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

apply clang-format

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-02-16 06:14:19 -05:00
parent 32cde04000
commit 08968cbdbf
7 changed files with 498 additions and 484 deletions
Download Patch File Download Diff File Expand all files Collapse all files

31
src/INTERLAYER/pair_ilp_graphene_hbn.cpp
View File

@ -58,8 +58,7 @@ static const char cite_ilp[] =
/* ---------------------------------------------------------------------- */
PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp)
: Pair(lmp), variant(ILP_GrhBN)
PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp), variant(ILP_GrhBN)
{
restartinfo = 0;
one_coeff = 1;
@ -212,20 +211,20 @@ void PairILPGrapheneHBN::read_file(char *filename)
if (comm->me == 0) {
std::string potential_name;
switch (variant) {
case ILP_GrhBN:
potential_name = "ilp/graphene/hbn";
break;
case ILP_GrhBN:
potential_name = "ilp/graphene/hbn";
break;
case ILP_TMD:
potential_name = "ilp/tmd";
break;
case ILP_TMD:
potential_name = "ilp/tmd";
break;
case SAIP_METAL:
potential_name = "saip/metal";
break;
case SAIP_METAL:
potential_name = "saip/metal";
break;
default:
error->one(FLERR,"Unknown ILP style variant {}",variant);
default:
error->one(FLERR, "Unknown ILP style variant {}", variant);
}
PotentialFileReader reader(lmp, filename, potential_name, unit_convert_flag);
char *line;
@ -342,10 +341,8 @@ void PairILPGrapheneHBN::read_file(char *filename)
void PairILPGrapheneHBN::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR, "Pair style ilp/* requires newton pair on");
if (!atom->molecule_flag)
error->all(FLERR, "Pair style ilp/* requires atom attribute molecule");
if (force->newton_pair == 0) error->all(FLERR, "Pair style ilp/* requires newton pair on");
if (!atom->molecule_flag) error->all(FLERR, "Pair style ilp/* requires atom attribute molecule");
// need a full neighbor list, including neighbors of ghosts

4
src/INTERLAYER/pair_ilp_graphene_hbn.h
View File

@ -68,8 +68,8 @@ class PairILPGrapheneHBN : public Pair {
double ***dnormdri;
double ****dnormal;
// adds for ilp/tmd
int Nnei; // max # of nearest neighbors for one atom
// adds for ilp/tmd
int Nnei; // max # of nearest neighbors for one atom
double **dnn;
double **vect;
double **pvet;

779
src/INTERLAYER/pair_ilp_tmd.cpp
View File

File diff suppressed because it is too large Load Diff

1
src/INTERLAYER/pair_ilp_tmd.h
View File

@ -43,7 +43,6 @@ class PairILPTMD : public PairILPGrapheneHBN {
return k % range;
}
/**************************************************************/
};
} // namespace LAMMPS_NS

12
src/INTERLAYER/pair_kolmogorov_crespi_z.cpp
View File

@ -28,8 +28,8 @@
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "potential_file_reader.h"
#include <cmath>
@ -160,15 +160,15 @@ void PairKolmogorovCrespiZ::compute(int eflag, int vflag)
if (evflag) {
ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
if (vflag_either) {
double fi[3],fj[3];
double fi[3], fj[3];
fi[0] = delx * fpair1;
fi[1] = dely * fpair1;
fi[2] = 0;
fj[0] = -delx * fpair1;
fj[1] = -dely * fpair1;
fj[2] = 0;
v_tally2_newton(i,fi,x[i]);
v_tally2_newton(j,fj,x[j]);
v_tally2_newton(i, fi, x[i]);
v_tally2_newton(j, fj, x[j]);
}
}
}
@ -246,9 +246,9 @@ void PairKolmogorovCrespiZ::coeff(int narg, char **arg)
void PairKolmogorovCrespiZ::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR,"Pair style kolmogorov/crespi/z requires newton pair on");
error->all(FLERR, "Pair style kolmogorov/crespi/z requires newton pair on");
neighbor->request(this,instance_me);
neighbor->request(this, instance_me);
}
/* ----------------------------------------------------------------------

