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patch_16De
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patch_21De
| Author | SHA1 | Date | |
|---|---|---|---|
| 62dea1bb63 | |||
| 800ff43413 | |||
| 9161bd98bf | |||
| c4e02a5d2b | |||
| 2ba424e1a3 | |||
| 81a2db8a0c | |||
| 0a176841e7 |
@ -1,7 +1,7 @@
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<!-- HTML_ONLY -->
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<HEAD>
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<TITLE>LAMMPS Users Manual</TITLE>
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<META NAME="docnumber" CONTENT="16 Dec 2016 version">
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<META NAME="docnumber" CONTENT="21 Dec 2016 version">
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<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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</HEAD>
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@ -21,7 +21,7 @@
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<H1></H1>
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LAMMPS Documentation :c,h3
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16 Dec 2016 version :c,h4
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21 Dec 2016 version :c,h4
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Version info: :h4
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@ -43,7 +43,7 @@ ComputeDpdAtom::ComputeDpdAtom(LAMMPS *lmp, int narg, char **arg) :
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size_peratom_cols = 4;
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nmax = 0;
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if (atom->dpd_flag != 1) error->all(FLERR,"compute dpd requires atom_style with internal temperature and energies (e.g. dpd)");
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}
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@ -34,7 +34,7 @@ using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixEOStableRX::FixEOStableRX(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg), ntables(0), tables(NULL),
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Fix(lmp, narg, arg), ntables(0), tables(NULL),
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tables2(NULL), dHf(NULL), eosSpecies(NULL)
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{
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if (narg != 8) error->all(FLERR,"Illegal fix eos/table/rx command");
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@ -60,12 +60,12 @@ double getElapsedTime( const TimerType &t0, const TimerType &t1) { return t1-t0;
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/* ---------------------------------------------------------------------- */
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FixRX::FixRX(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg), mol2param(NULL), nreactions(0),
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params(NULL), Arr(NULL), nArr(NULL), Ea(NULL), tempExp(NULL),
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stoich(NULL), stoichReactants(NULL), stoichProducts(NULL), kR(NULL),
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pairDPDE(NULL), dpdThetaLocal(NULL), sumWeights(NULL), sparseKinetics_nu(NULL),
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sparseKinetics_nuk(NULL), sparseKinetics_inu(NULL), sparseKinetics_isIntegralReaction(NULL),
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kineticsFile(NULL), id_fix_species(NULL),
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Fix(lmp, narg, arg), mol2param(NULL), nreactions(0),
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params(NULL), Arr(NULL), nArr(NULL), Ea(NULL), tempExp(NULL),
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stoich(NULL), stoichReactants(NULL), stoichProducts(NULL), kR(NULL),
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pairDPDE(NULL), dpdThetaLocal(NULL), sumWeights(NULL), sparseKinetics_nu(NULL),
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sparseKinetics_nuk(NULL), sparseKinetics_inu(NULL), sparseKinetics_isIntegralReaction(NULL),
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kineticsFile(NULL), id_fix_species(NULL),
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id_fix_species_old(NULL), fix_species(NULL), fix_species_old(NULL)
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{
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if (narg < 7 || narg > 12) error->all(FLERR,"Illegal fix rx command");
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@ -656,7 +656,7 @@ void FixRX::setup_pre_force(int vflag)
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memset(dpdThetaLocal, 0, sizeof(double)*count);
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computeLocalTemperature();
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}
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for (int id = 0; id < nlocal; id++)
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for (int ispecies=0; ispecies<nspecies; ispecies++){
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tmp = atom->dvector[ispecies][id];
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@ -667,14 +667,14 @@ void FixRX::setup_pre_force(int vflag)
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// Set the reaction rate constants to zero: no reactions occur at step 0
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for(int irxn=0;irxn<nreactions;irxn++)
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kR[irxn] = 0.0;
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kR[irxn] = 0.0;
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if (odeIntegrationFlag == ODE_LAMMPS_RK4)
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rk4(i,NULL);
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rk4(i,NULL);
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else if (odeIntegrationFlag == ODE_LAMMPS_RKF45)
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rkf45(i,NULL);
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rkf45(i,NULL);
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}
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// Communicate the updated momenta and velocities to all nodes
