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Merge branch 'master' into collected-small-changes

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Axel Kohlmeyer 2019-04-06 19:52:39 -04:00
parent b25657c67b ce1040a103
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19
doc/src/pair_ilp_graphene_hbn.txt
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@ -47,11 +47,16 @@ 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 is intended for interactions between two different
layers of graphene or hexagonal boron nitride. 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.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.
To perform a realistic simulation, this potential must be used in combination with
intra-layer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intra-layer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intra-layer potential and atoms residing on different layers
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,
@ -62,6 +67,10 @@ 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

14
doc/src/pair_kolmogorov_crespi_full.txt
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@ -42,10 +42,16 @@ 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.
NOTE: This potential (ILP) is intended for interlayer interactions between two
different layers of graphene. To perform a realistic simulation, this potential
must be used in combination with intra-layer potential, such as
"AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
To keep the intra-layer properties unaffected, the interlayer interaction
within the same layers should be avoided. Hence, each atom has to have a layer
identifier such that atoms residing on the same layer interact via the
appropriate intra-layer potential and atoms residing on different layers
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},

66
src/USER-MISC/pair_ilp_graphene_hbn.cpp
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@ -111,7 +111,7 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
tagint itag,jtag;
double prodnorm1,prodnorm2,fkcx,fkcy,fkcz;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2;
double rsq,r,Rcut,rhosq1,rhosq2,exp0,exp1,exp2,r2inv,r6inv,r8inv,Tap,dTap,Vkc;
double rsq,r,Rcut,rhosq1,rhosq2,exp0,exp1,exp2,r2inv,r6inv,r8inv,Tap,dTap,Vilp;
double frho1,frho2,TSvdw,TSvdw2inv,Erep,fsum,rdsq1,rdsq2;
int *ilist,*jlist,*numneigh,**firstneigh;
int *ILP_neighs_i,*ILP_neighs_j;
@ -131,6 +131,10 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
double fp2[3] = {0.0, 0.0, 0.0};
double fprod1[3] = {0.0, 0.0, 0.0};
double fprod2[3] = {0.0, 0.0, 0.0};
double fk[3] = {0.0, 0.0, 0.0};
double fl[3] = {0.0, 0.0, 0.0};
double delkj[3] = {0.0, 0.0, 0.0};
double delli[3] = {0.0, 0.0, 0.0};
inum = list->inum;
ilist = list->ilist;
@ -213,7 +217,7 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
frho1 = exp1*p.C;
frho2 = exp2*p.C;
Erep = p.epsilon + frho1 + frho2;
Vkc = -p.C6*r6inv/TSvdw + exp0*Erep;
Vilp = -p.C6*r6inv/TSvdw + exp0*Erep;
// derivatives
fpair = -6.0*p.C6*r8inv/TSvdw + p.d/p.seff*p.C6*(TSvdw-1.0)*TSvdw2inv*r8inv*r + p.lambda*exp0/r*Erep;
@ -240,9 +244,9 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
fprod2[0] = prodnorm2*dprodnorm2[0]*fpair2;
fprod2[1] = prodnorm2*dprodnorm2[1]*fpair2;
fprod2[2] = prodnorm2*dprodnorm2[2]*fpair2;
fkcx = (delx*fsum - fp1[0] - fp2[0])*Tap - Vkc*dTap*delx/r;
fkcy = (dely*fsum - fp1[1] - fp2[1])*Tap - Vkc*dTap*dely/r;
fkcz = (delz*fsum - fp1[2] - fp2[2])*Tap - Vkc*dTap*delz/r;
fkcx = (delx*fsum - fp1[0] - fp2[0])*Tap - Vilp*dTap*delx/r;
fkcy = (dely*fsum - fp1[1] - fp2[1])*Tap - Vilp*dTap*dely/r;
fkcz = (delz*fsum - fp1[2] - fp2[2])*Tap - Vilp*dTap*delz/r;
f[i][0] += fkcx - fprod1[0]*Tap;
f[i][1] += fkcy - fprod1[1]*Tap;
@ -260,9 +264,16 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz;
dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz;
dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz;
f[k][0] += (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
f[k][1] += (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
f[k][2] += (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
delkj[0] = x[k][0] - x[j][0];
delkj[1] = x[k][1] - x[j][1];
delkj[2] = x[k][2] - x[j][2];
if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]);
}
// calculate the forces acted on the neighbors of atom j from atom i
@ -274,20 +285,24 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
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;
fl[0] = (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
fl[1] = (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
fl[2] = (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
f[l][0] += fl[0];
f[l][1] += fl[1];
f[l][2] += fl[2];
delli[0] = x[l][0] - x[i][0];
delli[1] = x[l][1] - x[i][1];
delli[2] = x[l][2] - x[i][2];
if (evflag) ev_tally_xyz(l,i,nlocal,newton_pair,0.0,0.0,fl[0],fl[1],fl[2],delli[0],delli[1],delli[2]);
}
if (eflag) {
if (tap_flag) evdwl = Tap*Vkc;
else evdwl = Vkc - offset[itype][jtype];
if (tap_flag) evdwl = Tap*Vilp;
else evdwl = Vilp - offset[itype][jtype];
}
if (evflag){
ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,
fkcx,fkcy,fkcz,delx,dely,delz);
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,fkcx,fkcy,fkcz,delx,dely,delz);
}
}
}
@ -433,7 +448,7 @@ void PairILPGrapheneHBN::calc_normal()
// the magnitude of the normal vector
nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
nn = sqrt(nn2);
if (nn == 0) error->all(FLERR,"The magnitude of the normal vector is zero");
if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
// the unit normal vector
normal[i][0] = n1[0]/nn;
normal[i][1] = n1[1]/nn;
@ -576,7 +591,7 @@ void PairILPGrapheneHBN::calc_normal()
// the magnitude of the normal vector
nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
nn = sqrt(nn2);
if (nn == 0) error->all(FLERR,"The magnitude of the normal vector is zero");
if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
// the unit normal vector
normal[i][0] = n1[0]/nn;
normal[i][1] = n1[1]/nn;
@ -616,7 +631,7 @@ void PairILPGrapheneHBN::calc_normal()
}
}
else {
error->all(FLERR,"There are too many neighbors for calculating normals");
error->one(FLERR,"There are too many neighbors for calculating normals");
}
//##############################################################################################
@ -723,8 +738,7 @@ void PairILPGrapheneHBN::ILP_neigh()
ILP_firstneigh[i] = neighptr;
ILP_numneigh[i] = n;
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");
if (n > 3) error->one(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");
@ -1010,7 +1024,7 @@ double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, do
double &fforce)
{
double r,r2inv,r6inv,r8inv,forcelj,philj,fpair;
double Tap,dTap,Vkc,TSvdw,TSvdw2inv;
double Tap,dTap,Vilp,TSvdw,TSvdw2inv;
int iparam_ij = elem2param[map[itype]][map[jtype]];
Param& p = params[iparam_ij];
@ -1028,13 +1042,13 @@ double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, do
TSvdw = 1.0 + exp(-p.d*(r/p.seff - 1.0));
TSvdw2inv = pow(TSvdw,-2.0);
Vkc = -p.C6*r6inv/TSvdw;
Vilp = -p.C6*r6inv/TSvdw;
// derivatives
fpair = -6.0*p.C6*r8inv/TSvdw + p.d/p.seff*p.C6*(TSvdw - 1.0)*r6inv*TSvdw2inv/r;
forcelj = fpair;
fforce = factor_lj*(forcelj*Tap - Vkc*dTap/r);
fforce = factor_lj*(forcelj*Tap - Vilp*dTap/r);
philj = Vkc*Tap;
philj = Vilp*Tap;
return factor_lj*philj;
}

