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timings, energy, virial tallying

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This commit is contained in:
Steve Plimpton
2022-05-18 08:49:31 -06:00
parent dbcc08ba00
commit df2ecf5bf8
12 changed files with 230 additions and 244 deletions
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31
src/AMOEBA/amoeba_charge_transfer.cpp
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@ -148,25 +148,20 @@ void PairAmoeba::charge_transfer()
// increment the internal virial tensor components // increment the internal virial tensor components
vxx = xr * frcx; if (vflag_global) {
vxy = yr * frcx; vxx = xr * frcx;
vxz = zr * frcx; vxy = yr * frcx;
vyy = yr * frcy; vxz = zr * frcx;
vyz = zr * frcy; vyy = yr * frcy;
vzz = zr * frcz; vyz = zr * frcy;
vzz = zr * frcz;
virqxfer[0] -= vxx; virqxfer[0] -= vxx;
virqxfer[1] -= vyy; virqxfer[1] -= vyy;
virqxfer[2] -= vzz; virqxfer[2] -= vzz;
virqxfer[3] -= vxy; virqxfer[3] -= vxy;
virqxfer[4] -= vxz; virqxfer[4] -= vxz;
virqxfer[5] -= vyz; virqxfer[5] -= vyz;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
} }
} }
} }

55
src/AMOEBA/amoeba_dispersion.cpp
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@ -212,25 +212,20 @@ void PairAmoeba::dispersion_real()
// increment the internal virial tensor components // increment the internal virial tensor components
vxx = xr * dedx; if (vflag_global) {
vyx = yr * dedx; vxx = xr * dedx;
vzx = zr * dedx; vyx = yr * dedx;
vyy = yr * dedy; vzx = zr * dedx;
vzy = zr * dedy; vyy = yr * dedy;
vzz = zr * dedz; vzy = zr * dedy;
vzz = zr * dedz;
virdisp[0] -= vxx; virdisp[0] -= vxx;
virdisp[1] -= vyy; virdisp[1] -= vyy;
virdisp[2] -= vzz; virdisp[2] -= vzz;
virdisp[3] -= vyx; virdisp[3] -= vyx;
virdisp[4] -= vzx; virdisp[4] -= vzx;
virdisp[5] -= vzy; virdisp[5] -= vzy;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
} }
} }
} }
@ -350,13 +345,15 @@ void PairAmoeba::dispersion_kspace()
struc2 = gridfft[n]*gridfft[n] + gridfft[n+1]*gridfft[n+1]; struc2 = gridfft[n]*gridfft[n] + gridfft[n+1]*gridfft[n+1];
e = -(term1 / denom) * struc2; e = -(term1 / denom) * struc2;
edisp += e; edisp += e;
vterm = 3.0 * (fac1*erfcterm*h + fac3*expterm) * struc2/denom; if (vflag_global) {
virdisp[0] -= h1*h1*vterm - e; vterm = 3.0 * (fac1*erfcterm*h + fac3*expterm) * struc2/denom;
virdisp[1] -= h2*h2*vterm - e; virdisp[0] -= h1*h1*vterm - e;
virdisp[2] -= h3*h3*vterm - e; virdisp[1] -= h2*h2*vterm - e;
virdisp[3] -= h1*h2*vterm; virdisp[2] -= h3*h3*vterm - e;
virdisp[4] -= h1*h3*vterm; virdisp[3] -= h1*h2*vterm;
virdisp[5] -= h2*h3*vterm; virdisp[4] -= h1*h3*vterm;
virdisp[5] -= h2*h3*vterm;
}
} else term1 = 0.0; } else term1 = 0.0;
// NOTE: pre-calc this division only once // NOTE: pre-calc this division only once
gridfft[n] *= -(term1/denom); gridfft[n] *= -(term1/denom);
@ -418,8 +415,10 @@ void PairAmoeba::dispersion_kspace()
if (me == 0) { if (me == 0) {
edisp -= term; edisp -= term;
virdisp[0] -= term; if (vflag_global) {
virdisp[1] -= term; virdisp[0] -= term;
virdisp[2] -= term; virdisp[1] -= term;
virdisp[2] -= term;
}
} }
} }

