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Merge pull request #2203 from akohlmey/collected-small-changes 

Various small fixes and cleanups. Bugfixes for atom style hybrid
This commit is contained in:
Axel Kohlmeyer 2020-07-01 06:24:28 -04:00 committed by GitHub
parent a73f1d4f03 0a9dd81288
commit 558d2eb84f
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
37 changed files with 158 additions and 165 deletions
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32
src/BODY/pair_body_rounded_polygon.cpp
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@ -236,7 +236,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
edge[jefirst+nj][4] = 0;
}
int interact, num_contacts, done;
int num_contacts, done;
double delta_a, j_a;
Contact contact_list[MAX_CONTACTS];
@ -244,15 +244,13 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
// check interaction between i's vertices and j' edges
interact = vertex_against_edge(i, j, k_nij, k_naij,
x, f, torque, tag, contact_list,
num_contacts, evdwl, facc);
vertex_against_edge(i, j, k_nij, k_naij, x, f, torque, tag,
contact_list, num_contacts, evdwl, facc);
// check interaction between j's vertices and i' edges
interact = vertex_against_edge(j, i, k_nij, k_naij,
x, f, torque, tag, contact_list,
num_contacts, evdwl, facc);
vertex_against_edge(j, i, k_nij, k_naij, x, f, torque, tag,
contact_list, num_contacts, evdwl, facc);
if (num_contacts >= 2) {
@ -595,7 +593,7 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
{
double rradi,rradj;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@ -641,6 +639,23 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// normal friction term at contact
fn[0] = -c_n * vn1;
fn[1] = -c_n * vn2;
fn[2] = -c_n * vn3;
// tangential friction term at contact,
// excluding the tangential deformation term for now
ft[0] = -c_t * vt1;
ft[1] = -c_t * vt2;
ft[2] = -c_t * vt3;
fx += fn[0] + ft[0];
fy += fn[1] + ft[1];
fz += fn[2] + ft[2];
}
f[i][0] += fx;
@ -1349,4 +1364,3 @@ void PairBodyRoundedPolygon::distance(const double* x2, const double* x1,
+ (x2[1] - x1[1]) * (x2[1] - x1[1])
+ (x2[2] - x1[2]) * (x2[2] - x1[2]));
}

12
src/KOKKOS/atom_vec_kokkos.h
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@ -103,14 +103,14 @@ class AtomVecKokkos : public AtomVec {
ExecutionSpace space) = 0;
virtual int
pack_border_vel_kokkos(int n, DAT::tdual_int_2d k_sendlist,
DAT::tdual_xfloat_2d buf,int iswap,
int pbc_flag, int *pbc, ExecutionSpace space) { return 0; }
pack_border_vel_kokkos(int /*n*/, DAT::tdual_int_2d /*k_sendlist*/,
DAT::tdual_xfloat_2d /*buf*/,int /*iswap*/,
int /*pbc_flag*/, int * /*pbc*/, ExecutionSpace /*space*/) { return 0; }
virtual void
unpack_border_vel_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf,
ExecutionSpace space) {}
unpack_border_vel_kokkos(const int &/*n*/, const int & /*nfirst*/,
const DAT::tdual_xfloat_2d & /*buf*/,
ExecutionSpace /*space*/) {}
virtual int
pack_exchange_kokkos(const int &nsend, DAT::tdual_xfloat_2d &buf,

4
src/KOKKOS/kokkos_type.h
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@ -272,7 +272,7 @@ template<typename T1, typename T2>
class ScatterViewHelper<Kokkos::Experimental::ScatterDuplicated,T1,T2> {
public:
KOKKOS_INLINE_FUNCTION
static T1 get(const T1 &dup, const T2 &nondup) {
static T1 get(const T1 &dup, const T2 & /*nondup*/) {
return dup;
}
};
@ -1025,7 +1025,7 @@ struct params_lj_coul {
KOKKOS_INLINE_FUNCTION
params_lj_coul(){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
KOKKOS_INLINE_FUNCTION
params_lj_coul(int i){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
params_lj_coul(int /*i*/){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
F_FLOAT cut_ljsq,cut_coulsq,lj1,lj2,lj3,lj4,offset;
};

