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Merge pull request #544 from akohlmey/tip4p-triclinic

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Correct handling of triclinic box support in pppm/tip4p and pppm/tip4p/omp
This commit is contained in:
sjplimp
2017-07-03 12:24:18 -06:00
committed by GitHub
parent 883b7aaa0e 73b948dcfc
commit 9eeb97b039
4 changed files with 195 additions and 75 deletions
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4
src/KSPACE/pppm.cpp
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@ -186,6 +186,10 @@ void PPPM::init()
// error check
triclinic_check();
if (triclinic != domain->triclinic)
error->all(FLERR,"Must redefine kspace_style after changing to triclinic box");
if (domain->triclinic && differentiation_flag == 1)
error->all(FLERR,"Cannot (yet) use PPPM with triclinic box "
"and kspace_modify diff ad");

157
src/KSPACE/pppm_tip4p.cpp
View File

@ -332,9 +332,9 @@ void PPPMTIP4P::fieldforce_ad()
const double qfactor = qqrd2e * scale;
s1 = x[i][0]*hx_inv;
s2 = x[i][1]*hy_inv;
s3 = x[i][2]*hz_inv;
s1 = xi[0]*hx_inv;
s2 = xi[1]*hy_inv;
s3 = xi[2]*hz_inv;
sf = sf_coeff[0]*sin(2*MY_PI*s1);
sf += sf_coeff[1]*sin(4*MY_PI*s1);
sf *= 2.0*q[i]*q[i];
@ -486,6 +486,8 @@ void PPPMTIP4P::fieldforce_peratom()
void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
{
double **x = atom->x;
iH1 = atom->map(atom->tag[i] + 1);
iH2 = atom->map(atom->tag[i] + 2);
@ -493,63 +495,98 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
// set iH1,iH2 to index of closest image to O
iH1 = domain->closest_image(i,iH1);
iH2 = domain->closest_image(i,iH2);
if (triclinic) {
find_M_triclinic(i,iH1,iH2,xM);
return;
// need to use custom code to find the closest image for triclinic,
// since local atoms are in lambda coordinates, but ghosts are not.
int *sametag = atom->sametag;
double xo[3],xh1[3],xh2[3];
domain->lamda2x(x[i],xo);
domain->lamda2x(x[iH1],xh1);
domain->lamda2x(x[iH2],xh2);
double delx = xo[0] - xh1[0];
double dely = xo[1] - xh1[1];
double delz = xo[2] - xh1[2];
double rsqmin = delx*delx + dely*dely + delz*delz;
double rsq;
int closest = iH1;
while (sametag[iH1] >= 0) {
iH1 = sametag[iH1];
delx = xo[0] - x[iH1][0];
dely = xo[1] - x[iH1][1];
delz = xo[2] - x[iH1][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rsqmin) {
rsqmin = rsq;
closest = iH1;
xh1[0] = x[iH1][0];
xh1[1] = x[iH1][1];
xh1[2] = x[iH1][2];
}
}
iH1 = closest;
closest = iH2;
delx = xo[0] - xh2[0];
dely = xo[1] - xh2[1];
delz = xo[2] - xh2[2];
rsqmin = delx*delx + dely*dely + delz*delz;
while (sametag[iH2] >= 0) {
iH2 = sametag[iH2];
delx = xo[0] - x[iH2][0];
dely = xo[1] - x[iH2][1];
delz = xo[2] - x[iH2][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rsqmin) {
rsqmin = rsq;
closest = iH2;
xh2[0] = x[iH2][0];
xh2[1] = x[iH2][1];
xh2[2] = x[iH2][2];
}
}
iH2 = closest;
// finally compute M in real coordinates ...
double delx1 = xh1[0] - xo[0];
double dely1 = xh1[1] - xo[1];
double delz1 = xh1[2] - xo[2];
double delx2 = xh2[0] - xo[0];
double dely2 = xh2[1] - xo[1];
double delz2 = xh2[2] - xo[2];
xM[0] = xo[0] + alpha * 0.5 * (delx1 + delx2);
xM[1] = xo[1] + alpha * 0.5 * (dely1 + dely2);
xM[2] = xo[2] + alpha * 0.5 * (delz1 + delz2);
// ... and convert M to lamda space for PPPM
domain->x2lamda(xM,xM);
} else {
// set iH1,iH2 to index of closest image to O
iH1 = domain->closest_image(i,iH1);
iH2 = domain->closest_image(i,iH2);
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
double delz1 = x[iH1][2] - x[i][2];
double delx2 = x[iH2][0] - x[i][0];
double dely2 = x[iH2][1] - x[i][1];
double delz2 = x[iH2][2] - x[i][2];
xM[0] = x[i][0] + alpha * 0.5 * (delx1 + delx2);
xM[1] = x[i][1] + alpha * 0.5 * (dely1 + dely2);
xM[2] = x[i][2] + alpha * 0.5 * (delz1 + delz2);
}
double **x = atom->x;
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
double delz1 = x[iH1][2] - x[i][2];
double delx2 = x[iH2][0] - x[i][0];
double dely2 = x[iH2][1] - x[i][1];
double delz2 = x[iH2][2] - x[i][2];
xM[0] = x[i][0] + alpha * 0.5 * (delx1 + delx2);
xM[1] = x[i][1] + alpha * 0.5 * (dely1 + dely2);
xM[2] = x[i][2] + alpha * 0.5 * (delz1 + delz2);
}
/* ----------------------------------------------------------------------
triclinic version of find_M()
calculation of M coords done in real space
------------------------------------------------------------------------- */
void PPPMTIP4P::find_M_triclinic(int i, int iH1, int iH2, double *xM)
{
double **x = atom->x;
// convert from lamda to real space
// may be possible to do this more efficiently in lamda space
domain->lamda2x(x[i],x[i]);
domain->lamda2x(x[iH1],x[iH1]);
domain->lamda2x(x[iH2],x[iH2]);
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
double delz1 = x[iH1][2] - x[i][2];
double delx2 = x[iH2][0] - x[i][0];
double dely2 = x[iH2][1] - x[i][1];
double delz2 = x[iH2][2] - x[i][2];
xM[0] = x[i][0] + alpha * 0.5 * (delx1 + delx2);
xM[1] = x[i][1] + alpha * 0.5 * (dely1 + dely2);
xM[2] = x[i][2] + alpha * 0.5 * (delz1 + delz2);
// convert back to lamda space
domain->x2lamda(x[i],x[i]);
domain->x2lamda(x[iH1],x[iH1]);
domain->x2lamda(x[iH2],x[iH2]);
domain->x2lamda(xM,xM);
}

