git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -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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certain 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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@ -80,7 +80,7 @@ PairTersoffTable::~PairTersoffTable()
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memory->destroy(setflag);
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memory->destroy(cutsq);
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delete [] map;
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deallocateGrids();
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deallocatePreLoops();
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}
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@ -103,7 +103,7 @@ void PairTersoffTable::compute(int eflag, int vflag)
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double invR_ij, invR_ik, cosTeta;
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double repulsivePotential, attractivePotential;
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double exponentRepulsivePotential, exponentAttractivePotential,interpolTMP,interpolDeltaX,interpolY1;
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double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
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double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
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double gtetaFunctionIJK,gtetaFunctionDerivedIJK,cutoffFunctionIK;
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double cutoffFunctionDerivedIK,factor_force3_ij,factor_1_force3_ik;
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double factor_2_force3_ik,betaZetaPowerIJK,betaZetaPowerDerivedIJK,factor_force_tot;
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@ -142,8 +142,8 @@ void PairTersoffTable::compute(int eflag, int vflag)
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if (jnum > leadingDimensionInteractionList) {
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char errmsg[256];
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sprintf(errmsg,"Too many neighbors for interaction list: %d vs %d.\n"
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"Check your system or increase 'leadingDimensionInteractionList'",
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jnum, leadingDimensionInteractionList);
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"Check your system or increase 'leadingDimensionInteractionList'",
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jnum, leadingDimensionInteractionList);
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error->one(FLERR,errmsg);
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}
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@ -168,11 +168,11 @@ void PairTersoffTable::compute(int eflag, int vflag)
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r_ij = sqrt(r_ij);
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invR_ij = 1.0 / r_ij;
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directorCos_ij_x = invR_ij * dr_ij[0];
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directorCos_ij_y = invR_ij * dr_ij[1];
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directorCos_ij_z = invR_ij * dr_ij[2];
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// preCutoffFunction
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interpolDeltaX = r_ij - GRIDSTART;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_FCUTOFF);
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@ -187,47 +187,47 @@ void PairTersoffTable::compute(int eflag, int vflag)
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for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) {
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double dr_ik[3], r_ik;
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double dr_ik[3], r_ik;
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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if (r_ik > params[ikparam].cutsq) continue;
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if (r_ik > params[ikparam].cutsq) continue;
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r_ik = sqrt(r_ik);
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r_ik = sqrt(r_ik);
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * dr_ik[0];
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directorCos_ik_y = invR_ik * dr_ik[1];
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directorCos_ik_z = invR_ik * dr_ik[2];
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cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
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// preGtetaFunction
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interpolDeltaX=cosTeta+1.0;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
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interpolIDX = (int) interpolTMP;
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interpolY1 = gtetaFunction[itype][interpolIDX];
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interpolY2 = gtetaFunction[itype][interpolIDX+1];
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gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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// preGtetaFunctionDerived
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interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
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interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
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gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
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preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
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preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
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preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * dr_ik[0];
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directorCos_ik_y = invR_ik * dr_ik[1];
