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Merge pull request #1507 from athomps/yarray 

Back-porting of Zombie SNAP improvements
This commit is contained in:
Axel Kohlmeyer 2019-06-17 14:13:28 -04:00 committed by GitHub
parent 6536399fc3 4d7d3a5d53
commit 93fd33aad9
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GPG Key ID: 4AEE18F83AFDEB23
18 changed files with 1024 additions and 2720 deletions
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36
doc/src/compute_sna_atom.txt
View File

@ -24,12 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
w_1, w_2,... = list of neighbor weights, one for each type :l
zero or more keyword/value pairs may be appended :l
keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
{diagonal} value = {0} or {1} or {2} or {3}
{0} = all j1, j2, j <= twojmax, j2 <= j1
{1} = subset satisfying j1 == j2
{2} = subset satisfying j1 == j2 == j3
{3} = subset satisfying j2 <= j1 <= j
keyword = {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
{rmin0} value = parameter in distance to angle conversion (distance units)
{switchflag} value = {0} or {1}
{0} = do not use switching function
@ -44,7 +39,7 @@ keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag
[Examples:]
compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 diagonal 3 rmin0 0.0
compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
compute db all sna/atom 1.4 0.95 6 2.0 1.0
compute vb all sna/atom 1.4 0.95 6 2.0 1.0 :pre
@ -151,7 +146,7 @@ The argument {rfac0} and the optional keyword {rmin0} define the
linear mapping from radial distance to polar angle {theta0} on the
3-sphere.
The argument {twojmax} and the keyword {diagonal} define which
The argument {twojmax} defines which
bispectrum components are generated. See section below on output for a
detailed explanation of the number of bispectrum components and the
ordered in which they are listed.
@ -192,23 +187,18 @@ command that includes all pairs in the neighbor list.
Compute {sna/atom} calculates a per-atom array, each column
corresponding to a particular bispectrum component. The total number
of columns and the identity of the bispectrum component contained in
each column depend on the values of {twojmax} and {diagonal}, as
each column depend of the value of {twojmax}, as
described by the following piece of python code:
for j1 in range(0,twojmax+1):
if(diagonal==2):
print j1/2.,j1/2.,j1/2.
elif(diagonal==1):
for j in range(0,min(twojmax,2*j1)+1,2):
print j1/2.,j1/2.,j/2.
elif(diagonal==0):
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
print j1/2.,j2/2.,j/2.
elif(diagonal==3):
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
if (j>=j1): print j1/2.,j2/2.,j/2. :pre
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
if (j>=j1): print j1/2.,j2/2.,j/2. :pre
NOTE: the {diagonal} keyword allowing other possible choices
for the number of bispectrum components was removed in 2019,
since all potentials use the value of 3, corresponding to the
above set of bispectrum components.
Compute {snad/atom} evaluates a per-atom array. The columns are
arranged into {ntypes} blocks, listed in order of atom type {I}. Each
@ -259,7 +249,7 @@ package"_Build_package.html doc page for more info.
[Default:]
The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
The optional keyword defaults are {rmin0} = 0,
{switchflag} = 1, {bzeroflag} = 1, {quadraticflag} = 0,
:line

8
doc/src/pair_snap.txt
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@ -38,7 +38,7 @@ where {B_k^i} is the {k}-th bispectrum component of atom {i},
and {beta_k^alpha_i} is the corresponding linear coefficient
that depends on {alpha_i}, the SNAP element of atom {i}. The
number of bispectrum components used and their definitions
depend on the values of {twojmax} and {diagonalstyle}
depend on the value of {twojmax}
defined in the SNAP parameter file described below.
The bispectrum calculation is described in more detail
in "compute sna/atom"_compute_sna_atom.html.
@ -125,14 +125,13 @@ This line is followed by {ncoeff} coefficients, one per line.
The SNAP parameter file can contain blank and comment lines (start
with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are {rcutfac} and
{twojmax}. Optional keywords are {rfac0}, {rmin0}, {diagonalstyle},
{twojmax}. Optional keywords are {rfac0}, {rmin0},
{switchflag}, and {bzeroflag}.
The default values for these keywords are
{rfac0} = 0.99363
{rmin0} = 0.0
{diagonalstyle} = 3
{switchflag} = 0
{bzeroflag} = 1
{quadraticflag} = 1 :ul
@ -144,6 +143,9 @@ If {quadraticflag} is set to 1, then the SNAP energy expression includes the qua
The SNAP element file should contain {K}({K}+1)/2 additional coefficients
for each element, the upper-triangular elements of alpha.
NOTE: The previously used {diagonalstyle} keyword was removed in 2019,
since all known SNAP potentials use the default value of 3.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:

