forked from lijiext/lammps
In PairAIREBO::bondorderLJ: p^sigma pi account for d/drij derivatives.
The bonderorderLJ function operates on a facticious distance |rij|, i.e. everything gets calculated "as if" atoms i and j were a given distance alpha apart. Mathematically, bondorderLJ is a function of rij (a vector), that is (in terms of the real distance Rij) rij = alpha * Rij/|Rij|. When we calculate the forces in bondorderLJ, we have to make sure to chain in this derivative whenever we calculate derivatives w.r.t. rij. The right correction, as it turns our, is Fij = alpha / |Rij| * (Identity(3,3) - Rij * Rij^T / |Rij|^2) * fij. This commit only fixes this for the p_ij^sigma pi terms, which were modified to separate out the d/drij derivative in the cosine calculation. Now, derivatives are taken w.r.t. the connecting edges instead of the edge points.
This commit is contained in:
Markus Hoehnerbach
parent
1b3f6e257a
commit
0e16dc3ead
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@ -2130,6 +2130,12 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
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Stb = 0.0;
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Stb = 0.0;
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dStb = 0.0;
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dStb = 0.0;
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double realrij[3];
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realrij[0] = x[atomi][0] - x[atomj][0];
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realrij[1] = x[atomi][1] - x[atomj][1];
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realrij[2] = x[atomi][2] - x[atomj][2];
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double realrijmag = sqrt(realrij[0] * realrij[0] + realrij[1] * realrij[1] + realrij[2] * realrij[2]);
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REBO_neighs = REBO_firstneigh[i];
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REBO_neighs = REBO_firstneigh[i];
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for (k = 0; k < REBO_numneigh[i]; k++) {
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for (k = 0; k < REBO_numneigh[i]; k++) {
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atomk = REBO_neighs[k];
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atomk = REBO_neighs[k];
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@ -2319,50 +2325,55 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
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lamdajik = 4.0*kronecker(itype,1) *
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lamdajik = 4.0*kronecker(itype,1) *
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((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
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((rho[ktype][1]-rikmag)-(rho[jtype][1]-rijmag));
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wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
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wik = Sp(rikmag,rcmin[itype][ktype],rcmax[itype][ktype],dwik);
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cosjik = ((rij[0]*rik[0])+(rij[1]*rik[1])+(rij[2]*rik[2])) /
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double rjk[3];
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(rijmag*rikmag);
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rjk[0] = rik[0] - rij[0];
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rjk[1] = rik[1] - rij[1];
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rjk[2] = rik[2] - rij[2];
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double rjkmag = sqrt(rjk[0] * rjk[0] + rjk[1] * rjk[1] + rjk[2] * rjk[2]);
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double rijrik = 2 * rijmag * rikmag;
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double rr = rijmag * rijmag - rikmag * rikmag;
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cosjik = (rr + rikmag * rikmag - rjkmag * rjkmag) / rijrik;
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cosjik = MIN(cosjik,1.0);
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cosjik = MIN(cosjik,1.0);
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cosjik = MAX(cosjik,-1.0);
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cosjik = MAX(cosjik,-1.0);
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double dctdjk = -2 / rijrik;
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dcosjikdri[0] = ((rij[0]+rik[0])/(rijmag*rikmag)) -
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double dctdik = (-rr + rjkmag * rjkmag) / (rijrik * rikmag * rikmag);
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(cosjik*((rij[0]/(rijmag*rijmag))+(rik[0]/(rikmag*rikmag))));
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// evaluate splines g and derivatives dg
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dcosjikdri[1] = ((rij[1]+rik[1])/(rijmag*rikmag)) -
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(cosjik*((rij[1]/(rijmag*rijmag))+(rik[1]/(rikmag*rikmag))));
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dcosjikdri[2] = ((rij[2]+rik[2])/(rijmag*rikmag)) -
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(cosjik*((rij[2]/(rijmag*rijmag))+(rik[2]/(rikmag*rikmag))));
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dcosjikdrk[0] = (-rij[0]/(rijmag*rikmag)) +