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directorCos_ik_z = invR_ik * dr_ik[2];
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cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
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// preGtetaFunction
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interpolDeltaX=cosTeta+1.0;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
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interpolIDX = (int) interpolTMP;
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interpolY1 = gtetaFunction[itype][interpolIDX];
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interpolY2 = gtetaFunction[itype][interpolIDX+1];
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gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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// preGtetaFunctionDerived
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interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
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interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
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gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
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preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
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preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
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preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
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} // loop on K
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@ -254,7 +254,7 @@ void PairTersoffTable::compute(int eflag, int vflag)
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r_ij = sqrt(r_ij);
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invR_ij = 1.0 / r_ij;
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directorCos_ij_x = invR_ij * dr_ij[0];
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directorCos_ij_y = invR_ij * dr_ij[1];
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directorCos_ij_z = invR_ij * dr_ij[2];
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@ -284,72 +284,72 @@ void PairTersoffTable::compute(int eflag, int vflag)
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cutoffFunctionDerivedIJ = preCutoffFunctionDerived[neighbor_j];
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zeta = 0.0;
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// first loop over neighbours of atom i except j - part 1/2
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for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
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double dr_ik[3], r_ik;
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double dr_ik[3], r_ik;
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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if (r_ik > params[ikparam].cutsq) continue;
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if (r_ik > params[ikparam].cutsq) continue;
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r_ik = sqrt(r_ik);
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r_ik = sqrt(r_ik);
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * r_ik_x;
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directorCos_ik_y = invR_ik * r_ik_y;
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directorCos_ik_z = invR_ik * r_ik_z;
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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zeta += cutoffFunctionIK * gtetaFunctionIJK;
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * r_ik_x;
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directorCos_ik_y = invR_ik * r_ik_y;
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directorCos_ik_z = invR_ik * r_ik_z;
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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zeta += cutoffFunctionIK * gtetaFunctionIJK;
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}
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// first loop over neighbours of atom i except j - part 2/2
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for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
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double dr_ik[3], r_ik;
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double dr_ik[3], r_ik;
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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if (r_ik > params[ikparam].cutsq) continue;
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if (r_ik > params[ikparam].cutsq) continue;
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r_ik = sqrt(r_ik);
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * dr_ik[0];
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directorCos_ik_y = invR_ik * dr_ik[1];
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directorCos_ik_z = invR_ik * dr_ik[2];
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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zeta += cutoffFunctionIK * gtetaFunctionIJK;
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r_ik = sqrt(r_ik);
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * dr_ik[0];
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directorCos_ik_y = invR_ik * dr_ik[1];
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directorCos_ik_z = invR_ik * dr_ik[2];
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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zeta += cutoffFunctionIK * gtetaFunctionIJK;
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}
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// betaZetaPowerIJK
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// betaZetaPowerIJK
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interpolDeltaX= params[ijparam].beta * zeta;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_BIJ);
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interpolIDX = (int) interpolTMP;
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@ -386,133 +386,133 @@ void PairTersoffTable::compute(int eflag, int vflag)