1
potentials/Ta06A.snapparam
View File

@ -10,6 +10,5 @@ twojmax 6
rfac0 0.99363
rmin0 0
diagonalstyle 3
bzeroflag 0
quadraticflag 0

1
potentials/W_2940_2017_2.snapparam
View File

@ -8,6 +8,5 @@ twojmax 8
rfac0 0.99363
rmin0 0
diagonalstyle 3
bzeroflag 0
quadraticflag 0

18
src/KOKKOS/pair_snap_kokkos_impl.h
View File

@ -85,9 +85,6 @@ void PairSNAPKokkos<DeviceType>::init_style()
if (force->newton_pair == 0)
error->all(FLERR,"Pair style SNAP requires newton pair on");
if (diagonalstyle != 3)
error->all(FLERR,"Must use diagonal style = 3 with pair snap/kk");
// irequest = neigh request made by parent class
neighflag = lmp->kokkos->neighflag;
@ -343,23 +340,12 @@ void PairSNAPKokkos<DeviceType>::coeff(int narg, char **arg)
Kokkos::deep_copy(d_coeffelem,h_coeffelem);
Kokkos::deep_copy(d_map,h_map);
// deallocate non-kokkos sna
if (sna) {
for (int tid = 0; tid<nthreads; tid++)
delete sna[tid];
delete [] sna;
sna = NULL;
}
// allocate memory for per OpenMP thread data which
// is wrapped into the sna class
snaKK = SNAKokkos<DeviceType>(rfac0,twojmax,
diagonalstyle,use_shared_arrays,
rmin0,switchflag,bzeroflag);
//if (!use_shared_arrays)
snaKK.grow_rij(nmax);
snaKK.grow_rij(0);
snaKK.init();
}
@ -667,8 +653,6 @@ double PairSNAPKokkos<DeviceType>::memory_usage()
int n = atom->ntypes+1;
bytes += n*n*sizeof(int);
bytes += n*n*sizeof(double);
bytes += 3*nmax*sizeof(double);
bytes += nmax*sizeof(int);
bytes += (2*ncoeffall)*sizeof(double);
bytes += (ncoeff*3)*sizeof(double);
bytes += snaKK.memory_usage();

8
src/KOKKOS/sna_kokkos.h
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@ -48,7 +48,7 @@ inline
SNAKokkos(const SNAKokkos<DeviceType>& sna, const typename Kokkos::TeamPolicy<DeviceType>::member_type& team);
inline
SNAKokkos(double, int, int, int, double, int, int);
SNAKokkos(double, int, double, int, int);
KOKKOS_INLINE_FUNCTION
~SNAKokkos();
@ -178,12 +178,6 @@ inline
double, double, double, // compute_duidrj
double, double, double, double, double);
// if number of atoms are small use per atom arrays
// for twojmax arrays, rij, inside, bvec
// this will increase the memory footprint considerably,
// but allows parallel filling and reuse of these arrays
int use_shared_arrays;
// Sets the style for the switching function
// 0 = none
// 1 = cosine