31
src/AMOEBA/amoeba_hal.cpp
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@ -188,25 +188,20 @@ void PairAmoeba::hal()
// increment the internal virial tensor components // increment the internal virial tensor components
vxx = xr * dedx; if (vflag_global) {
vyx = yr * dedx; vxx = xr * dedx;
vzx = zr * dedx; vyx = yr * dedx;
vyy = yr * dedy; vzx = zr * dedx;
vzy = zr * dedy; vyy = yr * dedy;
vzz = zr * dedz; vzy = zr * dedy;
vzz = zr * dedz;
virhal[0] -= vxx; virhal[0] -= vxx;
virhal[1] -= vyy; virhal[1] -= vyy;
virhal[2] -= vzz; virhal[2] -= vzz;
virhal[3] -= vyx; virhal[3] -= vyx;
virhal[4] -= vzx; virhal[4] -= vzx;
virhal[5] -= vzy; virhal[5] -= vzy;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
} }
} }
} }

131
src/AMOEBA/amoeba_multipole.cpp
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@ -497,25 +497,20 @@ void PairAmoeba::multipole_real()
// increment the virial due to pairwise Cartesian forces // increment the virial due to pairwise Cartesian forces
vxx = -xr * frcx; if (vflag_global) {
vxy = -0.5 * (yr*frcx+xr*frcy); vxx = -xr * frcx;
vxz = -0.5 * (zr*frcx+xr*frcz); vxy = -0.5 * (yr*frcx+xr*frcy);
vyy = -yr * frcy; vxz = -0.5 * (zr*frcx+xr*frcz);
vyz = -0.5 * (zr*frcy+yr*frcz); vyy = -yr * frcy;
vzz = -zr * frcz; vyz = -0.5 * (zr*frcy+yr*frcz);
vzz = -zr * frcz;
virmpole[0] -= vxx;
virmpole[1] -= vyy; virmpole[0] -= vxx;
virmpole[2] -= vzz; virmpole[1] -= vyy;
virmpole[3] -= vxy; virmpole[2] -= vzz;
virmpole[4] -= vxz; virmpole[3] -= vxy;
virmpole[5] -= vyz; virmpole[4] -= vxz;
virmpole[5] -= vyz;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
} }
} }
} }
@ -530,6 +525,8 @@ void PairAmoeba::multipole_real()
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {
torque2force(i,tq[i],fix,fiy,fiz,f); torque2force(i,tq[i],fix,fiy,fiz,f);
if (!vflag_global) continue;
iz = zaxis2local[i]; iz = zaxis2local[i];
ix = xaxis2local[i]; ix = xaxis2local[i];
iy = yaxis2local[i]; iy = yaxis2local[i];
@ -543,7 +540,7 @@ void PairAmoeba::multipole_real()
xiy = x[iy][0] - x[i][0]; xiy = x[iy][0] - x[i][0];
yiy = x[iy][1] - x[i][1]; yiy = x[iy][1] - x[i][1];
ziy = x[iy][2] - x[i][2]; ziy = x[iy][2] - x[i][2];
vxx = xix*fix[0] + xiy*fiy[0] + xiz*fiz[0]; vxx = xix*fix[0] + xiy*fiy[0] + xiz*fiz[0];
vxy = 0.5 * (yix*fix[0] + yiy*fiy[0] + yiz*fiz[0] + vxy = 0.5 * (yix*fix[0] + yiy*fiy[0] + yiz*fiz[0] +
xix*fix[1] + xiy*fiy[1] + xiz*fiz[1]); xix*fix[1] + xiy*fiy[1] + xiz*fiz[1]);
@ -553,7 +550,7 @@ void PairAmoeba::multipole_real()
vyz = 0.5 * (zix*fix[1] + ziy*fiy[1] + ziz*fiz[1] + vyz = 0.5 * (zix*fix[1] + ziy*fiy[1] + ziz*fiz[1] +
yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]); yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]);
vzz = zix*fix[2] + ziy*fiy[2] + ziz*fiz[2]; vzz = zix*fix[2] + ziy*fiy[2] + ziz*fiz[2];
virmpole[0] -= vxx; virmpole[0] -= vxx;
virmpole[1] -= vyy; virmpole[1] -= vyy;
virmpole[2] -= vzz; virmpole[2] -= vzz;
@ -768,22 +765,24 @@ void PairAmoeba::multipole_kspace()
// augment the permanent multipole virial contributions // augment the permanent multipole virial contributions
for (i = 0; i < nlocal; i++) { if (vflag_global) {
vxx = vxx - cmp[i][1]*cphi[i][1] - 2.0*cmp[i][4]*cphi[i][4] - for (i = 0; i < nlocal; i++) {
cmp[i][7]*cphi[i][7] - cmp[i][8]*cphi[i][8]; vxx = vxx - cmp[i][1]*cphi[i][1] - 2.0*cmp[i][4]*cphi[i][4] -
vxy = vxy - 0.5*(cmp[i][2]*cphi[i][1]+cmp[i][1]*cphi[i][2]) - cmp[i][7]*cphi[i][7] - cmp[i][8]*cphi[i][8];
(cmp[i][4]+cmp[i][5])*cphi[i][7] - 0.5*cmp[i][7]*(cphi[i][4]+cphi[i][5]) - vxy = vxy - 0.5*(cmp[i][2]*cphi[i][1]+cmp[i][1]*cphi[i][2]) -