44
src/USER-MISC/pair_kolmogorov_crespi_full.cpp
View File

@ -129,6 +129,10 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
double fp2[3] = {0.0, 0.0, 0.0};
double fprod1[3] = {0.0, 0.0, 0.0};
double fprod2[3] = {0.0, 0.0, 0.0};
double fk[3] = {0.0, 0.0, 0.0};
double fl[3] = {0.0, 0.0, 0.0};
double delkj[3] = {0.0, 0.0, 0.0};
double delli[3] = {0.0, 0.0, 0.0};
inum = list->inum;
ilist = list->ilist;
@ -259,9 +263,16 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz;
dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz;
dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz;
f[k][0] += (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
f[k][1] += (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
f[k][2] += (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
delkj[0] = x[k][0] - x[j][0];
delkj[1] = x[k][1] - x[j][1];
delkj[2] = x[k][2] - x[j][2];
if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]);
}
// calculate the forces acted on the neighbors of atom j from atom i
@ -273,9 +284,16 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
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;
fl[0] = (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
fl[1] = (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
fl[2] = (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
f[l][0] += fl[0];
f[l][1] += fl[1];
f[l][2] += fl[2];
delli[0] = x[l][0] - x[i][0];
delli[1] = x[l][1] - x[i][1];
delli[2] = x[l][2] - x[i][2];
if (evflag) ev_tally_xyz(l,i,nlocal,newton_pair,0.0,0.0,fl[0],fl[1],fl[2],delli[0],delli[1],delli[2]);
}
if (eflag) {
@ -283,10 +301,7 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
else evdwl = Vkc - offset[itype][jtype];
}
if (evflag){
ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,
fkcx,fkcy,fkcz,delx,dely,delz);
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,fkcx,fkcy,fkcz,delx,dely,delz);
}
}
}
@ -431,7 +446,7 @@ void PairKolmogorovCrespiFull::calc_normal()
// the magnitude of the normal vector
nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
nn = sqrt(nn2);
if (nn == 0) error->all(FLERR,"The magnitude of the normal vector is zero");
if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
// the unit normal vector
normal[i][0] = n1[0]/nn;
normal[i][1] = n1[1]/nn;
@ -579,7 +594,7 @@ void PairKolmogorovCrespiFull::calc_normal()
// the magnitude of the normal vector
nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2];
nn = sqrt(nn2);
if (nn == 0) error->all(FLERR,"The magnitude of the normal vector is zero");
if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero");
// the unit normal vector
normal[i][0] = n1[0]/nn;
normal[i][1] = n1[1]/nn;
@ -619,7 +634,7 @@ void PairKolmogorovCrespiFull::calc_normal()
}
}
else {
error->all(FLERR,"There are too many neighbors for calculating normals");
error->one(FLERR,"There are too many neighbors for calculating normals");
}
//##############################################################################################
@ -727,8 +742,7 @@ void PairKolmogorovCrespiFull::KC_neigh()
KC_firstneigh[i] = neighptr;
KC_numneigh[i] = n;
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");
if (n > 3) error->one(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");