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comm->forward_comm_fix(this);
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if(localTempFlag) delete [] dpdThetaLocal;
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@ -12,7 +12,7 @@
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing authors:
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Contributing authors:
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James Larentzos and Timothy I. Mattox (Engility Corporation)
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------------------------------------------------------------------------- */
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@ -147,7 +147,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
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// loop over all local atoms in other bins in "half" stencil
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for (k = 0; k < nstencil_half; k++) {
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for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
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for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
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j = bins_ssa[j]) {
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jtype = type[j];
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@ -183,7 +183,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
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// Note2: only non-pure locals can have ghosts as neighbors
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if (ssaAIR[i] == 1) for (k = 0; k < nstencil_full; k++) {
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for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0;
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for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0;
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j = bins_ssa[j]) {
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jtype = type[j];
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@ -12,7 +12,7 @@
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing authors:
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Contributing authors:
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James Larentzos and Timothy I. Mattox (Engility Corporation)
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------------------------------------------------------------------------- */
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@ -15,7 +15,7 @@
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NPairStyle(halffull/newton/ssa,
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NPairHalffullNewtonSSA,
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NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
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NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
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NP_ORTHO | NP_TRI | NP_SSA)
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#else
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@ -12,7 +12,7 @@
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing authors:
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Contributing authors:
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James Larentzos and Timothy I. Mattox (Engility Corporation)
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------------------------------------------------------------------------- */
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@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
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NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
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NStencilSSA(lmp) {}
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/* ----------------------------------------------------------------------
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@ -12,7 +12,7 @@
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing authors:
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Contributing authors:
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James Larentzos and Timothy I. Mattox (Engility Corporation)
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------------------------------------------------------------------------- */
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@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
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NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
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NStencilSSA(lmp) {}
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/* ----------------------------------------------------------------------
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@ -62,7 +62,7 @@ void NStencilHalfBin3dNewtonSSA::create()
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// For k==0, make sure to skip already included bins
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k = 0;
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k = 0;
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for (j = -sy; j <= 0; j++)
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for (i = -sx; i <= sx; i++) {
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if (j == 0 && i > 0) continue;
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@ -182,7 +182,7 @@ void PairDPDfdt::compute(int eflag, int vflag)
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wr = 1.0 - r/cut[itype][jtype];
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wd = wr*wr;
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randnum = random->gaussian();
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gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
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gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
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/ (2.0*force->boltz*temperature);
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// conservative force = a0 * wd