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// second loop over neighbours of atom i except j, forces and virial only - part 1/2
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for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
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double dr_ik[3], r_ik, f_ik[3];
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double dr_ik[3], r_ik, f_ik[3];
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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if (r_ik > params[ikparam].cutsq) continue;
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if (r_ik > params[ikparam].cutsq) continue;
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r_ik = sqrt(r_ik);
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * dr_ik[0];
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directorCos_ik_y = invR_ik * dr_ik[1];
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directorCos_ik_z = invR_ik * dr_ik[2];
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cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
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factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
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f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
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f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
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f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
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factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
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factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
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f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
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f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
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f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
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f[j][0] -= f_ij[0];
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f[j][1] -= f_ij[1];
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f[j][2] -= f_ij[2];
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r_ik = sqrt(r_ik);
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invR_ik = 1.0 / r_ik;
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f[k][0] -= f_ik[0];
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f[k][1] -= f_ik[1];
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f[k][2] -= f_ik[2];
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directorCos_ik_x = invR_ik * dr_ik[0];
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directorCos_ik_y = invR_ik * dr_ik[1];
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directorCos_ik_z = invR_ik * dr_ik[2];
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fxtmp += f_ij[0] + f_ik[0];
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fytmp += f_ij[1] + f_ik[1];
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fztmp += f_ij[2] + f_ik[2];
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cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
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// potential energy
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evdwl = 0.0;
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
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gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
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factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
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f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
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f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
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f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
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factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
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factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
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|
||||
f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
|
||||
f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
|
||||
f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
|
||||
|
||||
f[j][0] -= f_ij[0];
|
||||
f[j][1] -= f_ij[1];
|
||||
f[j][2] -= f_ij[2];
|
||||
|
||||
f[k][0] -= f_ik[0];
|
||||
f[k][1] -= f_ik[1];
|
||||
f[k][2] -= f_ik[2];
|
||||
|
||||
fxtmp += f_ij[0] + f_ik[0];
|
||||
fytmp += f_ij[1] + f_ik[1];
|
||||
fztmp += f_ij[2] + f_ik[2];
|
||||
|
||||
// potential energy
|
||||
evdwl = 0.0;
|
||||
|
||||
if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
|
||||
}
|
||||
|
||||
|
||||
// second loop over neighbours of atom i except j, forces and virial only - part 2/2
|
||||
for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
|
||||
double dr_ik[3], r_ik, f_ik[3];
|
||||
double dr_ik[3], r_ik, f_ik[3];
|
||||
|
||||
k = jlist[neighbor_k];
|
||||
k &= NEIGHMASK;
|
||||
ktype = map[type[k]];
|
||||
ikparam = elem2param[itype][ktype][ktype];
|
||||
ijkparam = elem2param[itype][jtype][ktype];
|
||||
k = jlist[neighbor_k];
|
||||
k &= NEIGHMASK;
|
||||
ktype = map[type[k]];
|
||||
ikparam = elem2param[itype][ktype][ktype];
|
||||
ijkparam = elem2param[itype][jtype][ktype];
|
||||
|
||||
dr_ik[0] = xtmp -x[k][0];
|
||||
dr_ik[1] = ytmp -x[k][1];
|
||||
dr_ik[2] = ztmp -x[k][2];
|
||||
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
|
||||
dr_ik[0] = xtmp -x[k][0];
|
||||
dr_ik[1] = ytmp -x[k][1];
|
||||
dr_ik[2] = ztmp -x[k][2];
|
||||
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
|
||||
|
||||
if (r_ik > params[ikparam].cutsq) continue;
|
||||
if (r_ik > params[ikparam].cutsq) continue;
|
||||
|
||||
r_ik = sqrt(r_ik);
|
||||
invR_ik = 1.0 / r_ik;
|
||||
|
||||
directorCos_ik_x = invR_ik * dr_ik[0];
|
||||
directorCos_ik_y = invR_ik * dr_ik[1];
|
||||
