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Merge pull request #696 from wmbrownIntel/intel-update-oct17

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Bug fix for unexpected case where a Intel bonded style is specified but there are no types
This commit is contained in:
Steve Plimpton
2017-10-18 13:25:07 -06:00
committed by GitHub
parent 7dfc6b7eab bb141aaae0
commit 382de50341
19 changed files with 42 additions and 36 deletions
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2
src/USER-INTEL/angle_charmm_intel.cpp
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@ -336,7 +336,7 @@ void AngleCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].theta0 = theta0[i];
fc.fc[i].k_ub = k_ub[i];

2
src/USER-INTEL/angle_harmonic_intel.cpp
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@ -318,7 +318,7 @@ void AngleHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].theta0 = theta0[i];
}

2
src/USER-INTEL/bond_fene_intel.cpp
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@ -295,7 +295,7 @@ void BondFENEIntel::pack_force_const(ForceConst<flt_t> &fc,
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].ir0sq = 1.0 / (r0[i] * r0[i]);
fc.fc[i].sigma = sigma[i];

2
src/USER-INTEL/bond_harmonic_intel.cpp
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@ -266,7 +266,7 @@ void BondHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].r0 = r0[i];
}

6
src/USER-INTEL/dihedral_charmm_intel.cpp
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@ -942,8 +942,8 @@ void DihedralCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
buffers->set_ntypes(tp1);
if (weightflag) {
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.ljp[i][j].lj1 = lj14_1[i][j];
fc.ljp[i][j].lj2 = lj14_2[i][j];
fc.ljp[i][j].lj3 = lj14_3[i][j];
@ -952,7 +952,7 @@ void DihedralCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
}
}
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.bp[i].multiplicity = multiplicity[i];
fc.bp[i].cos_shift = cos_shift[i];
fc.bp[i].sin_shift = sin_shift[i];

2
src/USER-INTEL/dihedral_harmonic_intel.cpp
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@ -400,7 +400,7 @@ void DihedralHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.bp[i].multiplicity = multiplicity[i];
fc.bp[i].cos_shift = cos_shift[i];
fc.bp[i].sin_shift = sin_shift[i];

2
src/USER-INTEL/dihedral_opls_intel.cpp
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@ -427,7 +427,7 @@ void DihedralOPLSIntel::pack_force_const(ForceConst<flt_t> &fc,
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.bp[i].k1 = k1[i];
fc.bp[i].k2 = k2[i];
fc.bp[i].k3 = k3[i];

2
src/USER-INTEL/improper_cvff_intel.cpp
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@ -433,7 +433,7 @@ void ImproperCvffIntel::pack_force_const(ForceConst<flt_t> &fc,
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].sign = sign[i];
fc.fc[i].multiplicity = multiplicity[i];

2
src/USER-INTEL/improper_harmonic_intel.cpp
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@ -389,7 +389,7 @@ void ImproperHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
for (int i = 1; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].chi = chi[i];
}

20
src/USER-INTEL/intel_preprocess.h
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@ -211,10 +211,9 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
datasize); \
}
#define IP_PRE_omp_range_id_vec(ifrom, ito, tid, inum, \
nthreads, vecsize) \
#define IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthreads, \
vecsize) \
{ \
tid = omp_get_thread_num(); \
int idelta = static_cast<int>(ceil(static_cast<float>(inum) \
/vecsize/nthreads)); \
idelta *= vecsize; \
@ -223,6 +222,14 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
if (ito > inum) ito = inum; \
}
#define IP_PRE_omp_range_id_vec(ifrom, ito, tid, inum, \
nthreads, vecsize) \
{ \
tid = omp_get_thread_num(); \
IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthreads, \
vecsize); \
}
#define IP_PRE_omp_stride_id_vec(ifrom, ip, ito, tid, inum, \
nthr, vecsize) \
{ \
@ -235,13 +242,12 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
int nd = nthr / INTEL_HTHREADS; \
int td = tid / INTEL_HTHREADS; \
int tm = tid % INTEL_HTHREADS; \
IP_PRE_omp_range_id_vec(ifrom, ito, td, inum, nd, \
vecsize); \
IP_PRE_omp_range_vec(ifrom, ito, td, inum, nd, vecsize); \
ifrom += tm * vecsize; \
ip = INTEL_HTHREADS * vecsize; \
} else { \
IP_PRE_omp_range_id_vec(ifrom, ito, tid, inum, nthr, \
vecsize); \
IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthr, \
vecsize); \
ip = vecsize; \
} \
}