6
src/KOKKOS/sna_kokkos_impl.h
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@ -368,7 +368,6 @@ void SNAKokkos<DeviceType>::compute_ui(const typename Kokkos::TeamPolicy<DeviceT
for (int j = 1; j <= twojmax; j++) {
const int jju = idxu_block[j];
const int jjup = idxu_block[j-1];
// fill in left side of matrix layer from previous layer
@ -1080,7 +1079,6 @@ void SNAKokkos<DeviceType>::compute_bi_cpu(const typename Kokkos::TeamPolicy<Dev
Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxb_max),
[&] (const int& jjb) {
//for(int jjb = 0; jjb < idxb_max; jjb++) {
const auto jjballoy = itriple;
const int j1 = idxb(jjb, 0);
const int j2 = idxb(jjb, 1);
const int j = idxb(jjb, 2);
@ -2024,7 +2022,6 @@ double SNAKokkos<DeviceType>::memory_usage()
{
int jdimpq = twojmax + 2;
int jdim = twojmax + 1;
int natom_pad = ((natom + 32 - 1) / 32) * 32; // for AoSoA layouts
double bytes;
bytes = 0;
@ -2032,10 +2029,9 @@ double SNAKokkos<DeviceType>::memory_usage()
bytes += jdimpq*jdimpq * sizeof(double); // pqarray
bytes += idxcg_max * sizeof(double); // cglist
#ifdef KOKKOS_ENABLE_CUDA
if (std::is_same<DeviceType,Kokkos::Cuda>::value) {
int natom_pad = ((natom + 32 - 1) / 32) * 32; // for AoSoA layouts
bytes += natom * idxu_max * nelements * sizeof(double); // ulisttot_re
bytes += natom * idxu_max * nelements * sizeof(double); // ulisttot_im

1
src/KSPACE/pppm_disp.cpp
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@ -316,7 +316,6 @@ void PPPMDisp::init()
for (int i=0; i<=EWALD_MAXORDER; ++i) // transcribe order
if (ewald_order&(1<<i)) { // from pair_style
int k=0;
char str[128];
switch (i) {
case 1:
k = 0; break;

4
src/MLIAP/mliap_descriptor_snap.cpp
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@ -149,15 +149,13 @@ void MLIAPDescriptorSNAP::forward(int* map, NeighList* list, double **descriptor
void MLIAPDescriptorSNAP::backward(PairMLIAP* pairmliap, NeighList* list, double **beta, int vflag)
{
int i,j,jnum,ninside;
double delx,dely,delz,evdwl,rsq;
double delx,dely,delz,rsq;
double fij[3];
int *jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
numneigh = list->numneigh;
firstneigh = list->firstneigh;

3
src/MLIAP/mliap_model.cpp
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@ -142,7 +142,6 @@ void MLIAPModel::read_coeffs(char *coefffilename)
}
if (comm->me == 0) fclose(fpcoeff);
}
/* ----------------------------------------------------------------------
@ -153,9 +152,7 @@ double MLIAPModel::memory_usage()
{
double bytes = 0;
int n = atom->ntypes+1;
bytes += nelements*nparams*sizeof(double); // coeffelem
return bytes;
}

4
src/RIGID/fix_rigid_small.cpp
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@ -410,9 +410,9 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
if (comm->me == 0) {
if (screen)
fprintf(screen," create bodies CPU = %g secs\n",time2-time1);
fprintf(screen," create bodies CPU = %g seconds\n",time2-time1);
if (logfile)
fprintf(logfile," create bodies CPU = %g secs\n",time2-time1);
fprintf(logfile," create bodies CPU = %g seconds\n",time2-time1);
}
// set nlocal_body and allocate bodies I own

4
src/RIGID/fix_shake.cpp
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@ -229,9 +229,9 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
if (comm->me == 0) {
if (screen)
fprintf(screen," find clusters CPU = %g secs\n",time2-time1);
fprintf(screen," find clusters CPU = %g seconds\n",time2-time1);
if (logfile)
fprintf(logfile," find clusters CPU = %g secs\n",time2-time1);
fprintf(logfile," find clusters CPU = %g seconds\n",time2-time1);
}
// initialize list of SHAKE clusters to constrain

2
src/SNAP/compute_sna_atom.cpp
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@ -259,7 +259,7 @@ void ComputeSNAAtom::compute_peratom()
int jtype = type[j];
int jelem = 0;
if (chemflag)
int jelem = map[jtype];
jelem = map[jtype];
if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;