directorCos_ik_z = invR_ik * dr_ik[2];
|
||||
|
||||
cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
|
||||
|
||||
gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
|
||||
|
||||
gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
|
||||
|
||||
cutoffFunctionIK = preCutoffFunction[neighbor_k];
|
||||
|
||||
cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
|
||||
|
||||
factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
|
||||
|
||||
f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
|
||||
f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
|
||||
f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
|
||||
|
||||
factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
|
||||
factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
|
||||
|
||||
f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
|
||||
f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
|
||||
f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
|
||||
|
||||
f[j][0] -= f_ij[0];
|
||||
f[j][1] -= f_ij[1];
|
||||
f[j][2] -= f_ij[2];
|
||||
r_ik = sqrt(r_ik);
|
||||
invR_ik = 1.0 / r_ik;
|
||||
|
||||
f[k][0] -= f_ik[0];
|
||||
f[k][1] -= f_ik[1];
|
||||
f[k][2] -= f_ik[2];
|
||||
directorCos_ik_x = invR_ik * dr_ik[0];
|
||||
directorCos_ik_y = invR_ik * dr_ik[1];
|
||||
directorCos_ik_z = invR_ik * dr_ik[2];
|
||||
|
||||
fxtmp += f_ij[0] + f_ik[0];
|
||||
fytmp += f_ij[1] + f_ik[1];
|
||||
fztmp += f_ij[2] + f_ik[2];
|
||||
cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
|
||||
|
||||
// potential energy
|
||||
evdwl = 0.0;
|
||||
gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
|
||||
|
||||
gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
|
||||
|
||||
cutoffFunctionIK = preCutoffFunction[neighbor_k];
|
||||
|
||||
cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
|
||||
|
||||
factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
|
||||
|
||||
f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
|
||||
f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
|
||||
f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
|
||||
|
||||
factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
|
||||
factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
|
||||
|
||||
f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
|
||||
f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
|
||||
f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
|
||||
|
||||
f[j][0] -= f_ij[0];
|
||||
f[j][1] -= f_ij[1];
|
||||
f[j][2] -= f_ij[2];
|
||||
|
||||
f[k][0] -= f_ik[0];
|
||||
f[k][1] -= f_ik[1];
|
||||
f[k][2] -= f_ik[2];
|
||||
|
||||
fxtmp += f_ij[0] + f_ik[0];
|
||||
fytmp += f_ij[1] + f_ik[1];
|
||||
fztmp += f_ij[2] + f_ik[2];
|
||||
|
||||
// potential energy
|
||||
evdwl = 0.0;
|
||||
|
||||
if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
|
||||
|
||||
if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
|
||||
|
||||
}
|
||||
} // loop on J
|
||||
f[i][0] += fxtmp;
|
||||
@ -525,7 +525,7 @@ void PairTersoffTable::compute(int eflag, int vflag)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTersoffTable::deallocatePreLoops(void)
|
||||
void PairTersoffTable::deallocatePreLoops(void)
|
||||
{
|
||||
memory->destroy (preGtetaFunction);
|
||||
memory->destroy (preGtetaFunctionDerived);
|
||||
@ -538,14 +538,14 @@ void PairTersoffTable::allocatePreLoops(void)
|
||||
memory->create(preGtetaFunction,leadingDimensionInteractionList,leadingDimensionInteractionList,"tersofftable:preGtetaFunction");
|
||||
|
||||
memory->create(preGtetaFunctionDerived,leadingDimensionInteractionList,leadingDimensionInteractionList,"tersofftable:preGtetaFunctionDerived");
|
||||
|
||||
|
||||
memory->create(preCutoffFunction,leadingDimensionInteractionList,"tersofftable:preCutoffFunction");
|
||||
|
||||
|
||||
memory->create(preCutoffFunctionDerived,leadingDimensionInteractionList,"tersofftable:preCutoffFunctionDerived");
|
||||
}
|
||||
|
||||
void PairTersoffTable::deallocateGrids()
|
||||
{
|
||||
void PairTersoffTable::deallocateGrids()
|
||||
{
|
||||
int i,j;
|
||||
|
||||
memory->destroy(exponential);
|
||||
@ -560,7 +560,7 @@ void PairTersoffTable::deallocateGrids()
|
||||
void PairTersoffTable::allocateGrids(void)
|
||||
{
|
||||
int i, j, l;
|
||||
|
||||
|
||||
int numGridPointsExponential, numGridPointsGtetaFunction, numGridPointsOneCutoffFunction;
|
||||
int numGridPointsNotOneCutoffFunction, numGridPointsCutoffFunction, numGridPointsBetaZetaPower;
|
||||
// double minArgumentExponential;
|
||||
@ -569,7 +569,7 @@ void PairTersoffTable::allocateGrids(void)
|
||||
double r, minMu, maxLambda, maxCutoff;
|
||||
double const PI=acos(-1.0);
|
||||
|
||||
// exponential
|
||||
// exponential
|
||||
|
||||
// find min and max argument
|
||||
minMu=params[0].lam2;
|
||||
@ -579,9 +579,9 @@ void PairTersoffTable::allocateGrids(void)
|
||||
if (params[i].lam1 > maxLambda) maxLambda = params[i].lam1;
|
||||
}
|
||||
maxCutoff=cutmax;
|
||||
|
||||
|
||||
minArgumentExponential=minMu*GRIDSTART;
|
||||
|
||||
|
||||
numGridPointsExponential=(int)((maxLambda*maxCutoff-minArgumentExponential)*GRIDDENSITY_EXP)+2;
|
||||
|
||||
memory->create(exponential,numGridPointsExponential,"tersofftable:exponential");
|
||||
@ -593,7 +593,7 @@ void PairTersoffTable::allocateGrids(void)
|
||||
exponential[i] = exp(-r);
|
||||
r += deltaArgumentExponential;
|
||||
}
|
||||
|
||||
|
||||
|
||||
// gtetaFunction
|
||||
|
||||
@ -601,12 +601,12 @@ void PairTersoffTable::allocateGrids(void)
|
||||
|
||||
memory->create(gtetaFunction,nelements,numGridPointsGtetaFunction,"tersofftable:gtetaFunction");
|
||||
memory->create(gtetaFunctionDerived,nelements,numGridPointsGtetaFunction,"tersofftable:gtetaFunctionDerived");
|
||||
|
||||
|
||||
r = minArgumentExponential;
|
||||
for (i=0; i<nelements; i++) {
|
||||
r = -1.0;
|
||||
deltaArgumentGtetaFunction = 1.0 / GRIDDENSITY_GTETA;
|
||||
|
||||
|
||||
int iparam = elem2param[i][i][i];
|
||||
double c = params[iparam].c;
|
||||
double d = params[iparam].d;
|
||||
@ -619,7 +619,7 @@ void PairTersoffTable::allocateGrids(void)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
// cutoffFunction, zetaFunction, find grids.