97
src/KOKKOS/sna_kokkos_impl.h
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@ -27,19 +27,17 @@ static const double MY_PI = 3.14159265358979323846; // pi
template<class DeviceType>
inline
SNAKokkos<DeviceType>::SNAKokkos(double rfac0_in,
int twojmax_in, int diagonalstyle_in, int use_shared_arrays_in,
int twojmax_in,
double rmin0_in, int switch_flag_in, int bzero_flag_in)
{
wself = 1.0;
use_shared_arrays = use_shared_arrays_in;
rfac0 = rfac0_in;
rmin0 = rmin0_in;
switch_flag = switch_flag_in;
bzero_flag = bzero_flag_in;
twojmax = twojmax_in;
diagonalstyle = diagonalstyle_in;
ncoeff = compute_ncoeff();
@ -70,14 +68,12 @@ KOKKOS_INLINE_FUNCTION
SNAKokkos<DeviceType>::SNAKokkos(const SNAKokkos<DeviceType>& sna, const typename Kokkos::TeamPolicy<DeviceType>::member_type& team) {
wself = sna.wself;
use_shared_arrays = sna.use_shared_arrays;
rfac0 = sna.rfac0;
rmin0 = sna.rmin0;
switch_flag = sna.switch_flag;
bzero_flag = sna.bzero_flag;
twojmax = sna.twojmax;
diagonalstyle = sna.diagonalstyle;
ncoeff = sna.ncoeff;
nmax = sna.nmax;
@ -104,48 +100,45 @@ template<class DeviceType>
inline
void SNAKokkos<DeviceType>::build_indexlist()
{
if(diagonalstyle == 3) {
int idxj_count = 0;
int idxj_full_count = 0;
int idxj_count = 0;
int idxj_full_count = 0;
for(int j1 = 0; j1 <= twojmax; j1++)
for(int j2 = 0; j2 <= j1; j2++)
for(int j = abs(j1 - j2); j <= MIN(twojmax, j1 + j2); j += 2) {
if (j >= j1) idxj_count++;
idxj_full_count++;
}
for(int j1 = 0; j1 <= twojmax; j1++)
for(int j2 = 0; j2 <= j1; j2++)
for(int j = abs(j1 - j2); j <= MIN(twojmax, j1 + j2); j += 2) {
if (j >= j1) idxj_count++;
idxj_full_count++;
}
// indexList can be changed here
// indexList can be changed here
idxj = Kokkos::View<SNAKK_LOOPINDICES*, DeviceType>("SNAKokkos::idxj",idxj_count);
idxj_full = Kokkos::View<SNAKK_LOOPINDICES*, DeviceType>("SNAKokkos::idxj_full",idxj_full_count);
auto h_idxj = Kokkos::create_mirror_view(idxj);
auto h_idxj_full = Kokkos::create_mirror_view(idxj_full);
idxj = Kokkos::View<SNAKK_LOOPINDICES*, DeviceType>("SNAKokkos::idxj",idxj_count);
idxj_full = Kokkos::View<SNAKK_LOOPINDICES*, DeviceType>("SNAKokkos::idxj_full",idxj_full_count);
auto h_idxj = Kokkos::create_mirror_view(idxj);
auto h_idxj_full = Kokkos::create_mirror_view(idxj_full);
idxj_max = idxj_count;
idxj_full_max = idxj_full_count;
idxj_max = idxj_count;
idxj_full_max = idxj_full_count;
idxj_count = 0;
idxj_full_count = 0;
idxj_count = 0;
idxj_full_count = 0;
for(int j1 = 0; j1 <= twojmax; j1++)
for(int j2 = 0; j2 <= j1; j2++)
for(int j = abs(j1 - j2); j <= MIN(twojmax, j1 + j2); j += 2) {
if (j >= j1) {
h_idxj[idxj_count].j1 = j1;
h_idxj[idxj_count].j2 = j2;
h_idxj[idxj_count].j = j;
idxj_count++;
}
h_idxj_full[idxj_full_count].j1 = j1;
h_idxj_full[idxj_full_count].j2 = j2;
h_idxj_full[idxj_full_count].j = j;
idxj_full_count++;
}
Kokkos::deep_copy(idxj,h_idxj);
Kokkos::deep_copy(idxj_full,h_idxj_full);
}
for(int j1 = 0; j1 <= twojmax; j1++)
for(int j2 = 0; j2 <= j1; j2++)
for(int j = abs(j1 - j2); j <= MIN(twojmax, j1 + j2); j += 2) {
if (j >= j1) {
h_idxj[idxj_count].j1 = j1;
h_idxj[idxj_count].j2 = j2;
h_idxj[idxj_count].j = j;
idxj_count++;
}
h_idxj_full[idxj_full_count].j1 = j1;
h_idxj_full[idxj_full_count].j2 = j2;
h_idxj_full[idxj_full_count].j = j;
idxj_full_count++;
}
Kokkos::deep_copy(idxj,h_idxj);
Kokkos::deep_copy(idxj_full,h_idxj_full);
}
/* ---------------------------------------------------------------------- */
@ -1223,26 +1216,10 @@ int SNAKokkos<DeviceType>::compute_ncoeff()
ncount = 0;
for (int j1 = 0; j1 <= twojmax; j1++)
if(diagonalstyle == 0) {
for (int j2 = 0; j2 <= j1; j2++)
for (int j = abs(j1 - j2);
j <= MIN(twojmax, j1 + j2); j += 2)
ncount++;
} else if(diagonalstyle == 1) {
int j2 = j1;
for (int j2 = 0; j2 <= j1; j2++)
for (int j = abs(j1 - j2);
j <= MIN(twojmax, j1 + j2); j += 2)
ncount++;
} else if(diagonalstyle == 2) {
ncount++;
} else if(diagonalstyle == 3) {
for (int j2 = 0; j2 <= j1; j2++)
for (int j = abs(j1 - j2);
j <= MIN(twojmax, j1 + j2); j += 2)
if (j >= j1) ncount++;
}
j <= MIN(twojmax, j1 + j2); j += 2)
if (j >= j1) ncount++;
return ncount;
}

