forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1377 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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cetain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -35,7 +35,7 @@
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using namespace LAMMPS_NS;
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enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_ELLIPSE};
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enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
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/* ---------------------------------------------------------------------- */
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@ -105,11 +105,13 @@ void PairGayBerne::compute(int eflag, int vflag)
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i = ilist[ii];
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itype = type[i];
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MathExtra::quat_to_mat_trans(quat[i],a1);
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MathExtra::diag_times3(well[itype],a1,temp);
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MathExtra::transpose_times3(a1,temp,b1);
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MathExtra::diag_times3(shape[itype],a1,temp);
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MathExtra::transpose_times3(a1,temp,g1);
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if (form[itype][itype] == ELLIPSE_ELLIPSE) {
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MathExtra::quat_to_mat_trans(quat[i],a1);
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MathExtra::diag_times3(well[itype],a1,temp);
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MathExtra::transpose_times3(a1,temp,b1);
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MathExtra::diag_times3(shape[itype],a1,temp);
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MathExtra::transpose_times3(a1,temp,g1);
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}
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jlist = firstneigh[i];
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jnum = numneigh[i];
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@ -151,6 +153,20 @@ void PairGayBerne::compute(int eflag, int vflag)
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rtor[0] = rtor[1] = rtor[2] = 0.0;
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break;
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case SPHERE_ELLIPSE:
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MathExtra::quat_to_mat_trans(quat[j],a2);
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MathExtra::diag_times3(well[jtype],a2,temp);
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MathExtra::transpose_times3(a2,temp,b2);
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MathExtra::diag_times3(shape[jtype],a2,temp);
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MathExtra::transpose_times3(a2,temp,g2);
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one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
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break;
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case ELLIPSE_SPHERE:
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one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
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rtor[0] = rtor[1] = rtor[2] = 0.0;
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break;
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default:
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MathExtra::quat_to_mat_trans(quat[j],a2);
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MathExtra::diag_times3(well[jtype],a2,temp);
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@ -292,14 +308,14 @@ void PairGayBerne::coeff(int narg, char **arg)
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well[i][0] = pow(eia_one,-1.0/mu);
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well[i][1] = pow(eib_one,-1.0/mu);
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well[i][2] = pow(eic_one,-1.0/mu);
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if (eia_one == 1.0 && eib_one == 1.0 && eic_one == 1.0) setwell[i] = 2;
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if (eia_one == eib_one && eib_one == eic_one) setwell[i] = 2;
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else setwell[i] = 1;
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}
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if (eja_one != 0.0 || ejb_one != 0.0 || ejc_one != 0.0) {
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well[j][0] = pow(eja_one,-1.0/mu);
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well[j][1] = pow(ejb_one,-1.0/mu);
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well[j][2] = pow(ejc_one,-1.0/mu);
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if (eja_one == 1.0 && ejb_one == 1.0 && ejc_one == 1.0) setwell[j] = 2;
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if (eja_one == ejb_one && ejb_one == ejc_one) setwell[j] = 2;
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else setwell[j] = 1;
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}
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setflag[i][j] = 1;
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@ -372,11 +388,17 @@ double PairGayBerne::init_one(int i, int j)
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atom->shape[j][1] != atom->shape[j][2]) jshape = 1;
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if (setwell[j] == 1) jshape = 1;
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if (ishape == 0 && jshape == 0) form[i][j] = SPHERE_SPHERE;
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else if (ishape == 0 || jshape == 0) form[i][j] = SPHERE_ELLIPSE;
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else form[i][j] = ELLIPSE_ELLIPSE;
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if (ishape == 0 && jshape == 0)
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form[i][i] = form[j][j] = form[i][j] = form[j][i] = SPHERE_SPHERE;
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else if (ishape == 0) {
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form[i][i] = SPHERE_SPHERE; form[j][j] = ELLIPSE_ELLIPSE;
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form[i][j] = SPHERE_ELLIPSE; form[j][i] = ELLIPSE_SPHERE;
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} else if (jshape == 0) {
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form[j][j] = SPHERE_SPHERE; form[i][i] = ELLIPSE_ELLIPSE;
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form[j][i] = SPHERE_ELLIPSE; form[i][j] = ELLIPSE_SPHERE;
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} else
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form[i][i] = form[j][j] = form[i][j] = form[j][i] = ELLIPSE_ELLIPSE;
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form[j][i] = form[i][j];
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epsilon[j][i] = epsilon[i][j];
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sigma[j][i] = sigma[i][j];
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cut[j][i] = cut[i][j];
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@ -660,6 +682,156 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],
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return temp1*chi;
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}
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/* ----------------------------------------------------------------------
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compute analytic energy, force (fforce), and torque (ttor)
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between ellipsoid and lj particle
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------------------------------------------------------------------------- */
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double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
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double b1[3][3],double g1[3][3],
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double *r12,const double rsq,double *fforce,
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double *ttor)
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{
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double tempv[3], tempv2[3];
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double temp[3][3];
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double temp1,temp2,temp3;
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int *type = atom->type;
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int newton_pair = force->newton_pair;
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int nlocal = atom->nlocal;
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double r12hat[3];
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MathExtra::normalize3(r12,r12hat);
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double r = sqrt(rsq);
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// compute distance of closest approach
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double g12[3][3];
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g12[0][0] = g1[0][0]+shape[type[j]][0];
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g12[1][1] = g1[1][1]+shape[type[j]][0];
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g12[2][2] = g1[2][2]+shape[type[j]][0];