22
src/USER-CGDNA/bond_oxdna_fene.cpp
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@ -328,29 +328,9 @@ void BondOxdnaFene::coeff(int narg, char **arg)
void BondOxdnaFene::init_style()
{
/* special bonds have to be lj = 0 1 1 and coul = 1 1 1 to exclude
the ss excluded volume interaction between nearest neighbors */
force->special_lj[1] = 0.0;
force->special_lj[2] = 1.0;
force->special_lj[3] = 1.0;
force->special_coul[1] = 1.0;
force->special_coul[2] = 1.0;
force->special_coul[3] = 1.0;
fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
" Special bond factors lj: %-10g %-10g %-10g\n"
" Special bond factors coul: %-10g %-10g %-10g\n",
force->special_lj[1],force->special_lj[2],force->special_lj[3],
force->special_coul[1],force->special_coul[2],force->special_coul[3]);
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
{
if (comm->me == 0)
error->warning(FLERR,"Use special bonds lj = 0,1,1 and coul = 1,1,1 with bond style oxdna/fene");
}
error->all(FLERR,"Must use 'special_bonds lj 0 1 1 coul 1 1 1' with bond style oxdna/fene");
}
/* ---------------------------------------------------------------------- */

10
src/atom_vec_hybrid.cpp
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@ -57,8 +57,6 @@ AtomVecHybrid::~AtomVecHybrid()
delete [] styles;
for (int k = 0; k < nstyles; k++) delete [] keywords[k];
delete [] keywords;
for (int k = 0; k < nstyles_bonus; k++) delete styles_bonus[k];
delete [] styles_bonus;
if (!fields_allocated) return;
@ -225,6 +223,7 @@ void AtomVecHybrid::process_args(int narg, char **arg)
// set bonus_flag if any substyle has bonus data
// set nstyles_bonus & styles_bonus
// sum two sizes over contributions from each substyle with bonus data.
nstyles_bonus = 0;
for (int k = 0; k < nstyles; k++)
@ -234,9 +233,14 @@ void AtomVecHybrid::process_args(int narg, char **arg)
bonus_flag = 1;
styles_bonus = new AtomVec*[nstyles_bonus];
nstyles_bonus = 0;
size_forward_bonus = 0;
size_border_bonus = 0;
for (int k = 0; k < nstyles; k++) {
if (styles[k]->bonus_flag)
if (styles[k]->bonus_flag) {
styles_bonus[nstyles_bonus++] = styles[k];
size_forward_bonus += styles[k]->size_forward_bonus;
size_border_bonus += styles[k]->size_border_bonus;
}
}
}

11
src/domain.cpp
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@ -1939,12 +1939,13 @@ void Domain::print_box(const std::string &prefix)
if (comm->me == 0) {
std::string mesg = prefix;
if (triclinic == 0) {
mesg += fmt::format("orthogonal box = ({} {} {}) to ({} {} {})\n",
boxlo[0],boxlo[1],boxlo[2],
boxhi[0],boxhi[1],boxhi[2]);
mesg += fmt::format("orthogonal box = ({:.8g} {:.8g} {:.8g}) to "
"({:.8g} {:.8g} {:.8g})\n",boxlo[0],boxlo[1],
boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
} else {
mesg += fmt::format("triclinic box = ({} {} {}) to ({} {} {}) "
"with tilt ({} {} {})\n",boxlo[0],boxlo[1],
mesg += fmt::format("triclinic box = ({:.8g} {:.8g} {:.8g}) to "
"({:.8g} {:.8g} {:.8g}) with tilt "
"({:.8g} {:.8g} {:.8g})\n",boxlo[0],boxlo[1],
boxlo[2],boxhi[0],boxhi[1],boxhi[2],xy,xz,yz);
}
utils::logmesg(lmp,mesg);

4
src/fix_adapt.cpp
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@ -588,7 +588,7 @@ void FixAdapt::change_settings()
// for scaleflag, previous_diam_scale is the scale factor on previous step
if (ad->aparam == DIAMETER) {
double density,scale;
double scale;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
@ -691,7 +691,7 @@ void FixAdapt::restore_settings()
} else if (ad->which == ATOM) {
if (diamflag) {
double density,scale;
double scale;
double *vec = fix_diam->vstore;
double *radius = atom->radius;

1
src/info.cpp
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@ -793,7 +793,6 @@ bool Info::is_active(const char *category, const char *name)
{
if ((category == NULL) || (name == NULL)) return false;
const char *style = "none";
const int len = strlen(name);
if (strcmp(category,"package") == 0) {
if (strcmp(name,"gpu") == 0) {

3
src/lattice.cpp
View File

@ -304,7 +304,8 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
// print lattice spacings
if (comm->me == 0)
utils::logmesg(lmp,fmt::format("Lattice spacing in x,y,z = {} {} {}\n",
utils::logmesg(lmp,fmt::format("Lattice spacing in x,y,z = "
"{:.8g} {:.8g} {:.8g}\n",
xlattice,ylattice,zlattice));
}