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(cosjik*(rik[0]/(rikmag*rikmag)));
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dcosjikdrk[1] = (-rij[1]/(rijmag*rikmag)) +
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(cosjik*(rik[1]/(rikmag*rikmag)));
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dcosjikdrk[2] = (-rij[2]/(rijmag*rikmag)) +
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(cosjik*(rik[2]/(rikmag*rikmag)));
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dcosjikdrj[0] = (-rik[0]/(rijmag*rikmag)) +
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(cosjik*(rij[0]/(rijmag*rijmag)));
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dcosjikdrj[1] = (-rik[1]/(rijmag*rikmag)) +
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(cosjik*(rij[1]/(rijmag*rijmag)));
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dcosjikdrj[2] = (-rik[2]/(rijmag*rikmag)) +
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(cosjik*(rij[2]/(rijmag*rijmag)));
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g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
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g = gSpline(cosjik,(NijC+NijH),itype,&dgdc,&dgdN);
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tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik));
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tmp2 = VA*.5*(tmp*wik*dgdc*exp(lamdajik));
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fj[0] = -tmp2*dcosjikdrj[0];
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fj[1] = -tmp2*dcosjikdrj[1];
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fi[0] = tmp2 * dctdik * rik[0];
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fj[2] = -tmp2*dcosjikdrj[2];
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fi[1] = tmp2 * dctdik * rik[1];
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fi[0] = -tmp2*dcosjikdri[0];
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fi[2] = tmp2 * dctdik * rik[2];
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fi[1] = -tmp2*dcosjikdri[1];
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fk[0] = -tmp2 * dctdik * rik[0];
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fi[2] = -tmp2*dcosjikdri[2];
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fk[1] = -tmp2 * dctdik * rik[1];
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fk[0] = -tmp2*dcosjikdrk[0];
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fk[2] = -tmp2 * dctdik * rik[2];
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fk[1] = -tmp2*dcosjikdrk[1];
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fj[0] = 0;
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fk[2] = -tmp2*dcosjikdrk[2];
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fj[1] = 0;
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fj[2] = 0;
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double fjk[3];
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fjk[0] = tmp2 * dctdjk * rjk[0];
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fjk[1] = tmp2 * dctdjk * rjk[1];
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fjk[2] = tmp2 * dctdjk * rjk[2];
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fi[0] += fjk[0];
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fi[1] += fjk[1];
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fi[2] += fjk[2];
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fk[0] -= fjk[0];
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fk[1] -= fjk[1];
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fk[2] -= fjk[2];
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double rijmbr = rcmin[itype][jtype] / realrijmag;
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fj[0] += rijmbr * (fjk[0] - (realrij[0] * realrij[0] * fjk[0] + realrij[0] * realrij[1] * fjk[1] + realrij[0] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
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fj[1] += rijmbr * (fjk[1] - (realrij[1] * realrij[0] * fjk[0] + realrij[1] * realrij[1] * fjk[1] + realrij[1] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
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fj[2] += rijmbr * (fjk[2] - (realrij[2] * realrij[0] * fjk[0] + realrij[2] * realrij[1] * fjk[1] + realrij[2] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
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fi[0] -= rijmbr * (fjk[0] - (realrij[0] * realrij[0] * fjk[0] + realrij[0] * realrij[1] * fjk[1] + realrij[0] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
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fi[1] -= rijmbr * (fjk[1] - (realrij[1] * realrij[0] * fjk[0] + realrij[1] * realrij[1] * fjk[1] + realrij[1] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
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fi[2] -= rijmbr * (fjk[2] - (realrij[2] * realrij[0] * fjk[0] + realrij[2] * realrij[1] * fjk[1] + realrij[2] * realrij[2] * fjk[2]) / (realrijmag * realrijmag));
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tmp2 = VA*.5*(tmp*wik*g*exp(lamdajik)*4.0*kronecker(itype,1));
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tmp2 = VA*.5*(tmp*wik*g*exp(lamdajik)*4.0*kronecker(itype,1));
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fj[0] -= tmp2*(-rij[0]/rijmag);
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fi[0] += tmp2*(rik[0]/rikmag);
