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Merge pull request #304 from timattox/USER-DPD_whitespace 

USER-DPD: Whitespace cleanup to pair_dpd_fdt_energy.cpp
This commit is contained in:
sjplimp 2016-12-21 09:51:10 -07:00 committed by GitHub
parent 9161bd98bf c4e02a5d2b
commit 800ff43413
11 changed files with 65 additions and 65 deletions
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2
src/USER-DPD/compute_dpd_atom.cpp
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@ -43,7 +43,7 @@ ComputeDpdAtom::ComputeDpdAtom(LAMMPS *lmp, int narg, char **arg) :
size_peratom_cols = 4;
nmax = 0;
if (atom->dpd_flag != 1) error->all(FLERR,"compute dpd requires atom_style with internal temperature and energies (e.g. dpd)");
}

2
src/USER-DPD/fix_eos_table_rx.cpp
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@ -34,7 +34,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixEOStableRX::FixEOStableRX(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), ntables(0), tables(NULL),
Fix(lmp, narg, arg), ntables(0), tables(NULL),
tables2(NULL), dHf(NULL), eosSpecies(NULL)
{
if (narg != 8) error->all(FLERR,"Illegal fix eos/table/rx command");

22
src/USER-DPD/fix_rx.cpp
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@ -60,12 +60,12 @@ double getElapsedTime( const TimerType &t0, const TimerType &t1) { return t1-t0;
/* ---------------------------------------------------------------------- */
FixRX::FixRX(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), mol2param(NULL), nreactions(0),
params(NULL), Arr(NULL), nArr(NULL), Ea(NULL), tempExp(NULL),
stoich(NULL), stoichReactants(NULL), stoichProducts(NULL), kR(NULL),
pairDPDE(NULL), dpdThetaLocal(NULL), sumWeights(NULL), sparseKinetics_nu(NULL),
sparseKinetics_nuk(NULL), sparseKinetics_inu(NULL), sparseKinetics_isIntegralReaction(NULL),
kineticsFile(NULL), id_fix_species(NULL),
Fix(lmp, narg, arg), mol2param(NULL), nreactions(0),
params(NULL), Arr(NULL), nArr(NULL), Ea(NULL), tempExp(NULL),
stoich(NULL), stoichReactants(NULL), stoichProducts(NULL), kR(NULL),
pairDPDE(NULL), dpdThetaLocal(NULL), sumWeights(NULL), sparseKinetics_nu(NULL),
sparseKinetics_nuk(NULL), sparseKinetics_inu(NULL), sparseKinetics_isIntegralReaction(NULL),
kineticsFile(NULL), id_fix_species(NULL),
id_fix_species_old(NULL), fix_species(NULL), fix_species_old(NULL)
{
if (narg < 7 || narg > 12) error->all(FLERR,"Illegal fix rx command");
@ -656,7 +656,7 @@ void FixRX::setup_pre_force(int vflag)
memset(dpdThetaLocal, 0, sizeof(double)*count);
computeLocalTemperature();
}
for (int id = 0; id < nlocal; id++)
for (int ispecies=0; ispecies<nspecies; ispecies++){
tmp = atom->dvector[ispecies][id];
@ -667,14 +667,14 @@ void FixRX::setup_pre_force(int vflag)
// Set the reaction rate constants to zero: no reactions occur at step 0
for(int irxn=0;irxn<nreactions;irxn++)
kR[irxn] = 0.0;
kR[irxn] = 0.0;
if (odeIntegrationFlag == ODE_LAMMPS_RK4)
rk4(i,NULL);
rk4(i,NULL);
else if (odeIntegrationFlag == ODE_LAMMPS_RKF45)
rkf45(i,NULL);
rkf45(i,NULL);
}
// Communicate the updated momenta and velocities to all nodes
comm->forward_comm_fix(this);
if(localTempFlag) delete [] dpdThetaLocal;

6
src/USER-DPD/npair_half_bin_newton_ssa.cpp
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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
@ -147,7 +147,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
// loop over all local atoms in other bins in "half" stencil
for (k = 0; k < nstencil_half; k++) {
for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
for (j = binhead_ssa[ibin+stencil[k]]; j >= 0;
j = bins_ssa[j]) {
jtype = type[j];
@ -183,7 +183,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
// Note2: only non-pure locals can have ghosts as neighbors
if (ssaAIR[i] == 1) for (k = 0; k < nstencil_full; k++) {
for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0;
for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0;
j = bins_ssa[j]) {
jtype = type[j];

2
src/USER-DPD/npair_halffull_newton_ssa.cpp
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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */

2
src/USER-DPD/npair_halffull_newton_ssa.h
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@ -15,7 +15,7 @@
NPairStyle(halffull/newton/ssa,
NPairHalffullNewtonSSA,
NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON |
NP_ORTHO | NP_TRI | NP_SSA)
#else