0.5*(cmp[i][8]*cphi[i][9]+cmp[i][9]*cphi[i][8]); (cmp[i][4]+cmp[i][5])*cphi[i][7] - 0.5*cmp[i][7]*(cphi[i][4]+cphi[i][5]) -
vxz = vxz - 0.5*(cmp[i][3]*cphi[i][1]+cmp[i][1]*cphi[i][3]) - 0.5*(cmp[i][8]*cphi[i][9]+cmp[i][9]*cphi[i][8]);
(cmp[i][4]+cmp[i][6])*cphi[i][8] - 0.5*cmp[i][8]*(cphi[i][4]+cphi[i][6]) - vxz = vxz - 0.5*(cmp[i][3]*cphi[i][1]+cmp[i][1]*cphi[i][3]) -
0.5*(cmp[i][7]*cphi[i][9]+cmp[i][9]*cphi[i][7]); (cmp[i][4]+cmp[i][6])*cphi[i][8] - 0.5*cmp[i][8]*(cphi[i][4]+cphi[i][6]) -
vyy = vyy - cmp[i][2]*cphi[i][2] - 2.0*cmp[i][5]*cphi[i][5] - 0.5*(cmp[i][7]*cphi[i][9]+cmp[i][9]*cphi[i][7]);
cmp[i][7]*cphi[i][7] - cmp[i][9]*cphi[i][9]; vyy = vyy - cmp[i][2]*cphi[i][2] - 2.0*cmp[i][5]*cphi[i][5] -
vyz = vyz - 0.5*(cmp[i][3]*cphi[i][2]+cmp[i][2]*cphi[i][3]) - cmp[i][7]*cphi[i][7] - cmp[i][9]*cphi[i][9];
(cmp[i][5]+cmp[i][6])*cphi[i][9] - 0.5*cmp[i][9]*(cphi[i][5]+cphi[i][6]) - vyz = vyz - 0.5*(cmp[i][3]*cphi[i][2]+cmp[i][2]*cphi[i][3]) -
0.5*(cmp[i][7]*cphi[i][8]+cmp[i][8]*cphi[i][7]); (cmp[i][5]+cmp[i][6])*cphi[i][9] - 0.5*cmp[i][9]*(cphi[i][5]+cphi[i][6]) -
vzz = vzz - cmp[i][3]*cphi[i][3] - 2.0*cmp[i][6]*cphi[i][6] - 0.5*(cmp[i][7]*cphi[i][8]+cmp[i][8]*cphi[i][7]);
cmp[i][8]*cphi[i][8] - cmp[i][9]*cphi[i][9]; vzz = vzz - cmp[i][3]*cphi[i][3] - 2.0*cmp[i][6]*cphi[i][6] -
cmp[i][8]*cphi[i][8] - cmp[i][9]*cphi[i][9];
}
} }
// resolve site torques then increment forces and virial // resolve site torques then increment forces and virial
@ -804,39 +803,43 @@ void PairAmoeba::multipole_kspace()
torque2force(i,tem,fix,fiy,fiz,f); torque2force(i,tem,fix,fiy,fiz,f);
iz = zaxis2local[i]; if (vflag_global) {
ix = xaxis2local[i]; iz = zaxis2local[i];
iy = yaxis2local[i]; ix = xaxis2local[i];
iy = yaxis2local[i];
xiz = x[iz][0] - x[i][0]; xiz = x[iz][0] - x[i][0];
yiz = x[iz][1] - x[i][1]; yiz = x[iz][1] - x[i][1];
ziz = x[iz][2] - x[i][2]; ziz = x[iz][2] - x[i][2];
xix = x[ix][0] - x[i][0]; xix = x[ix][0] - x[i][0];
yix = x[ix][1] - x[i][1]; yix = x[ix][1] - x[i][1];
zix = x[ix][2] - x[i][2]; zix = x[ix][2] - x[i][2];
xiy = x[iy][0] - x[i][0]; xiy = x[iy][0] - x[i][0];
yiy = x[iy][1] - x[i][1]; yiy = x[iy][1] - x[i][1];
ziy = x[iy][2] - x[i][2]; ziy = x[iy][2] - x[i][2];
vxx += xix*fix[0] + xiy*fiy[0] + xiz*fiz[0]; vxx += xix*fix[0] + xiy*fiy[0] + xiz*fiz[0];
vxy += 0.5*(yix*fix[0] + yiy*fiy[0] + yiz*fiz[0] + vxy += 0.5*(yix*fix[0] + yiy*fiy[0] + yiz*fiz[0] +
xix*fix[1] + xiy*fiy[1] + xiz*fiz[1]); xix*fix[1] + xiy*fiy[1] + xiz*fiz[1]);
vxz += 0.5*(zix*fix[0] + ziy*fiy[0] + ziz*fiz[0] + vxz += 0.5*(zix*fix[0] + ziy*fiy[0] + ziz*fiz[0] +
xix*fix[2] + xiy*fiy[2] + xiz*fiz[2]); xix*fix[2] + xiy*fiy[2] + xiz*fiz[2]);
vyy += yix*fix[1] + yiy*fiy[1] + yiz*fiz[1]; vyy += yix*fix[1] + yiy*fiy[1] + yiz*fiz[1];
vyz += 0.5*(zix*fix[1] + ziy*fiy[1] + ziz*fiz[1] + vyz += 0.5*(zix*fix[1] + ziy*fiy[1] + ziz*fiz[1] +
yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]); yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]);
vzz += zix*fix[2] + ziy*fiy[2] + ziz*fiz[2]; vzz += zix*fix[2] + ziy*fiy[2] + ziz*fiz[2];
}
} }
// increment total internal virial tensor components // increment total internal virial tensor components
virmpole[0] -= vxx; if (vflag_global) {
virmpole[1] -= vyy; virmpole[0] -= vxx;
virmpole[2] -= vzz; virmpole[1] -= vyy;
virmpole[3] -= vxy; virmpole[2] -= vzz;
virmpole[4] -= vxz; virmpole[3] -= vxy;
virmpole[5] -= vyz; virmpole[4] -= vxz;
virmpole[5] -= vyz;
}
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

