameters provide a good description
in both short- and long-range interaction regime, while the old ILP parameters
published in "(Leven)"_#Leven 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 smaller than the equilibrium distance).
The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
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}.
@ -112,14 +116,17 @@ units, if your simulation does not use {metal} units.
:line
:link(Leven)
[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016)
: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)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
:link(Ouyang1)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
:link(Ouyang)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

39
doc/src/pair_kolmogorov_crespi_full.txt
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@ -19,11 +19,11 @@ tap_flag = 0/1 to turn off/on the taper function
pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
pair_coeff * * none
pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
pair_coeff * * rebo CH.airebo C C
pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
pair_coeff * * rebo CH.airebo C H
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre
[Description:]
@ -38,27 +38,32 @@ 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.
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 is intended for interactions between two different
graphene layers. Therefore, to avoid interaction within the same layers,
each layer should have a separate molecule id and is recommended to use
"full" atom style in the data file.
The parameter file (e.g. CC.KC), is intended for use with {metal}
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: A new set of parameters of KC potential for hydrocarbons (CH.KC)
is presented in "(Ouyang)"_#Ouyang2. The parameters in CH.KC provides
a good description in both short- and long-range interaction regime,
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 smaller than the equilibrium distance).
The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang2.
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}.
@ -84,7 +89,7 @@ package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
The CC.KC potential file provided with LAMMPS (see the potentials
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
@ -105,5 +110,5 @@ units.
:link(Kolmogorov1)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
:link(Ouyang2)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
:link(Ouyang1)
[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

2
potentials/BNCH.ILP
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@ -1,6 +1,6 @@
# Interlayer Potential (ILP) for graphene/graphene, graphene/hBN and hBN/hBN junctions
#
# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018).
# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
#
# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut

4
potentials/CH.KC
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@ -1,6 +1,6 @@
# Refined parameters for Kolmogorov-Crespi Potential
# Refined parameters for Kolmogorov-Crespi Potential without taper function
#
# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018).
# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
#
# z0 C0 C2 C4 C delta lambda A S rcut
C C 3.328819 21.847167 12.060173 4.711099 6.678908e-4 0.7718101 3.143921 12.660270 1.0 2.0

10
potentials/CH_taper.KC Normal file
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@ -0,0 +1,10 @@
# Refined parameters for Kolmogorov-Crespi Potential with taper function
#
# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
#
# z0 C0 C2 C4 C delta lambda A S rcut
C C 3.416084 20.021583 10.9055107 4.2756354 1.0010836E-2 0.8447122 2.9360584 14.3132588 1.0 2.0
C H 2.849054 72.557245 1.0164169E-2 65.923312 8.7962504E-5 0.3349237 3.0402632 14.7533201 1.0 1.5
H H 2.187478 3.915802E-5 5.0896431E-5 3.6657827 1.5373722446 0.9633581 0.4249989 1.570737E-4 1.0 1.2
H C 2.849054 72.557245 1.0164169E-2 65.923312 8.7962504E-5 0.3349237 3.0402632 14.7533201 1.0 2.2

27
src/USER-MISC/pair_ilp_graphene_hbn.cpp
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@ -249,11 +249,9 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
f[i][0] += fkcx - fprod1[0]*Tap;
f[i][1] += fkcy - fprod1[1]*Tap;
f[i][2] += fkcz - fprod1[2]*Tap;
if (newton_pair || j < nlocal) {
f[j][0] -= fkcx + fprod2[0]*Tap;
f[j][1] -= fkcy + fprod2[1]*Tap;
f[j][2] -= fkcz + fprod2[2]*Tap;
}
f[j][0] -= fkcx + fprod2[0]*Tap;
f[j][1] -= fkcy + fprod2[1]*Tap;
f[j][2] -= fkcz + fprod2[2]*Tap;
// calculate the forces acted on the neighbors of atom i from atom j
ILP_neighs_i = ILP_firstneigh[i];
@ -274,15 +272,13 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
for (ll = 0; ll < ILP_numneigh[j]; ll++) {
l = ILP_neighs_j[ll];
if (l == j) continue;
if (newton_pair || l < nlocal) {
// derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
}
// derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
}
if (eflag) {
@ -729,7 +725,8 @@ void PairILPGrapheneHBN::ILP_neigh()
ILP_firstneigh[i] = neighptr;
ILP_numneigh[i] = n;
if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please reduce the cutoff for normals");
if (n == 0) error->all(FLERR,"Could not build neighbor list to calculate normals, please check your configuration");
if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please check your configuration");
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

27
src/USER-MISC/pair_kolmogorov_crespi_full.cpp
View File

@ -249,11 +249,9 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
f[i][0] += fkcx - fprod1[0]*Tap;
f[i][1] += fkcy - fprod1[1]*Tap;
f[i][2] += fkcz - fprod1[2]*Tap;
if (newton_pair || j < nlocal) {
f[j][0] -= fkcx + fprod2[0]*Tap;
f[j][1] -= fkcy + fprod2[1]*Tap;
f[j][2] -= fkcz + fprod2[2]*Tap;
}
f[j][0] -= fkcx + fprod2[0]*Tap;
f[j][1] -= fkcy + fprod2[1]*Tap;
f[j][2] -= fkcz + fprod2[2]*Tap;
// calculate the forces acted on the neighbors of atom i from atom j
KC_neighs_i = KC_firstneigh[i];
@ -274,15 +272,13 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
for (ll = 0; ll < KC_numneigh[j]; ll++) {
l = KC_neighs_j[ll];
if (l == j) continue;
if (newton_pair || l < nlocal) {
// derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
}
// derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
}
if (eflag) {
@ -734,7 +730,8 @@ void PairKolmogorovCrespiFull::KC_neigh()
KC_firstneigh[i] = neighptr;
KC_numneigh[i] = n;
if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please reduce the cutoff for normals");
if (n == 0) error->all(FLERR,"Could not build neighbor list to calculate normals, please check your configuration");
if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please check your configuration");
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");