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Merge pull request #1005 from timattox/USER-DPD_alpha 

USER-DPD: propagate a minor performance bugfix throughout the DPDE code
This commit is contained in:
Steve Plimpton 2018-07-19 09:07:21 -06:00 committed by GitHub
parent fa73fab5df f9c7fa973b
commit 36081f9ffd
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GPG Key ID: 4AEE18F83AFDEB23
6 changed files with 18 additions and 12 deletions
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3
src/KOKKOS/fix_shardlow_kokkos.cpp
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@ -157,7 +157,6 @@ void FixShardlowKokkos<DeviceType>::init()
k_pairDPDE->k_cutsq.template sync<DeviceType>();
d_cutsq = k_pairDPDE->k_cutsq.template view<DeviceType>();
const double boltz2 = 2.0*force->boltz;
for (int i = 1; i <= ntypes; i++) {
for (int j = i; j <= ntypes; j++) {
F_FLOAT cutone = k_pairDPDE->cut[i][j];
@ -165,7 +164,7 @@ void FixShardlowKokkos<DeviceType>::init()
else k_params.h_view(i,j).cutinv = FLT_MAX;
k_params.h_view(i,j).halfsigma = 0.5*k_pairDPDE->sigma[i][j];
k_params.h_view(i,j).kappa = k_pairDPDE->kappa[i][j];
k_params.h_view(i,j).alpha = sqrt(boltz2*k_pairDPDE->kappa[i][j]);
k_params.h_view(i,j).alpha = k_pairDPDE->alpha[i][j];
k_params.h_view(j,i) = k_params.h_view(i,j);

3
src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
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@ -591,7 +591,7 @@ void PairDPDfdtEnergyKokkos<DeviceType>::operator()(TagPairDPDfdtEnergyComputeNo
// Compute uCond
randnum = rand_gen.normal();
kappa_ij = STACKPARAMS?m_params[itype][jtype].kappa:params(itype,jtype).kappa;
alpha_ij = sqrt(2.0*boltz*kappa_ij);
alpha_ij = STACKPARAMS?m_params[itype][jtype].alpha:params(itype,jtype).alpha;
randPair = alpha_ij*wr*randnum*dtinvsqrt;
uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
@ -676,6 +676,7 @@ double PairDPDfdtEnergyKokkos<DeviceType>::init_one(int i, int j)
k_params.h_view(i,j).a0 = a0[i][j];
k_params.h_view(i,j).sigma = sigma[i][j];
k_params.h_view(i,j).kappa = kappa[i][j];
k_params.h_view(i,j).alpha = alpha[i][j];
k_params.h_view(j,i) = k_params.h_view(i,j);
if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);

6
src/KOKKOS/pair_dpd_fdt_energy_kokkos.h
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@ -88,10 +88,10 @@ class PairDPDfdtEnergyKokkos : public PairDPDfdtEnergy {
struct params_dpd {
KOKKOS_INLINE_FUNCTION
params_dpd(){cut=0;a0=0;sigma=0;kappa=0;};
params_dpd(){cut=0;a0=0;sigma=0;kappa=0;alpha=0;};
KOKKOS_INLINE_FUNCTION
params_dpd(int i){cut=0;a0=0;sigma=0;kappa=0;};
F_FLOAT cut,a0,sigma,kappa;
params_dpd(int i){cut=0;a0=0;sigma=0;kappa=0;alpha=0;};
F_FLOAT cut,a0,sigma,kappa,alpha;
};
DAT::tdual_efloat_1d k_duCond,k_duMech;