8
src/neighbor.cpp
View File

@ -1438,7 +1438,7 @@ void Neighbor::init_topology()
void Neighbor::print_pairwise_info()
{
int i,m;
int i;
NeighRequest *rq;
const double cutghost = MAX(cutneighmax,comm->cutghostuser);
@ -1466,10 +1466,10 @@ void Neighbor::print_pairwise_info()
every,delay,dist_check ? "yes" : "no");
out += fmt::format(" max neighbors/atom: {}, page size: {}\n",
oneatom, pgsize);
out += fmt::format(" master list distance cutoff = {}\n",cutneighmax);
out += fmt::format(" ghost atom cutoff = {}\n",cutghost);
out += fmt::format(" master list distance cutoff = {:.8g}\n",cutneighmax);
out += fmt::format(" ghost atom cutoff = {:.8g}\n",cutghost);
if (style != Neighbor::NSQ)
out += fmt::format(" binsize = {}, bins = {} {} {}\n",binsize,
out += fmt::format(" binsize = {:.8g}, bins = {:g} {:g} {:g}\n",binsize,
ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
ceil(bbox[2]/binsize));

1
src/pair_table.cpp
View File

@ -70,7 +70,6 @@ void PairTable::compute(int eflag, int vflag)
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,factor_lj,fraction,value,a,b;
char estr[128];
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;

2
src/read_data.cpp
View File

@ -897,7 +897,7 @@ void ReadData::command(int narg, char **arg)
MPI_Barrier(world);
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" read_data CPU = {:.3f} secs\n",
utils::logmesg(lmp,fmt::format(" read_data CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}

2
src/read_restart.cpp
View File

@ -511,7 +511,7 @@ void ReadRestart::command(int narg, char **arg)
MPI_Barrier(world);
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" read_restart CPU = {:.3f} secs\n",
utils::logmesg(lmp,fmt::format(" read_restart CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}

2
src/replicate.cpp
View File

@ -779,6 +779,6 @@ void Replicate::command(int narg, char **arg)
MPI_Barrier(world);
if (me == 0)
utils::logmesg(lmp,fmt::format(" replicate CPU = {:.3f} secs\n",
utils::logmesg(lmp,fmt::format(" replicate CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}

6
src/special.cpp
View File

@ -63,8 +63,8 @@ void Special::build()
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
fmt::print(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
" special bond factors lj: {:<10g} {:<10g} {:<10g}\n"
" special bond factors coul: {:<10g} {:<10g} {:<10g}\n",
" special bond factors lj: {:<8g} {:<8g} {:<8g}\n"
" special bond factors coul: {:<8g} {:<8g} {:<8g}\n",
special_lj[1],special_lj[2],special_lj[3],
special_coul[1],special_coul[2],special_coul[3]);
}
@ -1314,6 +1314,6 @@ void Special::fix_alteration()
void Special::timer_output(double time1)
{
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" special bonds CPU = {:.3f} secs\n",
utils::logmesg(lmp,fmt::format(" special bonds CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
}

4
src/utils.cpp
View File

@ -549,9 +549,9 @@ bool utils::is_double(const std::string & str) {
std::string utils::path_basename(const std::string & path) {
#if defined(_WIN32)
size_t start = path.find_last_of('/\\');
size_t start = path.find_last_of("/\\");
#else
size_t start = path.find_last_of('/');
size_t start = path.find_last_of("/");
#endif
if (start == std::string::npos) {

5
unittest/force-styles/pair_style.cpp
View File

@ -1007,6 +1007,9 @@ TEST(PairStyle, single)
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
// need to add this dependency
test_config.prerequisites.push_back(std::make_pair("atom", "full"));
// create a LAMMPS instance with standard settings to detect the number of atom types
if (!verbose) ::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(argc, argv, test_config);
@ -1018,8 +1021,10 @@ TEST(PairStyle, single)
for (auto prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
test_config.prerequisites.pop_back();
GTEST_SKIP();
}
test_config.prerequisites.pop_back();
// gather some information and skip if unsupported
int ntypes = lmp->atom->ntypes;

2
unittest/force-styles/tests/atomic-pair-eam.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 15 Jun 2020
date_generated: Thu Jun 25 12:25:55 202
epsilon: 5e-12
epsilon: 6e-12
prerequisites: ! |
pair eam
pre_commands: ! |