53
src/AMOEBA/amoeba_polar.cpp
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@ -100,6 +100,8 @@ void PairAmoeba::polar()
torque2force(i,tep,fix,fiy,fiz,f); torque2force(i,tep,fix,fiy,fiz,f);
if (!vflag_global) continue;
iz = zaxis2local[i]; iz = zaxis2local[i];
ix = xaxis2local[i]; ix = xaxis2local[i];
iy = yaxis2local[i]; iy = yaxis2local[i];
@ -113,7 +115,7 @@ void PairAmoeba::polar()
xiy = x[iy][0] - x[i][0]; xiy = x[iy][0] - x[i][0];
yiy = x[iy][1] - x[i][1]; yiy = x[iy][1] - x[i][1];
ziy = x[iy][2] - x[i][2]; ziy = x[iy][2] - x[i][2];
vxx = xix*fix[0] + xiy*fiy[0] + xiz*fiz[0]; vxx = xix*fix[0] + xiy*fiy[0] + xiz*fiz[0];
vyy = yix*fix[1] + yiy*fiy[1] + yiz*fiz[1]; vyy = yix*fix[1] + yiy*fiy[1] + yiz*fiz[1];
vzz = zix*fix[2] + ziy*fiy[2] + ziz*fiz[2]; vzz = zix*fix[2] + ziy*fiy[2] + ziz*fiz[2];
@ -124,7 +126,7 @@ void PairAmoeba::polar()
xix*fix[2] + xiy*fiy[2] + xiz*fiz[2]); xix*fix[2] + xiy*fiy[2] + xiz*fiz[2]);
vyz = 0.5 * (zix*fix[1] + ziy*fiy[1] + ziz*fiz[1] + vyz = 0.5 * (zix*fix[1] + ziy*fiy[1] + ziz*fiz[1] +
yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]); yix*fix[2] + yiy*fiy[2] + yiz*fiz[2]);
virpolar[0] -= vxx; virpolar[0] -= vxx;
virpolar[1] -= vyy; virpolar[1] -= vyy;
virpolar[2] -= vzz; virpolar[2] -= vzz;
@ -1139,25 +1141,20 @@ void PairAmoeba::polar_real()
// increment the virial due to pairwise Cartesian forces // increment the virial due to pairwise Cartesian forces
vxx = xr * frcx; if (vflag_global) {
vxy = 0.5 * (yr*frcx+xr*frcy); vxx = xr * frcx;
vxz = 0.5 * (zr*frcx+xr*frcz); vxy = 0.5 * (yr*frcx+xr*frcy);
vyy = yr * frcy; vxz = 0.5 * (zr*frcx+xr*frcz);
vyz = 0.5 * (zr*frcy+yr*frcz); vyy = yr * frcy;
vzz = zr * frcz; vyz = 0.5 * (zr*frcy+yr*frcz);
vzz = zr * frcz;
virpolar[0] -= vxx; virpolar[0] -= vxx;
virpolar[1] -= vyy; virpolar[1] -= vyy;
virpolar[2] -= vzz; virpolar[2] -= vzz;
virpolar[3] -= vxy; virpolar[3] -= vxy;
virpolar[4] -= vxz; virpolar[4] -= vxz;
virpolar[5] -= vyz; virpolar[5] -= vyz;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
} }
} }
} }
@ -1191,6 +1188,8 @@ void PairAmoeba::polar_real()
torque2force(i,tep,fix,fiy,fiz,f); torque2force(i,tep,fix,fiy,fiz,f);
if (!vflag_global) continue;
iz = zaxis2local[i]; iz = zaxis2local[i];
ix = xaxis2local[i]; ix = xaxis2local[i];
iy = yaxis2local[i]; iy = yaxis2local[i];
@ -2163,10 +2162,12 @@ void PairAmoeba::polar_kspace()
// increment the total internal virial tensor components // increment the total internal virial tensor components
virpolar[0] -= vxx; if (vflag_global) {
virpolar[1] -= vyy; virpolar[0] -= vxx;
virpolar[2] -= vzz; virpolar[1] -= vyy;
virpolar[3] -= vxy; virpolar[2] -= vzz;
virpolar[4] -= vxz; virpolar[3] -= vxy;
virpolar[5] -= vyz; virpolar[4] -= vxz;
virpolar[5] -= vyz;
}
} }