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@ -206,7 +206,7 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
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if (r < EPSILON) continue; // r can be 0.0 in DPD systems
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rinv = 1.0/r;
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wr = 1.0 - r/cut[itype][jtype];
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wd = wr*wr;
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wd = wr*wr;
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delvx = vxtmp - v[j][0];
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delvy = vytmp - v[j][1];
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@ -214,11 +214,11 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
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dot = delx*delvx + dely*delvy + delz*delvz;
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randnum = random->gaussian();
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// Compute the current temperature
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theta_ij = 0.5*(1.0/dpdTheta[i] + 1.0/dpdTheta[j]);
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theta_ij = 1.0/theta_ij;
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gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
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// Compute the current temperature
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theta_ij = 0.5*(1.0/dpdTheta[i] + 1.0/dpdTheta[j]);
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theta_ij = 1.0/theta_ij;
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gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
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/ (2.0*force->boltz*theta_ij);
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// conservative force = a0 * wr
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@ -239,44 +239,44 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
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f[j][2] -= delz*fpair;
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}
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if (rmass) {
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mass_i = rmass[i];
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mass_j = rmass[j];
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} else {
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mass_i = mass[itype];
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mass_j = mass[jtype];
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}
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massinv_i = 1.0 / mass_i;
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massinv_j = 1.0 / mass_j;
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if (rmass) {
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mass_i = rmass[i];
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mass_j = rmass[j];
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} else {
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mass_i = mass[itype];
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mass_j = mass[jtype];
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}
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massinv_i = 1.0 / mass_i;
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massinv_j = 1.0 / mass_j;
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// Compute the mechanical and conductive energy, uMech and uCond
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mu_ij = massinv_i + massinv_j;
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mu_ij *= force->ftm2v;
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// Compute the mechanical and conductive energy, uMech and uCond
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mu_ij = massinv_i + massinv_j;
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mu_ij *= force->ftm2v;
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uTmp = gamma_ij*wd*rinv*rinv*dot*dot
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uTmp = gamma_ij*wd*rinv*rinv*dot*dot
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- 0.5*sigma[itype][jtype]*sigma[itype][jtype]*mu_ij*wd;
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uTmp -= sigma[itype][jtype]*wr*rinv*dot*randnum*dtinvsqrt;
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uTmp *= 0.5;
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uTmp -= sigma[itype][jtype]*wr*rinv*dot*randnum*dtinvsqrt;
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uTmp *= 0.5;
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duMech[i] += uTmp;
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if (newton_pair || j < nlocal) {
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duMech[j] += uTmp;
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}
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// Compute uCond
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randnum = random->gaussian();
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kappa_ij = kappa[itype][jtype];
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alpha_ij = sqrt(2.0*force->boltz*kappa_ij);
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randPair = alpha_ij*wr*randnum*dtinvsqrt;
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duMech[i] += uTmp;
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if (newton_pair || j < nlocal) {
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duMech[j] += uTmp;
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}
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// Compute uCond
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randnum = random->gaussian();
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kappa_ij = kappa[itype][jtype];
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alpha_ij = sqrt(2.0*force->boltz*kappa_ij);
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randPair = alpha_ij*wr*randnum*dtinvsqrt;
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uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
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uTmp += randPair;
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duCond[i] += uTmp;