79
src/SNAP/compute_sna_atom.cpp
View File

@ -25,7 +25,6 @@
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "openmp_snap.h"
using namespace LAMMPS_NS;
@ -45,7 +44,6 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
// default values
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 1;
@ -85,14 +83,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
int iarg = nargmin;
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/atom command");
diagonalstyle = atoi(arg[iarg+1]);
if (diagonalstyle < 0 || diagonalstyle > 3)
error->all(FLERR,"Illegal compute sna/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"rmin0") == 0) {
if (strcmp(arg[iarg],"rmin0") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/atom command");
rmin0 = atof(arg[iarg+1]);
@ -115,28 +106,16 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal compute sna/atom command");
}
nthreads = comm->nthreads;
snaptr = new SNA*[nthreads];
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag)
#endif
{
int tid = omp_get_thread_num();
snaptr = new SNA(lmp,rfac0,twojmax,
rmin0,switchflag,bzeroflag);
// always unset use_shared_arrays since it does not work with computes
snaptr[tid] = new SNA(lmp,rfac0,twojmax,diagonalstyle,
0 /*use_shared_arrays*/, rmin0,switchflag,bzeroflag);
}
ncoeff = snaptr[0]->ncoeff;
ncoeff = snaptr->ncoeff;
size_peratom_cols = ncoeff;
if (quadraticflag) size_peratom_cols += (ncoeff*(ncoeff+1))/2;
peratom_flag = 1;
nmax = 0;
njmax = 0;
sna = NULL;
}
/* ---------------------------------------------------------------------- */
@ -147,9 +126,7 @@ ComputeSNAAtom::~ComputeSNAAtom()
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
for (int tid = 0; tid<nthreads; tid++)
delete snaptr[tid];
delete [] snaptr;
delete snaptr;
}
/* ---------------------------------------------------------------------- */
@ -176,13 +153,7 @@ void ComputeSNAAtom::init()
if (strcmp(modify->compute[i]->style,"sna/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute sna/atom");
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
int tid = omp_get_thread_num();
snaptr[tid]->init();
}
snaptr->init();
}
/* ---------------------------------------------------------------------- */
@ -223,11 +194,7 @@ void ComputeSNAAtom::compute_peratom()
double** const x = atom->x;
const int* const mask = atom->mask;
#if defined(_OPENMP)
#pragma omp parallel for default(none)
#endif
for (int ii = 0; ii < inum; ii++) {
const int tid = omp_get_thread_num();
const int i = ilist[ii];
if (mask[i] & groupbit) {
@ -241,7 +208,7 @@ void ComputeSNAAtom::compute_peratom()
// insure rij, inside, and typej are of size jnum
snaptr[tid]->grow_rij(jnum);
snaptr->grow_rij(jnum);
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
@ -258,26 +225,25 @@ void ComputeSNAAtom::compute_peratom()
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
snaptr[tid]->rij[ninside][0] = delx;
snaptr[tid]->rij[ninside][1] = dely;
snaptr[tid]->rij[ninside][2] = delz;
snaptr[tid]->inside[ninside] = j;
snaptr[tid]->wj[ninside] = wjelem[jtype];
snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
ninside++;
}
}
snaptr[tid]->compute_ui(ninside);
snaptr[tid]->compute_zi();
snaptr[tid]->compute_bi();
snaptr[tid]->copy_bi2bvec();
snaptr->compute_ui(ninside);
snaptr->compute_zi();
snaptr->compute_bi();
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
sna[i][icoeff] = snaptr[tid]->bvec[icoeff];
sna[i][icoeff] = snaptr->blist[icoeff];
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
double bi = snaptr->blist[icoeff];
// diagonal element of quadratic matrix
@ -286,7 +252,7 @@ void ComputeSNAAtom::compute_peratom()
// upper-triangular elements of quadratic matrix
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
sna[i][ncount++] = bi*snaptr[tid]->bvec[jcoeff];
sna[i][ncount++] = bi*snaptr->blist[jcoeff];
}
}
} else {
@ -302,10 +268,9 @@ void ComputeSNAAtom::compute_peratom()
double ComputeSNAAtom::memory_usage()
{
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
bytes += snaptr[0]->memory_usage()*comm->nthreads;
double bytes = nmax*size_peratom_cols * sizeof(double); // sna
bytes += snaptr->memory_usage(); // SNA object
return bytes;
}

