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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6499 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-07-01 15:38:33 +00:00
parent 32a2028114
commit f19afbe481
3 changed files with 123 additions and 99 deletions
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185
src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
View File

@ -71,11 +71,11 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double delx1,dely1,delz1,delx2,dely2,delz2,delx3,dely3,delz3;
double r,r2inv,r6inv,forcecoul,forcelj,cforce,negforce;
double delxOM, delyOM, delzOM;
double r,r2inv,r6inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],v[6];
double grij,expm2,prefactor,t,erfc,ddotf;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],f1[3],v[6],xH1[3],xH2[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
@ -153,7 +153,7 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
evdwl,0.0,forcelj,delx,dely,delz);
}
// adjust rsq for off-site O charge(s)
// adjust rsq and delxyz for off-site O charge(s)
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
@ -199,11 +199,11 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
cforce = forcecoul * r2inv;
// if i,j are not O atoms, force is applied directly
// if i or j are O atoms, force is on fictitious atom
// if i or j are O atoms, force is on fictitious atom & partitioned
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
// preserves total force and torque on water molecule
// all virial terms are computed as distances to x2
// virial = sum(r x F) where each water's atoms are near xi and xj
// vlist stores 2,4,6 atoms whose forces contribute to virial
n = 0;
@ -214,59 +214,62 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
f[i][2] += delz * cforce;
if (vflag) {
v[0] = delx * delx * cforce;
v[1] = dely * dely * cforce;
v[2] = delz * delz * cforce;
v[3] = delx * dely * cforce;
v[4] = delx * delz * cforce;
v[5] = dely * delz * cforce;
v[0] = x[i][0] * delx * cforce;
v[1] = x[i][1] * dely * cforce;
v[2] = x[i][2] * delz * cforce;
v[3] = x[i][0] * dely * cforce;
v[4] = x[i][0] * delz * cforce;
v[5] = x[i][1] * delz * cforce;
vlist[n++] = i;
}
} else {
fO[0] = delx*cforce*(1.0-2.0*alpha);
fO[1] = dely*cforce*(1.0-2.0*alpha);
fO[2] = delz*cforce*(1.0-2.0*alpha);
fH[0] = alpha * (delx*cforce);
fH[1] = alpha * (dely*cforce);
fH[2] = alpha * (delz*cforce);
fd[0] = delx*cforce;
fd[1] = dely*cforce;
fd[2] = delz*cforce;
f[i][0] += fO[0];
f[i][1] += fO[1];
f[i][2] += fO[2];
delxOM = x[i][0] - x1[0];
delyOM = x[i][1] - x1[1];
delzOM = x[i][2] - x1[2];
f[iH1][0] += fH[0];
f[iH1][1] += fH[1];
f[iH1][2] += fH[2];
f[iH2][0] += fH[0];
f[iH2][1] += fH[1];
f[iH2][2] += fH[2];
ddotf = (delxOM * fd[0] + delyOM * fd[1] + delzOM * fd[2]) /
(qdist*qdist);
f1[0] = ddotf * delxOM;
f1[1] = ddotf * delyOM;
f1[2] = ddotf * delzOM;
fO[0] = fd[0] - alpha * (fd[0] - f1[0]);
fO[1] = fd[1] - alpha * (fd[1] - f1[1]);
fO[2] = fd[2] - alpha * (fd[2] - f1[2]);
fH[0] = 0.5 * alpha * (fd[0] - f1[0]);
fH[1] = 0.5 * alpha * (fd[1] - f1[1]);
fH[2] = 0.5 * alpha * (fd[2] - f1[2]);
f[i][0] += fO[0];
f[i][1] += fO[1];
f[i][2] += fO[2];
f[iH1][0] += fH[0];
f[iH1][1] += fH[1];
f[iH1][2] += fH[2];
f[iH2][0] += fH[0];
f[iH2][1] += fH[1];
f[iH2][2] += fH[2];
if (vflag) {
delx1 = x[i][0] - x2[0];
dely1 = x[i][1] - x2[1];
delz1 = x[i][2] - x2[2];
domain->minimum_image(delx1,dely1,delz1);
domain->closest_image(x[i],x[iH1],xH1);
domain->closest_image(x[i],x[iH2],xH2);
delx2 = x[iH1][0] - x2[0];
dely2 = x[iH1][1] - x2[1];
delz2 = x[iH1][2] - x2[2];
domain->minimum_image(delx2,dely2,delz2);
delx3 = x[iH2][0] - x2[0];
dely3 = x[iH2][1] - x2[1];
delz3 = x[iH2][2] - x2[2];
domain->minimum_image(delx3,dely3,delz3);
v[0] = delx1 * fO[0] + (delx2 + delx3) * fH[0];