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if (newton_pair || j < nlocal) {
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duCond[j] -= uTmp;
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}
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uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
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uTmp += randPair;
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duCond[i] += uTmp;
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if (newton_pair || j < nlocal) {
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duCond[j] -= uTmp;
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}
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if (eflag) {
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// unshifted eng of conservative term:
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// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
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@ -182,7 +182,7 @@ void PairMultiLucy::compute(int eflag, int vflag)
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f[j][2] -= delz*fpair;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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0.0,0.0,fpair,delx,dely,delz);
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0.0,0.0,fpair,delx,dely,delz);
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}
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}
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@ -201,7 +201,7 @@ void PairMultiLucy::compute(int eflag, int vflag)
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evdwl *=(pi*cutsq[itype][itype]*cutsq[itype][itype])/84.0;
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if (evflag) ev_tally(0,0,nlocal,newton_pair,
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evdwl,0.0,0.0,0.0,0.0,0.0);
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evdwl,0.0,0.0,0.0,0.0,0.0);
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}
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if (vflag_fdotr) virial_fdotr_compute();
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@ -847,6 +847,7 @@ void AtomVecBody::unpack_border(int n, int first, double *buf)
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inertia[2] = buf[m++];
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bonus[j].ninteger = (int) ubuf(buf[m++]).i;
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bonus[j].ndouble = (int) ubuf(buf[m++]).i;
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// corresponding put() calls are in clear_bonus()
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bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
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bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
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m += bptr->unpack_border_body(&bonus[j],&buf[m]);
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@ -897,6 +898,7 @@ void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
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inertia[2] = buf[m++];
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bonus[j].ninteger = (int) ubuf(buf[m++]).i;
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bonus[j].ndouble = (int) ubuf(buf[m++]).i;
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// corresponding put() calls are in clear_bonus()
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bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
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bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
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m += bptr->unpack_border_body(&bonus[j],&buf[m]);
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@ -946,6 +948,7 @@ int AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
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inertia[2] = buf[m++];
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bonus[j].ninteger = (int) ubuf(buf[m++]).i;
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bonus[j].ndouble = (int) ubuf(buf[m++]).i;
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// corresponding put() calls are in clear_bonus()
|
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bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
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bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
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m += bptr->unpack_border_body(&bonus[j],&buf[m]);
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@ -1050,6 +1053,7 @@ int AtomVecBody::unpack_exchange(double *buf)
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inertia[2] = buf[m++];
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bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
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bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
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// corresponding put() calls are in copy()
|
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bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
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bonus[nlocal_bonus].iindex);
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bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
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@ -57,10 +57,10 @@ namespace LAMMPS_NS {
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|
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template<class T>
|
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class MyPage {
|
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public:
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int ndatum; // total # of stored datums
|
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int nchunk; // total # of stored chunks
|
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|
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public:
|
||||
MyPage() {
|
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ndatum = nchunk = 0;
|
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pages = NULL;
|