|
||||
|
||||
int ngrid_max = -1;
|
||||
@ -638,55 +638,55 @@ void PairTersoffTable::allocateGrids(void)
|
||||
for (j=0; j<nelements; j++) {
|
||||
for (j=0; j<nelements; j++) {
|
||||
|
||||
int ijparam = elem2param[i][j][j];
|
||||
double cutoffR = params[ijparam].cutoffR;
|
||||
double cutoffS = params[ijparam].cutoffS;
|
||||
int ijparam = elem2param[i][j][j];
|
||||
double cutoffR = params[ijparam].cutoffR;
|
||||
double cutoffS = params[ijparam].cutoffS;
|
||||
|
||||
numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
|
||||
numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
|
||||
numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
|
||||
numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
|
||||
numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
|
||||
numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
|
||||
|
||||
ngrid_max = MAX(ngrid_max,numGridPointsCutoffFunction);
|
||||
ngrid_max = MAX(ngrid_max,numGridPointsCutoffFunction);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
memory->create(cutoffFunction,nelements,nelements,ngrid_max,"tersoff:cutfunc");
|
||||
memory->create(cutoffFunctionDerived,nelements,nelements,ngrid_max,"tersoff:cutfuncD");
|
||||
|
||||
|
||||
// cutoffFunction, compute.
|
||||
|
||||
for (i=0; i<nelements; i++) {
|
||||
for (j=0; j<nelements; j++) {
|
||||
for (j=0; j<nelements; j++) {
|
||||
int ijparam = elem2param[i][j][j];
|
||||
double cutoffR = params[ijparam].cutoffR;
|
||||
double cutoffS = params[ijparam].cutoffS;
|
||||
int ijparam = elem2param[i][j][j];
|
||||
double cutoffR = params[ijparam].cutoffR;
|
||||
double cutoffS = params[ijparam].cutoffS;
|
||||
|
||||
numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
|
||||
numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
|
||||
numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
|
||||
numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
|
||||
numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
|
||||
numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
|
||||
|
||||
r = GRIDSTART;
|
||||
deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY_FCUTOFF;
|
||||
|
||||
for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
|
||||
cutoffFunction[i][j][l] = 1.0;
|
||||
cutoffFunctionDerived[i][j][l]=0.0;
|
||||
r += deltaArgumentCutoffFunction;
|
||||
}
|
||||
r = GRIDSTART;
|
||||
deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY_FCUTOFF;
|
||||
|
||||
for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) {
|
||||
cutoffFunction[i][j][l] = 0.5 + 0.5 * cos (PI * (r - cutoffR)/(cutoffS-cutoffR)) ;
|
||||
cutoffFunctionDerived[i][j][l] = -0.5 * PI * sin (PI * (r - cutoffR)/(cutoffS-cutoffR)) / (cutoffS-cutoffR) ;
|
||||
r += deltaArgumentCutoffFunction;
|
||||
}
|
||||
for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
|
||||
cutoffFunction[i][j][l] = 1.0;
|
||||
cutoffFunctionDerived[i][j][l]=0.0;
|
||||
r += deltaArgumentCutoffFunction;
|
||||
}
|
||||
|
||||
for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) {
|
||||
cutoffFunction[i][j][l] = 0.5 + 0.5 * cos (PI * (r - cutoffR)/(cutoffS-cutoffR)) ;
|
||||
cutoffFunctionDerived[i][j][l] = -0.5 * PI * sin (PI * (r - cutoffR)/(cutoffS-cutoffR)) / (cutoffS-cutoffR) ;
|
||||
r += deltaArgumentCutoffFunction;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// betaZetaPower, compute
|
||||
|
||||
|
||||
memory->create(betaZetaPower,nelements,zeta_max,"tersoff:zetafunc");
|
||||
memory->create(betaZetaPowerDerived,nelements,zeta_max,"tersoff:zetafuncD");
|
||||
|
||||
@ -701,11 +701,11 @@ void PairTersoffTable::allocateGrids(void)
|
||||
|
||||
r=0.0;
|
||||
deltaArgumentBetaZetaPower = 1.0 / GRIDDENSITY_BIJ;
|
||||
|
||||
|
||||
betaZetaPower[i][0]=1.0;
|
||||
|
||||
r += deltaArgumentBetaZetaPower;
|
||||
|
||||
|
||||
for (j = 1; j < numGridPointsBetaZetaPower; j++) {
|
||||
double powern=params[iparam].powern;
|
||||
betaZetaPower[i][j]=pow((1+pow(r,powern)),-1/(2*powern));
|
||||
@ -728,7 +728,7 @@ void PairTersoffTable::allocate()