5
src/SNAP/compute_sna_atom.h
View File

@ -34,7 +34,7 @@ class ComputeSNAAtom : public Compute {
double memory_usage();
private:
int nmax, njmax, diagonalstyle;
int nmax;
int ncoeff;
double **cutsq;
class NeighList *list;
@ -42,10 +42,9 @@ class ComputeSNAAtom : public Compute {
double rcutfac;
double *radelem;
double *wjelem;
class SNA** snaptr;
class SNA* snaptr;
double cutmax;
int quadraticflag;
int nthreads;
};
}

118
src/SNAP/compute_snad_atom.cpp
View File

@ -25,7 +25,6 @@
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "openmp_snap.h"
using namespace LAMMPS_NS;
@ -45,7 +44,6 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
// default values
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 1;
@ -83,14 +81,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
int iarg = nargmin;
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snad/atom command");
diagonalstyle = atof(arg[iarg+1]);
if (diagonalstyle < 0 || diagonalstyle > 3)
error->all(FLERR,"Illegal compute snad/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"rmin0") == 0) {
if (strcmp(arg[iarg],"rmin0") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snad/atom command");
rmin0 = atof(arg[iarg+1]);
@ -113,20 +104,10 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal compute snad/atom command");
}
nthreads = comm->nthreads;
snaptr = new SNA*[nthreads];
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag)
#endif
{
int tid = omp_get_thread_num();
snaptr = new SNA(lmp,rfac0,twojmax,
rmin0,switchflag,bzeroflag);
// always unset use_shared_arrays since it does not work with computes
snaptr[tid] = new SNA(lmp,rfac0,twojmax,diagonalstyle,
0 /*use_shared_arrays*/, rmin0,switchflag,bzeroflag);
}
ncoeff = snaptr[0]->ncoeff;
ncoeff = snaptr->ncoeff;
nperdim = ncoeff;
if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
yoffset = nperdim;
@ -136,9 +117,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
nmax = 0;
njmax = 0;
snad = NULL;
}
/* ---------------------------------------------------------------------- */
@ -149,9 +128,7 @@ ComputeSNADAtom::~ComputeSNADAtom()
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
for (int tid = 0; tid<nthreads; tid++)
delete snaptr[tid];
delete [] snaptr;
delete snaptr;
}
/* ---------------------------------------------------------------------- */
@ -178,13 +155,7 @@ void ComputeSNADAtom::init()
if (strcmp(modify->compute[i]->style,"snad/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute snad/atom");
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
int tid = omp_get_thread_num();
snaptr[tid]->init();
}
snaptr->init();
}
/* ---------------------------------------------------------------------- */
@ -235,11 +206,7 @@ void ComputeSNADAtom::compute_peratom()
double** const x = atom->x;
const int* const mask = atom->mask;
#if defined(_OPENMP)
#pragma omp parallel for default(none)
#endif
for (int ii = 0; ii < inum; ii++) {
const int tid = omp_get_thread_num();
const int i = ilist[ii];
if (mask[i] & groupbit) {
@ -258,7 +225,7 @@ void ComputeSNADAtom::compute_peratom()
// insure rij, inside, and typej are of size jnum
snaptr[tid]->grow_rij(jnum);
snaptr->grow_rij(jnum);
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
@ -276,30 +243,28 @@ void ComputeSNADAtom::compute_peratom()
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
snaptr[tid]->rij[ninside][0] = delx;
snaptr[tid]->rij[ninside][1] = dely;