42
src/AMOEBA/amoeba_repulsion.cpp
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@ -354,32 +354,24 @@ void PairAmoeba::repulsion()
// increment the virial due to pairwise Cartesian forces // increment the virial due to pairwise Cartesian forces
vxx = -xr * frcx; if (vflag_global) {
vxy = -0.5 * (yr*frcx+xr*frcy); vxx = -xr * frcx;
vxz = -0.5 * (zr*frcx+xr*frcz); vxy = -0.5 * (yr*frcx+xr*frcy);
vyy = -yr * frcy; vxz = -0.5 * (zr*frcx+xr*frcz);
vyz = -0.5 * (zr*frcy+yr*frcz); vyy = -yr * frcy;
vzz = -zr * frcz; vyz = -0.5 * (zr*frcy+yr*frcz);
vzz = -zr * frcz;
virrepulse[0] -= vxx; virrepulse[0] -= vxx;
virrepulse[1] -= vyy; virrepulse[1] -= vyy;
virrepulse[2] -= vzz; virrepulse[2] -= vzz;
virrepulse[3] -= vxy; virrepulse[3] -= vxy;
virrepulse[4] -= vxz; virrepulse[4] -= vxz;
virrepulse[5] -= vyz; virrepulse[5] -= vyz;
// energy = e
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
} }
} }
} }
// DEBUG
//fclose(fp);
// reverse comm to sum torque from ghost atoms to owned atoms // reverse comm to sum torque from ghost atoms to owned atoms
crstyle = TORQUE; crstyle = TORQUE;
@ -390,6 +382,8 @@ void PairAmoeba::repulsion()
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {
torque2force(i,tq[i],fix,fiy,fiz,f); torque2force(i,tq[i],fix,fiy,fiz,f);
if (!vflag_global) continue;
iz = zaxis2local[i]; iz = zaxis2local[i];
ix = xaxis2local[i]; ix = xaxis2local[i];
iy = yaxis2local[i]; iy = yaxis2local[i];
@ -420,12 +414,6 @@ void PairAmoeba::repulsion()
virrepulse[3] -= vxy; virrepulse[3] -= vxy;
virrepulse[4] -= vxz; virrepulse[4] -= vxz;
virrepulse[5] -= vyz; virrepulse[5] -= vyz;
// virial = 6-vec vir
// NOTE: add tally function
if (evflag) {
}
} }
} }