6
src/USER-DPD/fix_shardlow.cpp
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@ -354,9 +354,8 @@ void FixShardlow::ssa_update_dpde(
double *uMech = atom->uMech;
double *dpdTheta = atom->dpdTheta;
double *cut_i, *cut2_i, *sigma_i, *kappa_i;
double *cut_i, *cut2_i, *sigma_i, *kappa_i, *alpha_i;
double theta_ij_inv, theta_i_inv;
const double boltz2 = 2.0*force->boltz;
const double boltz_inv = 1.0/force->boltz;
const double ftm2v = force->ftm2v;
@ -389,6 +388,7 @@ while (ct-- > 0) {
cut_i = pairDPDE->cut[itype];
sigma_i = pairDPDE->sigma[itype];
kappa_i = pairDPDE->kappa[itype];
alpha_i = pairDPDE->alpha[itype];
theta_i_inv = 1.0/dpdTheta[i];
const double mass_i = (rmass) ? rmass[i] : mass[itype];
const double massinv_i = 1.0 / mass_i;
@ -448,7 +448,7 @@ while (ct-- > 0) {
// Compute uCond
double kappa_ij = kappa_i[jtype];
double alpha_ij = sqrt(boltz2*kappa_ij);
double alpha_ij = alpha_i[jtype];
double del_uCond = alpha_ij*wr*dtsqrt * es_normal(RNGstate);
del_uCond += kappa_ij*(theta_i_inv - theta_j_inv)*wdt;

10
src/USER-DPD/pair_dpd_fdt_energy.cpp
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@ -65,6 +65,7 @@ PairDPDfdtEnergy::~PairDPDfdtEnergy()
memory->destroy(a0);
memory->destroy(sigma);
memory->destroy(kappa);
memory->destroy(alpha);
memory->destroy(duCond);
memory->destroy(duMech);
}
@ -269,7 +270,7 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag)
// Compute uCond
randnum = random->gaussian();
kappa_ij = kappa[itype][jtype];
alpha_ij = sqrt(2.0*force->boltz*kappa_ij);
alpha_ij = alpha[itype][jtype];
randPair = alpha_ij*wr*randnum*dtinvsqrt;
uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd;
@ -322,6 +323,7 @@ void PairDPDfdtEnergy::allocate()
memory->create(a0,n+1,n+1,"pair:a0");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(kappa,n+1,n+1,"pair:kappa");
memory->create(alpha,n+1,n+1,"pair:alpha");
if (!splitFDT_flag) {
memory->create(duCond,nlocal+nghost+1,"pair:duCond");
memory->create(duMech,nlocal+nghost+1,"pair:duMech");
@ -374,11 +376,12 @@ void PairDPDfdtEnergy::coeff(int narg, char **arg)
double a0_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double cut_one = cut_global;
double kappa_one;
double kappa_one, alpha_one;
a0_is_zero = (a0_one == 0.0); // Typical use with SSA is to set a0 to zero
kappa_one = force->numeric(FLERR,arg[4]);
alpha_one = sqrt(2.0*force->boltz*kappa_one);
if (narg == 6) cut_one = force->numeric(FLERR,arg[5]);
int count = 0;
@ -387,6 +390,7 @@ void PairDPDfdtEnergy::coeff(int narg, char **arg)
a0[i][j] = a0_one;
sigma[i][j] = sigma_one;
kappa[i][j] = kappa_one;
alpha[i][j] = alpha_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
@ -435,6 +439,7 @@ double PairDPDfdtEnergy::init_one(int i, int j)
a0[j][i] = a0[i][j];
sigma[j][i] = sigma[i][j];
kappa[j][i] = kappa[i][j];
alpha[j][i] = alpha[i][j];
return cut[i][j];
}
@ -488,6 +493,7 @@ void PairDPDfdtEnergy::read_restart(FILE *fp)
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&kappa[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
alpha[i][j] = sqrt(2.0*force->boltz*kappa[i][j]);
a0_is_zero = a0_is_zero && (a0[i][j] == 0.0); // verify the zero assumption
}
}

2
src/USER-DPD/pair_dpd_fdt_energy.h
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@ -43,7 +43,7 @@ class PairDPDfdtEnergy : public Pair {
double **cut;
double **a0;
double **sigma,**kappa;
double **sigma,**kappa,**alpha;
double *duCond,*duMech;
int seed;