snaptr[tid]->rij[ninside][2] = delz;
snaptr[tid]->inside[ninside] = j;
snaptr[tid]->wj[ninside] = wjelem[jtype];
snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
ninside++;
}
}
snaptr[tid]->compute_ui(ninside);
snaptr[tid]->compute_zi();
snaptr->compute_ui(ninside);
snaptr->compute_zi();
if (quadraticflag) {
snaptr[tid]->compute_bi();
snaptr[tid]->copy_bi2bvec();
snaptr->compute_bi();
}
for (int jj = 0; jj < ninside; jj++) {
const int j = snaptr[tid]->inside[jj];
snaptr[tid]->compute_duidrj(snaptr[tid]->rij[jj],
snaptr[tid]->wj[jj],
snaptr[tid]->rcutij[jj]);
snaptr[tid]->compute_dbidrj();
snaptr[tid]->copy_dbi2dbvec();
const int j = snaptr->inside[jj];
snaptr->compute_duidrj(snaptr->rij[jj],
snaptr->wj[jj],
snaptr->rcutij[jj]);
snaptr->compute_dbidrj();
// Accumulate -dBi/dRi, -dBi/dRj
@ -307,12 +272,12 @@ void ComputeSNADAtom::compute_peratom()
double *snadj = snad[j]+typeoffset;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0];
snadi[icoeff+yoffset] += snaptr[tid]->dbvec[icoeff][1];
snadi[icoeff+zoffset] += snaptr[tid]->dbvec[icoeff][2];
snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0];
snadj[icoeff+yoffset] -= snaptr[tid]->dbvec[icoeff][1];
snadj[icoeff+zoffset] -= snaptr[tid]->dbvec[icoeff][2];
snadi[icoeff] += snaptr->dblist[icoeff][0];
snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
snadj[icoeff] -= snaptr->dblist[icoeff][0];
snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
}
if (quadraticflag) {
@ -321,10 +286,10 @@ void ComputeSNADAtom::compute_peratom()
snadj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
double bix = snaptr[tid]->dbvec[icoeff][0];
double biy = snaptr[tid]->dbvec[icoeff][1];
double biz = snaptr[tid]->dbvec[icoeff][2];
double bi = snaptr->blist[icoeff];
double bix = snaptr->dblist[icoeff][0];
double biy = snaptr->dblist[icoeff][1];
double biz = snaptr->dblist[icoeff][2];
// diagonal elements of quadratic matrix
@ -343,12 +308,12 @@ void ComputeSNADAtom::compute_peratom()
// upper-triangular elements of quadratic matrix
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ bix*snaptr[tid]->bvec[jcoeff];
double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+ biy*snaptr[tid]->bvec[jcoeff];
double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+ biz*snaptr[tid]->bvec[jcoeff];
double dbxtmp = bi*snaptr->dblist[jcoeff][0]
+ bix*snaptr->blist[jcoeff];
double dbytmp = bi*snaptr->dblist[jcoeff][1]
+ biy*snaptr->blist[jcoeff];
double dbztmp = bi*snaptr->dblist[jcoeff][2]
+ biz*snaptr->blist[jcoeff];
snadi[ncount] += dbxtmp;
snadi[ncount+yoffset] += dbytmp;
@ -404,10 +369,9 @@ void ComputeSNADAtom::unpack_reverse_comm(int n, int *list, double *buf)
double ComputeSNADAtom::memory_usage()
{
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
bytes += 3*nperdim*atom->ntypes;
bytes += snaptr[0]->memory_usage()*comm->nthreads;
double bytes = nmax*size_peratom_cols * sizeof(double); // snad
bytes += snaptr->memory_usage(); // SNA object
return bytes;
}

5
src/SNAP/compute_snad_atom.h
View File

@ -36,7 +36,7 @@ class ComputeSNADAtom : public Compute {
double memory_usage();
private:
int nmax, njmax, diagonalstyle;
int nmax;
int ncoeff, nperdim, yoffset, zoffset;
double **cutsq;
class NeighList *list;
@ -44,10 +44,9 @@ class ComputeSNADAtom : public Compute {
double rcutfac;
double *radelem;
double *wjelem;
class SNA** snaptr;
class SNA* snaptr;
double cutmax;
int quadraticflag;
int nthreads;
};
}