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTersoffTable::settings(int narg, char **arg)
|
||||
@ -784,7 +784,7 @@ void PairTersoffTable::coeff(int narg, char **arg)
|
||||
}
|
||||
|
||||
// read potential file and initialize potential parameters
|
||||
|
||||
|
||||
read_file(arg[2]);
|
||||
setup();
|
||||
|
||||
@ -801,8 +801,8 @@ void PairTersoffTable::coeff(int narg, char **arg)
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
if (map[i] >= 0 && map[j] >= 0) {
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
@ -876,8 +876,8 @@ void PairTersoffTable::read_file(char *file)
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(line,MAXLINE,fp);
|
||||
if (ptr == NULL) {
|
||||
eof = 1;
|
||||
fclose(fp);
|
||||
eof = 1;
|
||||
fclose(fp);
|
||||
} else n = strlen(line) + 1;
|
||||
}
|
||||
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||
@ -898,8 +898,8 @@ void PairTersoffTable::read_file(char *file)
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(&line[n],MAXLINE-n,fp);
|
||||
if (ptr == NULL) {
|
||||
eof = 1;
|
||||
fclose(fp);
|
||||
eof = 1;
|
||||
fclose(fp);
|
||||
} else n = strlen(line) + 1;
|
||||
}
|
||||
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||
@ -938,7 +938,7 @@ void PairTersoffTable::read_file(char *file)
|
||||
if (nparams == maxparam) {
|
||||
maxparam += DELTA;
|
||||
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
|
||||
"pair:params");
|
||||
"pair:params");
|
||||
}
|
||||
|
||||
params[nparams].ielement = ielement;
|
||||
@ -966,16 +966,16 @@ void PairTersoffTable::read_file(char *file)
|
||||
// currently only allow m exponent of 1 or 3
|
||||
params[nparams].powermint = int(params[nparams].powerm);
|
||||
|
||||
if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
|
||||
params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
|
||||
params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
|
||||
params[nparams].cutoffR < 0.0 ||params[nparams].cutoffS < 0.0 ||
|
||||
params[nparams].cutoffR > params[nparams].cutoffS ||
|
||||
params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0
|
||||
if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
|
||||
params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
|
||||
params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
|
||||
params[nparams].cutoffR < 0.0 ||params[nparams].cutoffS < 0.0 ||
|
||||
params[nparams].cutoffR > params[nparams].cutoffS ||
|
||||
params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0
|
||||
) error->all(FLERR,"Illegal Tersoff parameter");
|
||||
|
||||
// only tersoff_2 parametrization is implemented
|
||||
if (params[nparams].gamma != 1.0 || params[nparams].lam3 != 0.0)
|
||||
if (params[nparams].gamma != 1.0 || params[nparams].lam3 != 0.0)
|
||||
error->all(FLERR,"Current tersoff/table pair_style implements only tersoff_2 parametrization");
|
||||
nparams++;
|
||||
}
|
||||
@ -999,16 +999,16 @@ void PairTersoffTable::setup()
|
||||
for (i = 0; i < nelements; i++)
|
||||
for (j = 0; j < nelements; j++)
|
||||
for (k = 0; k < nelements; k++) {
|
||||
n = -1;
|
||||
for (m = 0; m < nparams; m++) {
|
||||
if (i == params[m].ielement && j == params[m].jelement &&
|
||||
k == params[m].kelement) {
|
||||
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
|
||||
n = m;
|
||||
}
|
||||
}
|
||||
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
|
||||
elem2param[i][j][k] = n;
|
||||
n = -1;
|
||||
for (m = 0; m < nparams; m++) {
|
||||
if (i == params[m].ielement && j == params[m].jelement &&
|
||||
k == params[m].kelement) {
|
||||
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
|
||||
n = m;
|
||||
}
|
||||
}
|
||||
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
|
||||
elem2param[i][j][k] = n;
|
||||
}
|
||||
|
||||
// set cutoff square
|
||||
@ -1022,4 +1022,4 @@ void PairTersoffTable::setup()
|
||||
for (m = 0; m < nparams; m++) {
|
||||
if (params[m].cut > cutmax) cutmax = params[m].cut;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user