1
src/KSPACE/pppm_tip4p.h
View File

@ -39,7 +39,6 @@ class PPPMTIP4P : public PPPM {
private:
void find_M(int, int &, int &, double *);
void find_M_triclinic(int, int, int, double *);
};
}

108
src/USER-OMP/pppm_tip4p_omp.cpp
View File

@ -48,7 +48,7 @@ using namespace MathSpecial;
PPPMTIP4POMP::PPPMTIP4POMP(LAMMPS *lmp, int narg, char **arg) :
PPPMTIP4P(lmp, narg, arg), ThrOMP(lmp, THR_KSPACE)
{
triclinic_support = 0;
triclinic_support = 1;
suffix_flag |= Suffix::OMP;
}
@ -735,6 +735,8 @@ void PPPMTIP4POMP::fieldforce_ad()
void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM)
{
double **x = atom->x;
iH1 = atom->map(atom->tag[i] + 1);
iH2 = atom->map(atom->tag[i] + 2);
@ -742,24 +744,102 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM)
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
// set iH1,iH2 to index of closest image to O
if (triclinic) {
iH1 = domain->closest_image(i,iH1);
iH2 = domain->closest_image(i,iH2);
// need to use custom code to find the closest image for triclinic,
// since local atoms are in lambda coordinates, but ghosts are not.
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
int *sametag = atom->sametag;
double xo[3],xh1[3],xh2[3];
double delx1 = x[iH1].x - x[i].x;
double dely1 = x[iH1].y - x[i].y;
double delz1 = x[iH1].z - x[i].z;
domain->lamda2x(x[i],xo);
domain->lamda2x(x[iH1],xh1);
domain->lamda2x(x[iH2],xh2);
double delx2 = x[iH2].x - x[i].x;
double dely2 = x[iH2].y - x[i].y;
double delz2 = x[iH2].z - x[i].z;
double delx = xo[0] - xh1[0];
double dely = xo[1] - xh1[1];
double delz = xo[2] - xh1[2];
double rsqmin = delx*delx + dely*dely + delz*delz;
double rsq;
int closest = iH1;
xM.x = x[i].x + alpha * 0.5 * (delx1 + delx2);
xM.y = x[i].y + alpha * 0.5 * (dely1 + dely2);
xM.z = x[i].z + alpha * 0.5 * (delz1 + delz2);
while (sametag[iH1] >= 0) {
iH1 = sametag[iH1];
delx = xo[0] - x[iH1][0];
dely = xo[1] - x[iH1][1];
delz = xo[2] - x[iH1][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rsqmin) {
rsqmin = rsq;
closest = iH1;
xh1[0] = x[iH1][0];
xh1[1] = x[iH1][1];
xh1[2] = x[iH1][2];
}
}
iH1 = closest;
closest = iH2;
delx = xo[0] - xh2[0];
dely = xo[1] - xh2[1];
delz = xo[2] - xh2[2];
rsqmin = delx*delx + dely*dely + delz*delz;
while (sametag[iH2] >= 0) {
iH2 = sametag[iH2];
delx = xo[0] - x[iH2][0];
dely = xo[1] - x[iH2][1];
delz = xo[2] - x[iH2][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rsqmin) {
rsqmin = rsq;
closest = iH2;
xh2[0] = x[iH2][0];
xh2[1] = x[iH2][1];
xh2[2] = x[iH2][2];
}
}
iH2 = closest;
// finally compute M in real coordinates ...
double delx1 = xh1[0] - xo[0];
double dely1 = xh1[1] - xo[1];
double delz1 = xh1[2] - xo[2];
double delx2 = xh2[0] - xo[0];
double dely2 = xh2[1] - xo[1];
double delz2 = xh2[2] - xo[2];
xM.x = xo[0] + alpha * 0.5 * (delx1 + delx2);
xM.y = xo[1] + alpha * 0.5 * (dely1 + dely2);
xM.z = xo[2] + alpha * 0.5 * (delz1 + delz2);
// ... and convert M to lamda space for PPPM
domain->x2lamda((double *)&xM,(double *)&xM);
} else {
// set iH1,iH2 to index of closest image to O
iH1 = domain->closest_image(i,iH1);
iH2 = domain->closest_image(i,iH2);
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
double delx1 = x[iH1].x - x[i].x;
double dely1 = x[iH1].y - x[i].y;
double delz1 = x[iH1].z - x[i].z;
double delx2 = x[iH2].x - x[i].x;
double dely2 = x[iH2].y - x[i].y;
double delz2 = x[iH2].z - x[i].z;
xM.x = x[i].x + alpha * 0.5 * (delx1 + delx2);
xM.y = x[i].y + alpha * 0.5 * (dely1 + dely2);
xM.z = x[i].z + alpha * 0.5 * (delz1 + delz2);
}
}