129
src/SNAP/compute_snav_atom.cpp
View File

@ -25,7 +25,6 @@
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "openmp_snap.h"
using namespace LAMMPS_NS;
@ -45,7 +44,6 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
// default values
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 1;
@ -79,14 +77,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
int iarg = nargmin;
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snav/atom command");
diagonalstyle = atof(arg[iarg+1]);
if (diagonalstyle < 0 || diagonalstyle > 3)
error->all(FLERR,"Illegal compute snav/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"rmin0") == 0) {
if (strcmp(arg[iarg],"rmin0") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snav/atom command");
rmin0 = atof(arg[iarg+1]);
@ -109,20 +100,10 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal compute snav/atom command");
}
nthreads = comm->nthreads;
snaptr = new SNA*[nthreads];
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag)
#endif
{
int tid = omp_get_thread_num();
snaptr = new SNA(lmp,rfac0,twojmax,
rmin0,switchflag,bzeroflag);
// always unset use_shared_arrays since it does not work with computes
snaptr[tid] = new SNA(lmp,rfac0,twojmax,diagonalstyle,
0 /*use_shared_arrays*/, rmin0,switchflag,bzeroflag);
}
ncoeff = snaptr[0]->ncoeff;
ncoeff = snaptr->ncoeff;
nperdim = ncoeff;
if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
size_peratom_cols = 6*nperdim*atom->ntypes;
@ -130,7 +111,6 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
nmax = 0;
njmax = 0;
snav = NULL;
}
@ -144,9 +124,7 @@ ComputeSNAVAtom::~ComputeSNAVAtom()
memory->destroy(wjelem);
memory->destroy(cutsq);
for (int tid = 0; tid<nthreads; tid++)
delete snaptr[tid];
delete [] snaptr;
delete snaptr;
}
/* ---------------------------------------------------------------------- */
@ -174,13 +152,7 @@ void ComputeSNAVAtom::init()
if (strcmp(modify->compute[i]->style,"snav/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute snav/atom");
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
int tid = omp_get_thread_num();
snaptr[tid]->init();
}
snaptr->init();
}
/* ---------------------------------------------------------------------- */
@ -230,11 +202,7 @@ void ComputeSNAVAtom::compute_peratom()
double** const x = atom->x;
const int* const mask = atom->mask;
#if defined(_OPENMP)
#pragma omp parallel for default(none)
#endif
for (int ii = 0; ii < inum; ii++) {
const int tid = omp_get_thread_num();
const int i = ilist[ii];
if (mask[i] & groupbit) {
@ -251,7 +219,7 @@ void ComputeSNAVAtom::compute_peratom()
// insure rij, inside, and typej are of size jnum
snaptr[tid]->grow_rij(jnum);
snaptr->grow_rij(jnum);
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
@ -269,31 +237,29 @@ void ComputeSNAVAtom::compute_peratom()
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
snaptr[tid]->rij[ninside][0] = delx;
snaptr[tid]->rij[ninside][1] = dely;
snaptr[tid]->rij[ninside][2] = delz;
snaptr[tid]->inside[ninside] = j;
snaptr[tid]->wj[ninside] = wjelem[jtype];
snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
ninside++;
}
}
snaptr[tid]->compute_ui(ninside);
snaptr[tid]->compute_zi();
snaptr->compute_ui(ninside);
snaptr->compute_zi();
if (quadraticflag) {
snaptr[tid]->compute_bi();
snaptr[tid]->copy_bi2bvec();
snaptr->compute_bi();
}
for (int jj = 0; jj < ninside; jj++) {
const int j = snaptr[tid]->inside[jj];
const int j = snaptr->inside[jj];
snaptr[tid]->compute_duidrj(snaptr[tid]->rij[jj],
snaptr[tid]->wj[jj],
snaptr[tid]->rcutij[jj]);
snaptr[tid]->compute_dbidrj();
snaptr[tid]->copy_dbi2dbvec();
