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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@ -210,8 +210,8 @@ void PairEDIP::compute(int eflag, int vflag)
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interpolY1 = exp3B[interpolIDX];
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interpolY2 = exp3B[interpolIDX+1];
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exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
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@ -220,8 +220,8 @@ void PairEDIP::compute(int eflag, int vflag)
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interpolY1 = exp2B[interpolIDX];
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interpolY2 = exp2B[interpolIDX+1];
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exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
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@ -230,8 +230,8 @@ void PairEDIP::compute(int eflag, int vflag)
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interpolY1 = pow2B[interpolIDX];
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interpolY2 = pow2B[interpolIDX+1];
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pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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prePow2B_ij[neighbor_j] = pow2B_ij;
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@ -241,15 +241,15 @@ void PairEDIP::compute(int eflag, int vflag)
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else {
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interpolY1 = cutoffFunction[interpolIDX];
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interpolY2 = cutoffFunction[interpolIDX+1];
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cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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zeta_i += cutoffFunction_ij;
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interpolY1 = cutoffFunctionDerived[interpolIDX];
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interpolY2 = cutoffFunctionDerived[interpolIDX+1];
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zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
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@ -271,22 +271,22 @@ void PairEDIP::compute(int eflag, int vflag)
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interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
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interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1];
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expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
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expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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interpolY1 = qFunctionGrid[interpolIDX];
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interpolY2 = qFunctionGrid[interpolIDX+1];
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qFunction = interpolY1 + (interpolY2 - interpolY1) *
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qFunction = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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interpolY1 = tauFunctionGrid[interpolIDX];
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interpolY2 = tauFunctionGrid[interpolIDX+1];
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tauFunction = interpolY1 + (interpolY2 - interpolY1) *
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tauFunction = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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interpolY1 = tauFunctionDerivedGrid[interpolIDX];
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interpolY2 = tauFunctionDerivedGrid[interpolIDX+1];
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tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
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tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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qFunctionDerived = -mu * qFunction;
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@ -326,8 +326,8 @@ void PairEDIP::compute(int eflag, int vflag)
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forceModCoord += (forceModCoord_factor*exp2B_ij);
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exp2BDerived_ij = preExp2BDerived_ij[neighbor_j];
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forceMod2B = exp2BDerived_ij * potential2B_factor +
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exp2B_ij * pow2BDerived_ij;
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forceMod2B = exp2BDerived_ij * potential2B_factor +
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exp2B_ij * pow2BDerived_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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@ -381,56 +381,56 @@ void PairEDIP::compute(int eflag, int vflag)
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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 +
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directorCos_ij_y * directorCos_ik_y +
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directorCos_ij_z * directorCos_ik_z;
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cosTeta = directorCos_ij_x * directorCos_ik_x +
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directorCos_ij_y * directorCos_ik_y +
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directorCos_ij_z * directorCos_ik_z;
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cosTetaDiff = cosTeta + tauFunction;
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cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff;
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qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction;
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expMinusQFunctionCosTetaDiffCosTetaDiff =
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exp(-qFunctionCosTetaDiffCosTetaDiff);
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expMinusQFunctionCosTetaDiffCosTetaDiff =
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exp(-qFunctionCosTetaDiffCosTetaDiff);
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potentia3B_factor = lambda *
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((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
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eta * qFunctionCosTetaDiffCosTetaDiff);
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potentia3B_factor = lambda *
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((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
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eta * qFunctionCosTetaDiffCosTetaDiff);
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exp3B_ik = preExp3B_ij[neighbor_k];
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exp3BDerived_ik = preExp3BDerived_ij[neighbor_k];
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forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
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potentia3B_factor;
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forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
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qFunction * cosTetaDiff *
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(eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
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forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
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potentia3B_factor;
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forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
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qFunction * cosTetaDiff *
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(eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
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forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij;
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f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_x - directorCos_ik_x);
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f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_y - directorCos_ik_y);
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f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_z - directorCos_ik_z);