v[1] = dely1 * fO[1] + (dely2 + dely3) * fH[1];
v[2] = delz1 * fO[2] + (delz2 + delz3) * fH[2];
v[3] = delx1 * fO[1] + (delx2 + delx3) * fH[1];
v[4] = delx1 * fO[2] + (delx2 + delx3) * fH[2];
v[5] = dely1 * fO[2] + (dely2 + dely3) * fH[2];
v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
v[3] = x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
v[4] = x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
v[5] = x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
vlist[n++] = i;
vlist[n++] = iH1;
@ -279,23 +282,45 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
f[j][1] -= dely * cforce;
f[j][2] -= delz * cforce;
if (vflag) vlist[n++] = j;
if (vflag) {
v[0] -= x[j][0] * delx * cforce;
v[1] -= x[j][1] * dely * cforce;
v[2] -= x[j][2] * delz * cforce;
v[3] -= x[j][0] * dely * cforce;
v[4] -= x[j][0] * delz * cforce;
v[5] -= x[j][1] * delz * cforce;
vlist[n++] = j;
}
} else {
negforce = -cforce;
fO[0] = delx*negforce*(1.0-2.0*alpha);
fO[1] = dely*negforce*(1.0-2.0*alpha);
fO[2] = delz*negforce*(1.0-2.0*alpha);
fd[0] = -delx*cforce;
fd[1] = -dely*cforce;
fd[2] = -delz*cforce;
fH[0] = alpha * (delx*negforce);
fH[1] = alpha * (dely*negforce);
fH[2] = alpha * (delz*negforce);
delxOM = x[j][0] - x2[0];
delyOM = x[j][1] - x2[1];
delzOM = x[j][2] - x2[2];
ddotf = (delxOM * fd[0] + delyOM * fd[1] + delzOM * fd[2]) /
(qdist*qdist);
f1[0] = ddotf * delxOM;
f1[1] = ddotf * delyOM;
f1[2] = ddotf * delzOM;
fO[0] = fd[0] - alpha * (fd[0] - f1[0]);
fO[1] = fd[1] - alpha * (fd[1] - f1[1]);
fO[2] = fd[2] - alpha * (fd[2] - f1[2]);
fH[0] = 0.5 * alpha * (fd[0] - f1[0]);
fH[1] = 0.5 * alpha * (fd[1] - f1[1]);
fH[2] = 0.5 * alpha * (fd[2] - f1[2]);
f[j][0] += fO[0];
f[j][1] += fO[1];
f[j][2] += fO[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
f[j][2] += fO[2];
f[jH1][0] += fH[0];
f[jH1][1] += fH[1];
f[jH1][2] += fH[2];
@ -305,27 +330,15 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
f[jH2][2] += fH[2];
if (vflag) {
delx1 = x[j][0] - x2[0];
dely1 = x[j][1] - x2[1];
delz1 = x[j][2] - x2[2];
domain->minimum_image(delx1,dely1,delz1);
domain->closest_image(x[j],x[jH1],xH1);
domain->closest_image(x[j],x[jH2],xH2);
delx2 = x[jH1][0] - x2[0];
dely2 = x[jH1][1] - x2[1];
delz2 = x[jH1][2] - x2[2];
domain->minimum_image(delx2,dely2,delz2);
delx3 = x[jH2][0] - x2[0];
dely3 = x[jH2][1] - x2[1];
delz3 = x[jH2][2] - x2[2];
domain->minimum_image(delx3,dely3,delz3);
v[0] += delx1 * fO[0] + (delx2 + delx3) * fH[0];
v[1] += dely1 * fO[1] + (dely2 + dely3) * fH[1];
v[2] += delz1 * fO[2] + (delz2 + delz3) * fH[2];
v[3] += delx1 * fO[1] + (delx2 + delx3) * fH[1];
v[4] += delx1 * fO[2] + (delx2 + delx3) * fH[2];
v[5] += dely1 * fO[2] + (dely2 + dely3) * fH[2];
v[0] += x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] += x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] += x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
v[3] += x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
v[4] += x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
v[5] += x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
vlist[n++] = j;
vlist[n++] = jH1;
@ -403,7 +416,7 @@ void PairLJCutCoulLongTIP4P::init_style()
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
alpha = qdist / (2.0 * cos(0.5*theta) * blen);
alpha = qdist / (cos(0.5*theta) * blen);
}
/* ----------------------------------------------------------------------
@ -485,9 +498,9 @@ void PairLJCutCoulLongTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
double delz2 = x[iH2][2] - x[i][2];
domain->minimum_image(delx2,dely2,delz2);
xM[0] = x[i][0] + alpha * (delx1 + delx2);
xM[1] = x[i][1] + alpha * (dely1 + dely2);
xM[2] = x[i][2] + alpha * (delz1 + delz2);
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);
}
/* ---------------------------------------------------------------------- */