117
src/AMOEBA/pair_amoeba.cpp
View File

@ -49,8 +49,6 @@ enum{GEAR,ASPC,LSQR};
#define DELTASTACK 16 #define DELTASTACK 16
#define UIND_DEBUG 0 // also in amoeba_induce.cpp
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
PairAmoeba::PairAmoeba(LAMMPS *lmp) : Pair(lmp) PairAmoeba::PairAmoeba(LAMMPS *lmp) : Pair(lmp)
@ -67,10 +65,16 @@ PairAmoeba::PairAmoeba(LAMMPS *lmp) : Pair(lmp)
me = comm->me; me = comm->me;
nprocs = comm->nprocs; nprocs = comm->nprocs;
// force field settings // pair style settings
one_coeff = 1; one_coeff = 1;
single_enable = 0; single_enable = 0;
no_virial_fdotr_compute = 1;
nextra = 6;
pvector = new double[nextra];
// force field settings
amoeba = 1; amoeba = 1;
hippo = 0; hippo = 0;
@ -165,6 +169,8 @@ PairAmoeba::PairAmoeba(LAMMPS *lmp) : Pair(lmp)
PairAmoeba::~PairAmoeba() PairAmoeba::~PairAmoeba()
{ {
delete [] pvector;
// check nfix in case all fixes have already been deleted // check nfix in case all fixes have already been deleted
if (modify->nfix) { if (modify->nfix) {
@ -275,26 +281,12 @@ PairAmoeba::~PairAmoeba()
} }
delete [] factors; delete [] factors;
// DEBUG
if (me == 0 && UIND_DEBUG) fclose(fp_uind);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void PairAmoeba::compute(int eflag, int vflag) void PairAmoeba::compute(int eflag, int vflag)
{ {
// DEBUG timer init
if (update->ntimestep <= 1) {
time_init = time_hal = time_repulse = time_disp = time_mpole = 0.0;
time_induce = time_polar = time_qxfer = 0.0;
}
double evdwl;
evdwl = 0.0;
ev_init(eflag,vflag); ev_init(eflag,vflag);
// zero energy/virial components // zero energy/virial components
@ -358,6 +350,13 @@ void PairAmoeba::compute(int eflag, int vflag)
// end of one-time initializations // end of one-time initializations
// ------------------------------------------------------------------- // -------------------------------------------------------------------
// initialize timers on first compute() call after setup
if (update->ntimestep <= update->beginstep+1) {
time_init = time_hal = time_repulse = time_disp = time_mpole = 0.0;
time_induce = time_polar = time_qxfer = 0.0;
}
double time0,time1,time2,time3,time4,time5,time6,time7,time8; double time0,time1,time2,time3,time4,time5,time6,time7,time8;
MPI_Barrier(world); MPI_Barrier(world);
@ -462,29 +461,27 @@ void PairAmoeba::compute(int eflag, int vflag)
// charge transfer, pairwise // charge transfer, pairwise
if (hippo && qxfer_flag) charge_transfer(); if (hippo && qxfer_flag) charge_transfer();
time8 = MPI_Wtime(); time8 = MPI_Wtime();
// energy, force, virial summations // store energy components for output by compute pair command
eng_vdwl = ehal + erepulse + edisp + empole + epolar + eqxfer; pvector[0] = ehal;
pvector[2] = erepulse;
pvector[3] = edisp;
pvector[4] = empole;
pvector[5] = epolar;
pvector[6] = eqxfer;
double **f = atom->f; // energy & virial summations
nlocal = atom->nlocal;
int nall = nlocal + atom->nghost; eng_vdwl = ehal + edisp;
eng_coul = erepulse + empole + epolar + eqxfer;
for (int i = 0; i < 6; i++) for (int i = 0; i < 6; i++)
virial[i] = virhal[i] + virrepulse[i] + virdisp[i] + virial[i] = virhal[i] + virrepulse[i] + virdisp[i] +
virpolar[i] + virmpole[i] + virqxfer[i]; virpolar[i] + virmpole[i] + virqxfer[i];
// virial computation // accumulate timing information
// NOTE: how does this work for AMOEBA ?
// do all terms get summed this way, or only pairwise
// it is 2x what summed virial[6] above is
// if (vflag_fdotr) virial_fdotr_compute();
// timing information
time_init += time1 - time0; time_init += time1 - time0;
time_hal += time2 - time1; time_hal += time2 - time1;