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f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_x - directorCos_ik_x);
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f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_y - directorCos_ik_y);
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f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_z - directorCos_ik_z);
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forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
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potentia3B_factor;
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forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
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potentia3B_factor;
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forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
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f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_x - directorCos_ij_x);
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f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_y - directorCos_ij_y);
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f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_z - directorCos_ij_z);
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f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_x - directorCos_ij_x);
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f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_y - directorCos_ij_y);
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f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_z - directorCos_ij_z);
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forceModCoord += (forceMod3B_factor2 *
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(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
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forceModCoord += (forceMod3B_factor2 *
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(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
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f[j][0] += f_ij[0];
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f[j][1] += f_ij[1];
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@ -482,7 +482,7 @@ void PairEDIP::compute(int eflag, int vflag)
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evdwl = 0.0;
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if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0,
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forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
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forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
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}
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}
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@ -509,27 +509,27 @@ void PairEDIP::allocateGrids(void)
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// tauFunctionGrid
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maxArgumentTauFunctionGrid = leadDimInteractionList;
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numGridPointsTauFunctionGrid = (int)
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numGridPointsTauFunctionGrid = (int)
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((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
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memory->create(tauFunctionGrid,numGridPointsTauFunctionGrid,
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"edip:tauFunctionGrid");
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"edip:tauFunctionGrid");
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memory->create(tauFunctionDerivedGrid,numGridPointsTauFunctionGrid,
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"edip:tauFunctionDerivedGrid");
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"edip:tauFunctionDerivedGrid");
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// expMinusBetaZeta_iZeta_iGrid
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maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
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numGridPointsExpMinusBetaZeta_iZeta_i = (int)
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numGridPointsExpMinusBetaZeta_iZeta_i = (int)
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((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
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memory->create(expMinusBetaZeta_iZeta_iGrid,
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numGridPointsExpMinusBetaZeta_iZeta_i,
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"edip:expMinusBetaZeta_iZeta_iGrid");
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numGridPointsExpMinusBetaZeta_iZeta_i,
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"edip:expMinusBetaZeta_iZeta_iGrid");
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// qFunctionGrid
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maxArgumentQFunctionGrid = leadDimInteractionList;
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numGridPointsQFunctionGrid = (int)
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numGridPointsQFunctionGrid = (int)
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((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
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memory->create(qFunctionGrid,numGridPointsQFunctionGrid,"edip:qFunctionGrid");
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@ -537,17 +537,17 @@ void PairEDIP::allocateGrids(void)
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numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
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numGridPointsNotOneCutoffFunction = (int) ((cutoffA-cutoffC) * GRIDDENSITY);
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numGridPointsCutoffFunction = numGridPointsOneCutoffFunction +
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numGridPointsCutoffFunction = numGridPointsOneCutoffFunction +
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numGridPointsNotOneCutoffFunction+2;
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memory->create(cutoffFunction,numGridPointsCutoffFunction,
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"edip:cutoffFunction");
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"edip:cutoffFunction");
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memory->create(cutoffFunctionDerived,numGridPointsCutoffFunction,
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"edip:cutoffFunctionDerived");
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"edip:cutoffFunctionDerived");
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// pow2B
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numGridPointsR = (int)
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numGridPointsR = (int)
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((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
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numGridPointsRTotal = numGridPointsR + 2;
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@ -563,14 +563,14 @@ void PairEDIP::allocateGrids(void)
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void PairEDIP::allocatePreLoops(void)
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{
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int nthreads = comm->nthreads;
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memory->create(preInvR_ij,nthreads*leadDimInteractionList,"edip:preInvR_ij");
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memory->create(preExp3B_ij,nthreads*leadDimInteractionList,"edip:preExp3B_ij");
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memory->create(preExp3BDerived_ij,nthreads*leadDimInteractionList,
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"edip:preExp3BDerived_ij");
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"edip:preExp3BDerived_ij");
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memory->create(preExp2B_ij,nthreads*leadDimInteractionList,"edip:preExp2B_ij");
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memory->create(preExp2BDerived_ij,nthreads*leadDimInteractionList,
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"edip:preExp2BDerived_ij");