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|
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@ -33,7 +33,7 @@ methods:
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minchunk <= N <= maxchunk required
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put(index) = return indexed chunk to pool (same index returned by get)
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int size() = return total size of allocated pages in bytes
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public varaibles:
|
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public variables:
|
||||
ndatum = total # of stored datums
|
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nchunk = total # of stored chunks
|
||||
size = total size of all allocated pages in daums
|
||||
|
||||
@ -192,6 +192,7 @@ void NeighList::setup_pages(int pgsize_caller, int oneatom_caller)
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gran calls grow() in granhistory
|
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respaouter calls grow() in respainner, respamiddle
|
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triggered by neighbor list build
|
||||
not called if a copy list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NeighList::grow(int nlocal, int nall)
|
||||
|
||||
@ -1369,6 +1369,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
|
||||
"with ghost neighbors");
|
||||
|
||||
// flags for settings the request + system requires of NPair class
|
||||
// some are set to 0/1, others are set to mask bit
|
||||
// comparisons below in loop over classes reflect that
|
||||
// copyflag = no/yes copy request
|
||||
// skipflag = no/yes skip request
|
||||
// halfflag = half request (gran and respa are also half lists)
|
||||
@ -1402,7 +1404,7 @@ int Neighbor::choose_pair(NeighRequest *rq)
|
||||
// NOTE: exactly one of these request flags is set (see neigh_request.h)
|
||||
// this requires gran/respaouter also set halfflag
|
||||
// can simplify this logic, if follow NOTE in neigh_request.h
|
||||
// all why do size/off2on and size/off2on/oneside set NP_HALF
|
||||
// why do size/off2on and size/off2on/oneside set NP_HALF
|
||||
// either should set both half & full, or half should be in file name
|
||||
// to be consistent with how other NP classes use "half"
|
||||
|
||||
@ -1433,9 +1435,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
|
||||
else if (rq->newton == 1) newtflag = 1;
|
||||
else if (rq->newton == 2) newtflag = 0;
|
||||
|
||||
// use flags to match exactly one of NPair class masks, bit by bit
|
||||
// copyflag match returns with no further checks
|
||||
// exactly one of halfflag,fullflag,halffullflag is set and thus must match
|
||||
// use flags to match exactly one of NPair class masks
|
||||
// sequence of checks is bit by bit in NeighConst
|
||||
|
||||
int mask;
|
||||
|
||||
@ -1447,13 +1448,21 @@ int Neighbor::choose_pair(NeighRequest *rq)
|
||||
for (int i = 0; i < npclass; i++) {
|
||||
mask = pairmasks[i];
|
||||
|
||||
if (copyflag && (mask & NP_COPY)) {
|
||||
// if copyflag set, return or continue with no further checks
|
||||
|
||||
if (copyflag) {
|
||||
if (!(mask & NP_COPY)) continue;
|
||||
if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
|
||||
if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
|
||||
return i+1;
|
||||
}
|
||||
|
||||
// skipflag must match along with other flags, so do not return
|
||||
|
||||
if (skipflag != (mask & NP_SKIP)) continue;
|
||||
|
||||
// exactly one of halfflag,fullflag,halffullflag is set and must match
|
||||
|
||||
if (halfflag) {
|
||||
if (!(mask & NP_HALF)) continue;
|
||||
} else if (fullflag) {
|
||||
@ -1470,19 +1479,38 @@ int Neighbor::choose_pair(NeighRequest *rq)
|
||||
if (ssaflag != (mask & NP_SSA)) continue;
|
||||
if (ompflag != (mask & NP_OMP)) continue;
|
||||
if (intelflag != (mask & NP_INTEL)) continue;
|
||||
|
||||
// style is one of NSQ,BIN,MULTI and must match
|
||||
|
||||
if (style == NSQ) {
|
||||
if (!(mask & NP_NSQ)) continue;
|
||||
} else if (style == BIN) {
|
||||
if (!(mask & NP_BIN)) continue;
|
||||
} else if (style == MULTI) {
|
||||
if (!(mask & NP_MULTI)) continue;
|
||||
}
|
||||
|
||||
// newtflag is on or off and must match
|
||||
|
||||
if (newtflag) {
|
||||
if (!(mask & NP_NEWTON)) continue;
|
||||
} else if (!newtflag) {
|
||||
if (!(mask & NP_NEWTOFF)) continue;
|
||||
}
|
||||
|
||||
// triclinic flag is on or off and must match
|
||||
|
||||
if (triclinic) {
|
||||
if (!(mask & NP_TRI)) continue;
|
||||
} else if (!triclinic) {
|
||||
if (!(mask & NP_ORTHO)) continue;
|
||||
}
|
||||
|
||||
// Kokkos flags
|
||||
|
||||
if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
|
||||
if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
|
||||
|
||||
if (style == NSQ && !(mask & NP_NSQ)) continue;
|
||||
if (style == BIN && !(mask & NP_BIN)) continue;
|
||||
if (style == MULTI && !(mask & NP_MULTI)) continue;
|
||||
|
||||
if (newtflag && !(mask & NP_NEWTON)) continue;
|
||||
if (!newtflag && !(mask & NP_NEWTOFF)) continue;
|
||||
|
||||
if (!triclinic && !(mask & NP_ORTHO)) continue;
|
||||
if (triclinic && !(mask & NP_TRI)) continue;
|
||||
|
||||
return i+1;
|
||||
}
|
||||
|
||||
@ -1727,7 +1755,7 @@ void Neighbor::build(int topoflag)
|
||||
|
||||
for (i = 0; i < npair_perpetual; i++) {
|
||||
m = plist[i];
|
||||
lists[m]->grow(nlocal,nall);
|
||||
if (!lists[m]->copy) lists[m]->grow(nlocal,nall);
|
||||
neigh_pair[m]->build_setup();
|
||||
neigh_pair[m]->build(lists[m]);
|
||||
}
|
||||
|
||||
@ -15,7 +15,8 @@
|
||||
|
||||
NPairStyle(skip,
|
||||
NPairSkip,
|
||||
NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI |
|
||||
NP_SKIP | NP_HALF | NP_FULL | NP_HALFFULL |
|
||||
NP_NSQ | NP_BIN | NP_MULTI |
|
||||
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
|
||||
|
||||
#else
|
||||
|
||||
@ -38,7 +38,7 @@ class Python {
|
||||
void invoke_function(int, char *) {}
|
||||
int find(char *) {return -1;}
|
||||
int variable_match(char *, char *, int) {return -1;}
|
||||
|
||||
char *long_string(int) {return NULL;}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "16 Dec 2016"
|
||||
#define LAMMPS_VERSION "21 Dec 2016"
|
||||
|
||||
Reference in New Issue
Block a user