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g12[0][1] = g1[0][1]; g12[1][0] = g1[1][0];
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g12[0][2] = g1[0][2]; g12[2][0] = g1[2][0];
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g12[1][2] = g1[1][2]; g12[2][1] = g1[2][1];
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double kappa[3];
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MathExtra::mldivide3(g12,r12,kappa,error);
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// tempv = G12^-1*r12hat
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tempv[0] = kappa[0]/r;
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tempv[1] = kappa[1]/r;
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tempv[2] = kappa[2]/r;
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double sigma12 = MathExtra::dot3(r12hat,tempv);
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sigma12 = pow(0.5*sigma12,-0.5);
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double h12 = r-sigma12;
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// energy
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// compute u_r
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double varrho = sigma[type[i]][type[j]]/(h12+gamma*sigma[type[i]][type[j]]);
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double varrho6 = pow(varrho,6.0);
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double varrho12 = varrho6*varrho6;
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double u_r = 4.0*epsilon[type[i]][type[j]]*(varrho12-varrho6);
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// compute eta_12
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double eta = 2.0*lshape[type[i]]*lshape[type[j]];
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double det_g12 = MathExtra::det3(g12);
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eta = pow(eta/det_g12,upsilon);
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// compute chi_12
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double b12[3][3];
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double iota[3];
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b12[0][0] = b1[0][0] + well[type[j]][0];
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b12[1][1] = b1[1][1] + well[type[j]][0];
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b12[2][2] = b1[2][2] + well[type[j]][0];
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b12[0][1] = b1[0][1]; b12[1][0] = b1[1][0];
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b12[0][2] = b1[0][2]; b12[2][0] = b1[2][0];
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b12[1][2] = b1[1][2]; b12[2][1] = b1[2][1];
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MathExtra::mldivide3(b12,r12,iota,error);
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// tempv = G12^-1*r12hat
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tempv[0] = iota[0]/r;
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tempv[1] = iota[1]/r;
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tempv[2] = iota[2]/r;
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double chi = MathExtra::dot3(r12hat,tempv);
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chi = pow(chi*2.0,mu);
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// force
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// compute dUr/dr
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temp1 = (2.0*varrho12*varrho-varrho6*varrho)/sigma[type[i]][type[j]];
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temp1 = temp1*24.0*epsilon[type[i]][type[j]];
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double u_slj = temp1*pow(sigma12,3.0)/2.0;
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double dUr[3];
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temp2 = MathExtra::dot3(kappa,r12hat);
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double uslj_rsq = u_slj/rsq;
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dUr[0] = temp1*r12hat[0]+uslj_rsq*(kappa[0]-temp2*r12hat[0]);
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dUr[1] = temp1*r12hat[1]+uslj_rsq*(kappa[1]-temp2*r12hat[1]);
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dUr[2] = temp1*r12hat[2]+uslj_rsq*(kappa[2]-temp2*r12hat[2]);
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// compute dChi_12/dr
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double dchi[3];
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temp1 = MathExtra::dot3(iota,r12hat);
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temp2 = -4.0/rsq*mu*pow(chi,(mu-1.0)/mu);
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dchi[0] = temp2*(iota[0]-temp1*r12hat[0]);
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dchi[1] = temp2*(iota[1]-temp1*r12hat[1]);
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dchi[2] = temp2*(iota[2]-temp1*r12hat[2]);
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temp1 = -eta*u_r;
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temp2 = eta*chi;
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fforce[0] = temp1*dchi[0]-temp2*dUr[0];
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fforce[1] = temp1*dchi[1]-temp2*dUr[1];
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fforce[2] = temp1*dchi[2]-temp2*dUr[2];
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// torque for particle 1 and 2
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// compute dUr
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tempv[0] = -uslj_rsq*kappa[0];
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tempv[1] = -uslj_rsq*kappa[1];
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tempv[2] = -uslj_rsq*kappa[2];
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MathExtra::row_times3(kappa,g1,tempv2);
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MathExtra::cross3(tempv,tempv2,dUr);
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// compute d_chi
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MathExtra::row_times3(iota,b1,tempv);
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MathExtra::cross3(tempv,iota,dchi);
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temp1 = -4.0/rsq;
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dchi[0] *= temp1;
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dchi[1] *= temp1;
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dchi[2] *= temp1;
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// compute d_eta
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double deta[3];
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deta[0] = deta[1] = deta[2] = 0.0;
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compute_eta_torque(g12,a1,shape[type[i]],temp);
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temp1 = -eta*upsilon;
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for (int m = 0; m < 3; m++) {
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for (int y = 0; y < 3; y++) tempv[y] = temp1*temp[m][y];
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MathExtra::cross3(a1[m],tempv,tempv2);
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deta[0] += tempv2[0];
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deta[1] += tempv2[1];
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deta[2] += tempv2[2];
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}
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// torque
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temp1 = u_r*eta;
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temp2 = u_r*chi;
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temp3 = chi*eta;
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ttor[0] = (temp1*dchi[0]+temp2*deta[0]+temp3*dUr[0]) * -1.0;
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ttor[1] = (temp1*dchi[1]+temp2*deta[1]+temp3*dUr[1]) * -1.0;
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ttor[2] = (temp1*dchi[2]+temp2*deta[2]+temp3*dUr[2]) * -1.0;
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return temp1*chi;
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}
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/* ----------------------------------------------------------------------
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torque contribution from eta
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computes trace in the last doc equation for the torque derivative
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@ -53,6 +53,9 @@ class PairGayBerne : public Pair {
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double g1[3][3], double g2[3][3], double *r12,
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const double rsq, double *fforce, double *ttor,
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double *rtor);
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double gayberne_lj(const int i, const int j, double a1[3][3],
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double b1[3][3],double g1[3][3],double *r12,
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const double rsq, double *fforce, double *ttor);
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void compute_eta_torque(double m[3][3], double m2[3][3],
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double *s, double ans[3][3]);
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};
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