4
src/USER-INTEL/pair_buck_coul_cut_intel.cpp
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@ -458,8 +458,8 @@ void PairBuckCoulCutIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.special_lj[0] = 1.0;
}
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.c_cut[i][j].cutsq = cutsq[i][j];
fc.c_cut[i][j].cut_ljsq = cut_ljsq[i][j];
fc.c_cut[i][j].cut_coulsq = cut_coulsq[i][j];

4
src/USER-INTEL/pair_buck_coul_long_intel.cpp
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@ -545,8 +545,8 @@ void PairBuckCoulLongIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.special_lj[0] = 1.0;
}
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
if (cutsq[i][j] < cut_ljsq[i][j])
error->all(FLERR,
"Intel variant of lj/buck/coul/long expects lj cutoff<=coulombic");

4
src/USER-INTEL/pair_buck_intel.cpp
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@ -413,8 +413,8 @@ void PairBuckIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.special_lj[0] = 1.0;
}
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.c_force[i][j].buck1 = buck1[i][j];
fc.c_force[i][j].buck2 = buck2[i][j];
fc.c_force[i][j].rhoinv = rhoinv[i][j];

4
src/USER-INTEL/pair_dpd_intel.cpp
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@ -531,8 +531,8 @@ void PairDPDIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.special_lj[0] = 1.0;
}
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.param[i][j].a0 = a0[i][j];
fc.param[i][j].gamma = gamma[i][j];
fc.param[i][j].sigma = sigma[i][j];

4
src/USER-INTEL/pair_gayberne_intel.cpp
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@ -938,8 +938,8 @@ void PairGayBerneIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.upsilon = upsilon;
fc.mu = mu;
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.ijc[i][j].lj1 = lj1[i][j];
fc.ijc[i][j].lj2 = lj2[i][j];
fc.ijc[i][j].cutsq = cutsq[i][j];

4
src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
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@ -521,8 +521,8 @@ void PairLJCharmmCoulCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.special_lj[0] = 1.0;
}
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.lj[i][j].x = lj1[i][j];
fc.lj[i][j].y = lj2[i][j];
fc.lj[i][j].z = lj3[i][j];

4
src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
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@ -586,8 +586,8 @@ void PairLJCharmmCoulLongIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.special_lj[0] = 1.0;
}
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.lj[i][j].x = lj1[i][j];
fc.lj[i][j].y = lj2[i][j];
fc.lj[i][j].z = lj3[i][j];

4
src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
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@ -544,8 +544,8 @@ void PairLJCutCoulLongIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.special_lj[0] = 1.0;
}
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
if (cutsq[i][j] < cut_ljsq[i][j])
error->all(FLERR,
"Intel variant of lj/cut/coul/long expects lj cutoff<=coulombic");

4
src/USER-INTEL/pair_lj_cut_intel.cpp
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@ -437,8 +437,8 @@ void PairLJCutIntel::pack_force_const(ForceConst<flt_t> &fc,
fc.special_lj[0] = 1.0;
}
for (int i = 0; i < tp1; i++) {
for (int j = 0; j < tp1; j++) {
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.ljc12o[i][j].lj1 = lj1[i][j];
fc.ljc12o[i][j].lj2 = lj2[i][j];
fc.lj34[i][j].lj3 = lj3[i][j];