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fj[1] -= tmp2*(-rij[1]/rijmag);
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fi[1] += tmp2*(rik[1]/rikmag);
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fj[2] -= tmp2*(-rij[2]/rijmag);
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fi[2] += tmp2*(rik[2]/rikmag);
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fi[0] -= tmp2*((-rik[0]/rikmag)+(rij[0]/rijmag));
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fi[1] -= tmp2*((-rik[1]/rikmag)+(rij[1]/rijmag));
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fi[2] -= tmp2*((-rik[2]/rikmag)+(rij[2]/rijmag));
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fk[0] -= tmp2*(rik[0]/rikmag);
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fk[0] -= tmp2*(rik[0]/rikmag);
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fk[1] -= tmp2*(rik[1]/rikmag);
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fk[1] -= tmp2*(rik[1]/rikmag);
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fk[2] -= tmp2*(rik[2]/rikmag);
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fk[2] -= tmp2*(rik[2]/rikmag);
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@ -2427,51 +2438,55 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
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lamdaijl = 4.0*kronecker(jtype,1) *
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lamdaijl = 4.0*kronecker(jtype,1) *
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((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
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((rho[ltype][1]-rjlmag)-(rho[itype][1]-rijmag));
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wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
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wjl = Sp(rjlmag,rcmin[jtype][ltype],rcmax[jtype][ltype],dwjl);
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cosijl = (-1.0*((rij[0]*rjl[0])+(rij[1]*rjl[1])+(rij[2]*rjl[2]))) /
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double ril[3];
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(rijmag*rjlmag);
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ril[0] = rij[0] + rjl[0];
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ril[1] = rij[1] + rjl[1];
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ril[2] = rij[2] + rjl[2];
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double rilmag = sqrt(ril[0] * ril[0] + ril[1] * ril[1] + ril[2] * ril[2]);
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double rijrjl = 2 * rijmag * rjlmag;
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double rr = rijmag * rijmag - rjlmag * rjlmag;
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cosijl = (rr + rjlmag * rjlmag - rilmag * rilmag) / rijrjl;
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cosijl = MIN(cosijl,1.0);
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cosijl = MIN(cosijl,1.0);
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cosijl = MAX(cosijl,-1.0);
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cosijl = MAX(cosijl,-1.0);
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double dctdil = -2 / rijrjl;
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dcosijldri[0] = (-rjl[0]/(rijmag*rjlmag)) -
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double dctdjl = (-rr + rilmag * rilmag) / (rijrjl * rjlmag * rjlmag);
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(cosijl*rij[0]/(rijmag*rijmag));
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dcosijldri[1] = (-rjl[1]/(rijmag*rjlmag)) -
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(cosijl*rij[1]/(rijmag*rijmag));
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dcosijldri[2] = (-rjl[2]/(rijmag*rjlmag)) -
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(cosijl*rij[2]/(rijmag*rijmag));
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dcosijldrj[0] = ((-rij[0]+rjl[0])/(rijmag*rjlmag)) +
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(cosijl*((rij[0]/square(rijmag))-(rjl[0]/(rjlmag*rjlmag))));
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dcosijldrj[1] = ((-rij[1]+rjl[1])/(rijmag*rjlmag)) +
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(cosijl*((rij[1]/square(rijmag))-(rjl[1]/(rjlmag*rjlmag))));
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dcosijldrj[2] = ((-rij[2]+rjl[2])/(rijmag*rjlmag)) +
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(cosijl*((rij[2]/square(rijmag))-(rjl[2]/(rjlmag*rjlmag))));
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dcosijldrl[0] = (rij[0]/(rijmag*rjlmag)) +
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(cosijl*rjl[0]/(rjlmag*rjlmag));
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dcosijldrl[1] = (rij[1]/(rijmag*rjlmag)) +
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(cosijl*rjl[1]/(rjlmag*rjlmag));
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dcosijldrl[2] = (rij[2]/(rijmag*rjlmag)) +
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(cosijl*rjl[2]/(rjlmag*rjlmag));
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// evaluate splines g and derivatives dg
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// evaluate splines g and derivatives dg
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g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
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g = gSpline(cosijl,NjiC+NjiH,jtype,&dgdc,&dgdN);