@ -494,15 +491,18 @@ void PairAmoeba::compute(int eflag, int vflag)
time_induce += time6 - time5; time_induce += time6 - time5;
time_polar += time7 - time6; time_polar += time7 - time6;
time_qxfer += time8 - time7; time_qxfer += time8 - time7;
}
// timing output /* ----------------------------------------------------------------------
print out AMOEBA/HIPPO timing info at end of run
if (update->ntimestep < update->laststep) return; ------------------------------------------------------------------------- */
void PairAmoeba::finish()
{
double ave; double ave;
MPI_Allreduce(&time_init,&ave,1,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&time_init,&ave,1,MPI_DOUBLE,MPI_SUM,world);
time_init = ave/nprocs; time_init = ave/nprocs;
MPI_Allreduce(&time_hal,&ave,1,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&time_hal,&ave,1,MPI_DOUBLE,MPI_SUM,world);
time_hal = ave/nprocs; time_hal = ave/nprocs;
@ -524,32 +524,32 @@ void PairAmoeba::compute(int eflag, int vflag)
MPI_Allreduce(&time_qxfer,&ave,1,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&time_qxfer,&ave,1,MPI_DOUBLE,MPI_SUM,world);
time_qxfer = ave/nprocs; time_qxfer = ave/nprocs;
double time_amtot = time_init + time_hal + time_repulse + time_disp + double time_total = time_init + time_hal + time_repulse + time_disp +
time_mpole + time_induce + time_polar + time_qxfer; time_mpole + time_induce + time_polar + time_qxfer;
if (me == 0) { if (me == 0) {
utils::logmesg(lmp,"\nAMEOBA/HIPPO timing info:\n"); utils::logmesg(lmp,"\nAMEOBA/HIPPO timing breakdown:\n");
utils::logmesg(lmp," Init time: {:.6g} {:.6g}\n", utils::logmesg(lmp," Init time: {:.6g} {:.6g}\n",
time_init,time_init/time_amtot); time_init,time_init/time_total);
if (amoeba) if (amoeba)
utils::logmesg(lmp," Hal time: {:.6g} {:.6g}\n", utils::logmesg(lmp," Hal time: {:.6g} {:.6g}\n",
time_hal,time_hal/time_amtot*100); time_hal,time_hal/time_total*100);
if (hippo) if (hippo)
utils::logmesg(lmp," Repls time: {:.6g} {:.6g}\n", utils::logmesg(lmp," Repulse time: {:.6g} {:.6g}\n",
time_repulse,time_repulse/time_amtot*100); time_repulse,time_repulse/time_total*100);
if (hippo) if (hippo)
utils::logmesg(lmp," Disp time: {:.6g} {:.6g}\n", utils::logmesg(lmp," Disp time: {:.6g} {:.6g}\n",
time_disp,time_disp/time_amtot*100); time_disp,time_disp/time_total*100);
utils::logmesg(lmp," Mpole time: {:.6g} {:.6g}\n", utils::logmesg(lmp," Mpole time: {:.6g} {:.6g}\n",
time_mpole,time_mpole/time_amtot*100); time_mpole,time_mpole/time_total*100);
utils::logmesg(lmp," Induce time: {:.6g} {:.6g}\n", utils::logmesg(lmp," Induce time: {:.6g} {:.6g}\n",
time_induce,time_induce/time_amtot*100); time_induce,time_induce/time_total*100);
utils::logmesg(lmp," Polar time: {:.6g} {:.6g}\n", utils::logmesg(lmp," Polar time: {:.6g} {:.6g}\n",
time_polar,time_polar/time_amtot*100); time_polar,time_polar/time_total*100);
if (hippo) if (hippo)
utils::logmesg(lmp," Qxfer time: {:.6g} {:.6g}\n", utils::logmesg(lmp," Qxfer time: {:.6g} {:.6g}\n",
time_qxfer,time_qxfer/time_amtot*100); time_qxfer,time_qxfer/time_total*100);
utils::logmesg(lmp," Total time: {:.6g}\n\n",time_amtot); utils::logmesg(lmp," Total time: {:.6g}\n",time_total);
} }
} }
@ -1016,15 +1016,6 @@ void PairAmoeba::init_style()
// request neighbor lists // request neighbor lists
int irequest = neighbor->request(this,instance_me); int irequest = neighbor->request(this,instance_me);
// open debug output files
// names are hard-coded
if (me == 0) {
char fname[32];
sprintf(fname,"tmp.uind.kspace.%d",nprocs);
if (UIND_DEBUG) fp_uind = fopen(fname,"w");
}
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