145
src/INTERLAYER/pair_saip_metal.cpp
View File

@ -52,7 +52,8 @@ static const char cite_saip[] =
/* ---------------------------------------------------------------------- */
PairSAIPMETAL::PairSAIPMETAL(LAMMPS *lmp) : PairILPGrapheneHBN(lmp) {
PairSAIPMETAL::PairSAIPMETAL(LAMMPS *lmp) : PairILPGrapheneHBN(lmp)
{
variant = SAIP_METAL;
if (lmp->citeme) lmp->citeme->add(cite_saip);
}
@ -71,19 +72,18 @@ void PairSAIPMETAL::settings(int narg, char **arg)
if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
}
/* ----------------------------------------------------------------------
Repulsive forces and energy
------------------------------------------------------------------------- */
void PairSAIPMETAL::calc_FRep(int eflag, int /* vflag */)
{
int i,j,ii,jj,inum,jnum,itype,jtype,k,kk;
double prodnorm1,fkcx,fkcy,fkcz,filp;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1;
double rsq,r,Rcut,rhosq1,exp0,exp1,Tap,dTap,Vilp;
double frho1,Erep,fsum,rdsq1;
int *ilist,*jlist,*numneigh,**firstneigh;
int i, j, ii, jj, inum, jnum, itype, jtype, k, kk;
double prodnorm1, fkcx, fkcy, fkcz, filp;
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair, fpair1;
double rsq, r, Rcut, rhosq1, exp0, exp1, Tap, dTap, Vilp;
double frho1, Erep, fsum, rdsq1;
int *ilist, *jlist, *numneigh, **firstneigh;
int *ILP_neighs_i;
evdwl = 0.0;
@ -123,35 +123,38 @@ void PairSAIPMETAL::calc_FRep(int eflag, int /* vflag */)
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
// only include the interaction between different layers
if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
int iparam_ij = elem2param[map[itype]][map[jtype]];
Param& p = params[iparam_ij];
Param &p = params[iparam_ij];
r = sqrt(rsq);
// turn on/off taper function
if (tap_flag) {
Rcut = sqrt(cutsq[itype][jtype]);
Tap = calc_Tap(r,Rcut);
dTap = calc_dTap(r,Rcut);
} else {Tap = 1.0; dTap = 0.0;}
Tap = calc_Tap(r, Rcut);
dTap = calc_dTap(r, Rcut);
} else {
Tap = 1.0;
dTap = 0.0;
}
// for atoms in bulk materials
if (strcmp(elements[map[itype]],"C") != 0 && strcmp(elements[map[itype]],"H") != 0 &&
strcmp(elements[map[itype]],"B") != 0 && strcmp(elements[map[itype]],"N") != 0) {
if (strcmp(elements[map[itype]], "C") != 0 && strcmp(elements[map[itype]], "H") != 0 &&
strcmp(elements[map[itype]], "B") != 0 && strcmp(elements[map[itype]], "N") != 0) {
// Set ni along rij
exp0 = exp(-p.lambda*(r-p.z0));
frho1 = 1.0*p.C;
Erep = 0.5*p.epsilon + frho1;
Vilp = exp0*Erep;
exp0 = exp(-p.lambda * (r - p.z0));
frho1 = 1.0 * p.C;
Erep = 0.5 * p.epsilon + frho1;
Vilp = exp0 * Erep;
// derivatives
fpair = p.lambda*exp0/r*Erep;
filp = fpair*Tap - Vilp*dTap/r;
fkcx = delx*filp;
fkcy = dely*filp;
fkcz = delz*filp;
fpair = p.lambda * exp0 / r * Erep;
filp = fpair * Tap - Vilp * dTap / r;
fkcx = delx * filp;
fkcy = dely * filp;
fkcz = delz * filp;
f[i][0] += fkcx;
f[i][1] += fkcy;
@ -159,46 +162,48 @@ void PairSAIPMETAL::calc_FRep(int eflag, int /* vflag */)
f[j][0] -= fkcx;
f[j][1] -= fkcy;
f[j][2] -= fkcz;
if (eflag) pvector[1] += evdwl = Tap*Vilp;
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,filp,delx,dely,delz);
}
else { // for atoms in 2D materials
if (eflag) pvector[1] += evdwl = Tap * Vilp;
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, filp, delx, dely, delz);
} else { // for atoms in 2D materials
// Calculate the transverse distance
prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz;
rhosq1 = rsq - prodnorm1*prodnorm1; // rho_ij
rdsq1 = rhosq1*p.delta2inv; // (rho_ij/delta)^2
prodnorm1 = normal[i][0] * delx + normal[i][1] * dely + normal[i][2] * delz;