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tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl));
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tmp2 = VA*.5*(tmp*wjl*dgdc*exp(lamdaijl));
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fi[0] = -tmp2*dcosijldri[0];
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fj[0] = tmp2 * dctdjl * rjl[0];
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fi[1] = -tmp2*dcosijldri[1];
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fj[1] = tmp2 * dctdjl * rjl[1];
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fi[2] = -tmp2*dcosijldri[2];
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fj[2] = tmp2 * dctdjl * rjl[2];
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fj[0] = -tmp2*dcosijldrj[0];
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fl[0] = -tmp2 * dctdjl * rjl[0];
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fj[1] = -tmp2*dcosijldrj[1];
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fl[1] = -tmp2 * dctdjl * rjl[1];
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fj[2] = -tmp2*dcosijldrj[2];
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fl[2] = -tmp2 * dctdjl * rjl[2];
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fl[0] = -tmp2*dcosijldrl[0];
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fi[0] = 0;
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fl[1] = -tmp2*dcosijldrl[1];
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fi[1] = 0;
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fl[2] = -tmp2*dcosijldrl[2];
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fi[2] = 0;
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double fil[3];
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fil[0] = tmp2 * dctdil * ril[0];
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fil[1] = tmp2 * dctdil * ril[1];
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fil[2] = tmp2 * dctdil * ril[2];
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fj[0] += fil[0];
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fj[1] += fil[1];
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fj[2] += fil[2];
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fl[0] -= fil[0];
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fl[1] -= fil[1];
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fl[2] -= fil[2];
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double rijmbr = rcmin[itype][jtype] / realrijmag;
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fi[0] += rijmbr * (fil[0] - (realrij[0] * realrij[0] * fil[0] + realrij[0] * realrij[1] * fil[1] + realrij[0] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
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fi[1] += rijmbr * (fil[1] - (realrij[1] * realrij[0] * fil[0] + realrij[1] * realrij[1] * fil[1] + realrij[1] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
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fi[2] += rijmbr * (fil[2] - (realrij[2] * realrij[0] * fil[0] + realrij[2] * realrij[1] * fil[1] + realrij[2] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
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fj[0] -= rijmbr * (fil[0] - (realrij[0] * realrij[0] * fil[0] + realrij[0] * realrij[1] * fil[1] + realrij[0] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
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fj[1] -= rijmbr * (fil[1] - (realrij[1] * realrij[0] * fil[0] + realrij[1] * realrij[1] * fil[1] + realrij[1] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
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fj[2] -= rijmbr * (fil[2] - (realrij[2] * realrij[0] * fil[0] + realrij[2] * realrij[1] * fil[1] + realrij[2] * realrij[2] * fil[2]) / (realrijmag * realrijmag));
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tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
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tmp2 = VA*.5*(tmp*wjl*g*exp(lamdaijl)*4.0*kronecker(jtype,1));
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fi[0] -= tmp2*(rij[0]/rijmag);
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fj[0] += tmp2*(rjl[0]/rjlmag);
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fi[1] -= tmp2*(rij[1]/rijmag);
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fj[1] += tmp2*(rjl[1]/rjlmag);
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fi[2] -= tmp2*(rij[2]/rijmag);
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fj[2] += tmp2*(rjl[2]/rjlmag);
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fj[0] -= tmp2*((-rjl[0]/rjlmag)-(rij[0]/rijmag));
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fj[1] -= tmp2*((-rjl[1]/rjlmag)-(rij[1]/rijmag));
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fj[2] -= tmp2*((-rjl[2]/rjlmag)-(rij[2]/rijmag));
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fl[0] -= tmp2*(rjl[0]/rjlmag);
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fl[0] -= tmp2*(rjl[0]/rjlmag);
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fl[1] -= tmp2*(rjl[1]/rjlmag);
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fl[1] -= tmp2*(rjl[1]/rjlmag);
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fl[2] -= tmp2*(rjl[2]/rjlmag);
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fl[2] -= tmp2*(rjl[2]/rjlmag);
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