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"edip:preExp2BDerived_ij");
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memory->create(prePow2B_ij,nthreads*leadDimInteractionList,"edip:prePow2B_ij");
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memory->create(preForceCoord,5*nthreads*leadDimInteractionList,"edip:preForceCoord");
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}
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@ -621,7 +621,7 @@ void PairEDIP::allocate()
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}
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/* ----------------------------------------------------------------------
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global settings
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global settings
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------------------------------------------------------------------------- */
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void PairEDIP::settings(int narg, char **arg)
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@ -660,17 +660,17 @@ void PairEDIP::initGrids(void)
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maxArgumentTauFunctionGrid = leadDimInteractionList;
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numGridPointsTauFunctionGrid = (int)
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numGridPointsTauFunctionGrid = (int)
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((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
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r = 0.0;
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deltaArgumentTauFunctionGrid = 1.0 / GRIDDENSITY;
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for (l = 0; l < numGridPointsTauFunctionGrid; l++) {
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tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) -
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u2 * exp(-2.0 * u4 * r);
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tauFunctionDerivedGrid[l] = - u2 * u3 * u4 * exp(-u4 * r) +
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2.0 * u2 * u4 * exp(-2.0 * u4 * r);
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tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) -
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u2 * exp(-2.0 * u4 * r);
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tauFunctionDerivedGrid[l] = - u2 * u3 * u4 * exp(-u4 * r) +
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2.0 * u2 * u4 * exp(-2.0 * u4 * r);
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r += deltaArgumentTauFunctionGrid;
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}
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@ -678,7 +678,7 @@ void PairEDIP::initGrids(void)
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maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
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numGridPointsExpMinusBetaZeta_iZeta_i = (int)
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numGridPointsExpMinusBetaZeta_iZeta_i = (int)
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((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
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r = 0.0;
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@ -692,7 +692,7 @@ void PairEDIP::initGrids(void)
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// qFunctionGrid
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maxArgumentQFunctionGrid = leadDimInteractionList;
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numGridPointsQFunctionGrid =
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numGridPointsQFunctionGrid =
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(int) ((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
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r = 0.0;
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@ -705,11 +705,11 @@ void PairEDIP::initGrids(void)
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// cutoffFunction
|
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numGridPointsOneCutoffFunction =
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numGridPointsOneCutoffFunction =
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(int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
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numGridPointsNotOneCutoffFunction =
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numGridPointsNotOneCutoffFunction =
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(int) ((cutoffA-cutoffC) * GRIDDENSITY);
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numGridPointsCutoffFunction =
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numGridPointsCutoffFunction =
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numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction+2;
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r = GRIDSTART;
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@ -721,20 +721,20 @@ void PairEDIP::initGrids(void)
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r += deltaArgumentCutoffFunction;
|
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}
|
||||
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for (l = numGridPointsOneCutoffFunction;
|
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for (l = numGridPointsOneCutoffFunction;
|
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l < numGridPointsCutoffFunction; l++) {
|
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temp = (cutoffA - cutoffC)/(r - cutoffC);
|
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temp3 = temp * temp * temp;
|
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temp4 = temp3 * temp;
|
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cutoffFunction[l] = exp(alpha/(1.0-temp3));
|
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cutoffFunctionDerived[l] = (-3*alpha/(cutoffA-cutoffC)) *
|
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(temp4/((1-temp3)*(1-temp3)))*exp(alpha/(1.0-temp3));
|
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cutoffFunctionDerived[l] = (-3*alpha/(cutoffA-cutoffC)) *
|
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(temp4/((1-temp3)*(1-temp3)))*exp(alpha/(1.0-temp3));
|
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r += deltaArgumentCutoffFunction;
|
||||
}
|
||||
|
||||
// pow2B
|
||||
|
||||
numGridPointsR = (int)
|
||||
numGridPointsR = (int)
|
||||
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
|
||||
numGridPointsRTotal = numGridPointsR + 2;
|
||||
|
||||
@ -804,7 +804,7 @@ void PairEDIP::coeff(int narg, char **arg)
|
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}
|
||||
|
||||
// read potential file and initialize potential parameters
|
||||
|
||||
|
||||
read_file(arg[2]);
|
||||
setup();
|
||||
|
||||
@ -821,8 +821,8 @@ void PairEDIP::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");
|
||||
@ -898,8 +898,8 @@ void PairEDIP::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);
|
||||
@ -920,8 +920,8 @@ void PairEDIP::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);
|
||||
@ -960,7 +960,7 @@ void PairEDIP::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;
|
||||
@ -985,13 +985,13 @@ void PairEDIP::read_file(char *file)
|
||||
params[nparams].u4 = atof(words[19]);
|
||||
|
||||
if (params[nparams].A < 0.0 || params[nparams].B < 0.0 ||
|
||||
params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
|
||||
params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
|
||||
params[nparams].eta < 0.0 || params[nparams].gamm < 0.0 ||
|
||||
params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
|
||||
params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
|
||||
params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
|
||||
params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
|
||||
params[nparams].eta < 0.0 || params[nparams].gamm < 0.0 ||
|
||||
params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
|
||||
params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
|
||||
error->all(FLERR,"Illegal EDIP parameter");
|
||||
|
||||
|
||||
nparams++;
|
||||
}
|
||||
|
||||
@ -1015,16 +1015,16 @@ void PairEDIP::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
|
||||
|
||||
Reference in New Issue
Block a user