2
src/KSPACE/pppm.cpp
View File

@ -174,7 +174,7 @@ void PPPM::init()
error->all("Bad TIP4P bond type for PPPM/TIP4P");
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
alpha = qdist / (2.0 * cos(0.5*theta) * blen);
alpha = qdist / (cos(0.5*theta) * blen);
}
// compute qsum & qsqsum and warn if not charge-neutral

35
src/KSPACE/pppm_tip4p.cpp
View File

@ -149,6 +149,7 @@ void PPPMTIP4P::fieldforce()
int iH1,iH2;
double xM[3];
double fx,fy,fz;
double ddotf, rOM[3], f1[3];
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
@ -207,17 +208,27 @@ void PPPMTIP4P::fieldforce()
fz = qqrd2e * q[i] * ek[2];
find_M(i,iH1,iH2,xM);
f[i][0] += fx*(1.0-2.0*alpha);
f[i][1] += fy*(1.0-2.0*alpha);
f[i][2] += fz*(1.0-2.0*alpha);
rOM[0] = xM[0] - x[i][0];
rOM[1] = xM[1] - x[i][1];
rOM[2] = xM[2] - x[i][2];
ddotf = (rOM[0] * fx + rOM[1] * fy + rOM[2] * fz) / (qdist * qdist);
f[iH1][0] += alpha*(fx);
f[iH1][1] += alpha*(fy);
f[iH1][2] += alpha*(fz);
f1[0] = ddotf * rOM[0];
f1[1] = ddotf * rOM[1];
f1[2] = ddotf * rOM[2];
f[iH2][0] += alpha*(fx);
f[iH2][1] += alpha*(fy);
f[iH2][2] += alpha*(fz);
f[i][0] += fx - alpha * (fx - f1[0]);
f[i][1] += fy - alpha * (fy - f1[1]);
f[i][2] += fz - alpha * (fz - f1[2]);
f[iH1][0] += 0.5*alpha*(fx - f1[0]);
f[iH1][1] += 0.5*alpha*(fy - f1[1]);
f[iH1][2] += 0.5*alpha*(fz - f1[2]);
f[iH2][0] += 0.5*alpha*(fx - f1[0]);
f[iH2][1] += 0.5*alpha*(fy - f1[1]);
f[iH2][2] += 0.5*alpha*(fz - f1[2]);
}
}
}
@ -249,7 +260,7 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
double delz2 = x[iH2][2] - x[i][2];
domain->minimum_image(delx2,dely2,delz2);
xM[0] = x[i][0] + alpha * (delx1 + delx2);
xM[1] = x[i][1] + alpha * (dely1 + dely2);
xM[2] = x[i][2] + alpha * (delz1 + delz2);
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);
}