rhosq1 = rsq - prodnorm1 * prodnorm1; // rho_ij
rdsq1 = rhosq1 * p.delta2inv; // (rho_ij/delta)^2
// store exponents
exp0 = exp(-p.lambda*(r-p.z0));
exp0 = exp(-p.lambda * (r - p.z0));
exp1 = exp(-rdsq1);
frho1 = exp1*p.C;
Erep = 0.5*p.epsilon + frho1;
Vilp = exp0*Erep;
frho1 = exp1 * p.C;
Erep = 0.5 * p.epsilon + frho1;
Vilp = exp0 * Erep;
// derivatives
fpair = p.lambda*exp0/r*Erep;
fpair1 = 2.0*exp0*frho1*p.delta2inv;
fpair = p.lambda * exp0 / r * Erep;
fpair1 = 2.0 * exp0 * frho1 * p.delta2inv;
fsum = fpair + fpair1;
// derivatives of the product of rij and ni, the result is a vector
dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz;
dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz;
dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz;
fp1[0] = prodnorm1*normal[i][0]*fpair1;
fp1[1] = prodnorm1*normal[i][1]*fpair1;
fp1[2] = prodnorm1*normal[i][2]*fpair1;
fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1;
fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1;
fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1;
dprodnorm1[0] =
dnormdri[0][0][i] * delx + dnormdri[1][0][i] * dely + dnormdri[2][0][i] * delz;
dprodnorm1[1] =
dnormdri[0][1][i] * delx + dnormdri[1][1][i] * dely + dnormdri[2][1][i] * delz;
dprodnorm1[2] =
dnormdri[0][2][i] * delx + dnormdri[1][2][i] * dely + dnormdri[2][2][i] * delz;
fp1[0] = prodnorm1 * normal[i][0] * fpair1;
fp1[1] = prodnorm1 * normal[i][1] * fpair1;
fp1[2] = prodnorm1 * normal[i][2] * fpair1;
fprod1[0] = prodnorm1 * dprodnorm1[0] * fpair1;
fprod1[1] = prodnorm1 * dprodnorm1[1] * fpair1;
fprod1[2] = prodnorm1 * dprodnorm1[2] * fpair1;
fkcx = (delx*fsum - fp1[0])*Tap - Vilp*dTap*delx/r;
fkcy = (dely*fsum - fp1[1])*Tap - Vilp*dTap*dely/r;
fkcz = (delz*fsum - fp1[2])*Tap - Vilp*dTap*delz/r;
fkcx = (delx * fsum - fp1[0]) * Tap - Vilp * dTap * delx / r;
fkcy = (dely * fsum - fp1[1]) * Tap - Vilp * dTap * dely / r;
fkcz = (delz * fsum - fp1[2]) * Tap - Vilp * dTap * delz / r;
f[i][0] += fkcx - fprod1[0]*Tap;
f[i][1] += fkcy - fprod1[1]*Tap;
f[i][2] += fkcz - fprod1[2]*Tap;
f[i][0] += fkcx - fprod1[0] * Tap;
f[i][1] += fkcy - fprod1[1] * Tap;
f[i][2] += fkcz - fprod1[2] * Tap;
f[j][0] -= fkcx;
f[j][1] -= fkcy;
f[j][2] -= fkcz;
@ -209,25 +214,31 @@ void PairSAIPMETAL::calc_FRep(int eflag, int /* vflag */)
k = ILP_neighs_i[kk];
if (k == i) continue;
// derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i
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;
fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap;
fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap;
fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap;
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;
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];
delki[0] = x[k][0] - x[i][0];
delki[1] = x[k][1] - x[i][1];
delki[2] = x[k][2] - x[i][2];
if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delki[0],delki[1],delki[2]);
if (evflag)
ev_tally_xyz(k, j, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delki[0],
delki[1], delki[2]);
}
if (eflag) pvector[1] += evdwl = Tap*Vilp;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,fkcx,fkcy,fkcz,delx,dely,delz);
} // end of speration atoms for bulk materials
} // end of rsq < cutoff
} // loop over jj
} // loop over ii
if (eflag) pvector[1] += evdwl = Tap * Vilp;
if (evflag)
ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0.0, fkcx, fkcy, fkcz, delx, dely, delz);
} // end of speration atoms for bulk materials
} // end of rsq < cutoff
} // loop over jj
} // loop over ii
}