1
src/AMOEBA/pair_amoeba.h
View File

@ -46,6 +46,7 @@ class PairAmoeba : public Pair {
void coeff(int, char **); void coeff(int, char **);
void init_style(); void init_style();
double init_one(int, int); double init_one(int, int);
void finish();
int pack_forward_comm(int, int *, double *, int, int *); int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *); void unpack_forward_comm(int, int, double *);

5
src/finish.cpp
View File

@ -28,6 +28,7 @@
#include "neigh_request.h" #include "neigh_request.h"
#include "neighbor.h" // IWYU pragma: keep #include "neighbor.h" // IWYU pragma: keep
#include "output.h" #include "output.h"
#include "pair.h"
#include "thermo.h" #include "thermo.h"
#include "timer.h" // IWYU pragma: keep #include "timer.h" // IWYU pragma: keep
#include "universe.h" #include "universe.h"
@ -214,6 +215,10 @@ void Finish::end(int flag)
} }
} }
// pair_style timing stats if provided
if (force->pair) force->pair->finish();
// PRD stats // PRD stats
if (prdflag) { if (prdflag) {

1
src/pair.h
View File

@ -169,6 +169,7 @@ class Pair : protected Pointers {
return 0.0; return 0.0;
} }
virtual void finish() {}
virtual void settings(int, char **) = 0; virtual void settings(int, char **) = 0;
virtual void coeff(int, char **) = 0; virtual void coeff(int, char **) = 0;

6
src/pair_hybrid.cpp
View File

@ -192,6 +192,12 @@ void PairHybrid::compute(int eflag, int vflag)
if (vflag_fdotr) virial_fdotr_compute(); if (vflag_fdotr) virial_fdotr_compute();
} }
/* ---------------------------------------------------------------------- */
void PairHybrid::finish()
{
for (int m = 0; m < nstyles; m++) styles[m]->finish();
}
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

1
src/pair_hybrid.h
View File

@ -46,6 +46,7 @@ class PairHybrid : public Pair {
void init_style() override; void init_style() override;
double init_one(int, int) override; double init_one(int, int) override;
void setup() override; void setup() override;
void finish();
void write_restart(FILE *) override; void write_restart(FILE *) override;
void read_restart(FILE *) override; void read_restart(FILE *) override;
double single(int, int, int, int, double, double, double, double &) override; double single(int, int, int, int, double, double, double, double &) override;