4
src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp
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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
NStencilSSA(lmp) {}
/* ----------------------------------------------------------------------

6
src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp
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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
NStencilSSA(lmp) {}
/* ----------------------------------------------------------------------
@ -62,7 +62,7 @@ void NStencilHalfBin3dNewtonSSA::create()
// For k==0, make sure to skip already included bins
k = 0;
k = 0;
for (j = -sy; j <= 0; j++)
for (i = -sx; i <= sx; i++) {
if (j == 0 && i > 0) continue;

2
src/USER-DPD/pair_dpd_fdt.cpp
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@ -182,7 +182,7 @@ void PairDPDfdt::compute(int eflag, int vflag)
wr = 1.0 - r/cut[itype][jtype];
wd = wr*wr;
randnum = random->gaussian();
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
/ (2.0*force->boltz*temperature);
// conservative force = a0 * wd

78
src/USER-DPD/pair_dpd_fdt_energy.cpp
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@ -206,7 +206,7 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
if (r < EPSILON) continue; // r can be 0.0 in DPD systems
rinv = 1.0/r;
wr = 1.0 - r/cut[itype][jtype];
wd = wr*wr;
wd = wr*wr;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
@ -214,11 +214,11 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
dot = delx*delvx + dely*delvy + delz*delvz;
randnum = random->gaussian();
// Compute the current temperature
theta_ij = 0.5*(1.0/dpdTheta[i] + 1.0/dpdTheta[j]);
theta_ij = 1.0/theta_ij;
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
// Compute the current temperature
theta_ij = 0.5*(1.0/dpdTheta[i] + 1.0/dpdTheta[j]);
theta_ij = 1.0/theta_ij;
gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
/ (2.0*force->boltz*theta_ij);
// conservative force = a0 * wr
@ -239,44 +239,44 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
}
if (rmass) {
mass_i = rmass[i];
mass_j = rmass[j];
} else {
mass_i = mass[itype];
mass_j = mass[jtype];
}
massinv_i = 1.0 / mass_i;
massinv_j = 1.0 / mass_j;
if (rmass) {
mass_i = rmass[i];
mass_j = rmass[j];
} else {
mass_i = mass[itype];
mass_j = mass[jtype];
}
massinv_i = 1.0 / mass_i;
massinv_j = 1.0 / mass_j;
// Compute the mechanical and conductive energy, uMech and uCond
mu_ij = massinv_i + massinv_j;
mu_ij *= force->ftm2v;
// Compute the mechanical and conductive energy, uMech and uCond
mu_ij = massinv_i + massinv_j;
mu_ij *= force->ftm2v;
uTmp = gamma_ij*wd*rinv*rinv*dot*dot
uTmp = gamma_ij*wd*rinv*rinv*dot*dot
- 0.5*sigma[itype][jtype]*sigma[itype][jtype]*mu_ij*wd;
uTmp -= sigma[itype][jtype]*wr*rinv*dot*randnum*dtinvsqrt;
uTmp *= 0.5;
uTmp -= sigma[itype][jtype]*wr*rinv*dot*randnum*dtinvsqrt;
uTmp *= 0.5;
duMech[i] += uTmp;
if (newton_pair || j < nlocal) {
duMech[j] += uTmp;
}
// Compute uCond
randnum = random->gaussian();
kappa_ij = kappa[itype][jtype];
alpha_ij = sqrt(2.0*force->boltz*kappa_ij);
randPair = alpha_ij*wr*randnum*dtinvsqrt;
duMech[i] += uTmp;
if (newton_pair || j < nlocal) {
duMech[j] += uTmp;
}
// Compute uCond
randnum = random->gaussian();
kappa_ij = kappa[itype][jtype];
alpha_ij = sqrt(2.0*force->boltz*kappa_ij);
randPair = alpha_ij*wr*randnum*dtinvsqrt;
uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
uTmp += randPair;
duCond[i] += uTmp;
if (newton_pair || j < nlocal) {
duCond[j] -= uTmp;
}
uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
uTmp += randPair;
duCond[i] += uTmp;
if (newton_pair || j < nlocal) {
duCond[j] -= uTmp;
}
if (eflag) {
// unshifted eng of conservative term:
// evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);

4
src/USER-DPD/pair_multi_lucy.cpp
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@ -182,7 +182,7 @@ void PairMultiLucy::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0.0,0.0,fpair,delx,dely,delz);
0.0,0.0,fpair,delx,dely,delz);
}
}
@ -201,7 +201,7 @@ void PairMultiLucy::compute(int eflag, int vflag)
evdwl *=(pi*cutsq[itype][itype]*cutsq[itype][itype])/84.0;
if (evflag) ev_tally(0,0,nlocal,newton_pair,
evdwl,0.0,0.0,0.0,0.0,0.0);
evdwl,0.0,0.0,0.0,0.0,0.0);
}
if (vflag_fdotr) virial_fdotr_compute();