snaptr->compute_duidrj(snaptr->rij[jj],
snaptr->wj[jj],
snaptr->rcutij[jj]);
snaptr->compute_dbidrj();
// Accumulate -dBi/dRi*Ri, -dBi/dRj*Rj
@ -301,18 +267,18 @@ void ComputeSNAVAtom::compute_peratom()
double *snavj = snav[j]+typeoffset;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp;
snavi[icoeff+nperdim] += snaptr[tid]->dbvec[icoeff][1]*ytmp;
snavi[icoeff+2*nperdim] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
snavi[icoeff+3*nperdim] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
snavi[icoeff+4*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
snavi[icoeff+5*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
snavj[icoeff+nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
snavj[icoeff+2*nperdim] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
snavj[icoeff+3*nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
snavj[icoeff+4*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
snavj[icoeff+5*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
snavi[icoeff] += snaptr->dblist[icoeff][0]*xtmp;
snavi[icoeff+nperdim] += snaptr->dblist[icoeff][1]*ytmp;
snavi[icoeff+2*nperdim] += snaptr->dblist[icoeff][2]*ztmp;
snavi[icoeff+3*nperdim] += snaptr->dblist[icoeff][1]*ztmp;
snavi[icoeff+4*nperdim] += snaptr->dblist[icoeff][0]*ztmp;
snavi[icoeff+5*nperdim] += snaptr->dblist[icoeff][0]*ytmp;
snavj[icoeff] -= snaptr->dblist[icoeff][0]*x[j][0];
snavj[icoeff+nperdim] -= snaptr->dblist[icoeff][1]*x[j][1];
snavj[icoeff+2*nperdim] -= snaptr->dblist[icoeff][2]*x[j][2];
snavj[icoeff+3*nperdim] -= snaptr->dblist[icoeff][1]*x[j][2];
snavj[icoeff+4*nperdim] -= snaptr->dblist[icoeff][0]*x[j][2];
snavj[icoeff+5*nperdim] -= snaptr->dblist[icoeff][0]*x[j][1];
}
if (quadraticflag) {
@ -321,10 +287,10 @@ void ComputeSNAVAtom::compute_peratom()
snavj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
double bix = snaptr[tid]->dbvec[icoeff][0];
double biy = snaptr[tid]->dbvec[icoeff][1];
double biz = snaptr[tid]->dbvec[icoeff][2];
double bi = snaptr->blist[icoeff];
double bix = snaptr->dblist[icoeff][0];
double biy = snaptr->dblist[icoeff][1];
double biz = snaptr->dblist[icoeff][2];
// diagonal element of quadratic matrix
@ -348,12 +314,12 @@ void ComputeSNAVAtom::compute_peratom()
// upper-triangular elements of quadratic matrix
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ bix*snaptr[tid]->bvec[jcoeff];
double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+ biy*snaptr[tid]->bvec[jcoeff];
double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+ biz*snaptr[tid]->bvec[jcoeff];
double dbxtmp = bi*snaptr->dblist[jcoeff][0]
+ bix*snaptr->blist[jcoeff];
double dbytmp = bi*snaptr->dblist[jcoeff][1]
+ biy*snaptr->blist[jcoeff];
double dbztmp = bi*snaptr->dblist[jcoeff][2]
+ biz*snaptr->blist[jcoeff];
snavi[ncount] += dbxtmp*xtmp;
snavi[ncount+nperdim] += dbytmp*ytmp;
snavi[ncount+2*nperdim] += dbztmp*ztmp;
@ -414,11 +380,8 @@ void ComputeSNAVAtom::unpack_reverse_comm(int n, int *list, double *buf)
double ComputeSNAVAtom::memory_usage()
{
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
bytes += 6*nperdim*atom->ntypes;
if (quadraticflag) bytes += 6*nperdim*atom->ntypes;
bytes += snaptr[0]->memory_usage()*comm->nthreads;
double bytes = nmax*size_peratom_cols * sizeof(double); // snav
bytes += snaptr->memory_usage(); // SNA object
return bytes;
}

5
src/SNAP/compute_snav_atom.h
View File

@ -36,7 +36,7 @@ class ComputeSNAVAtom : public Compute {
double memory_usage();
private:
int nmax, njmax, diagonalstyle;
int nmax;
int ncoeff, nperdim;
double **cutsq;
class NeighList *list;
@ -44,9 +44,8 @@ class ComputeSNAVAtom : public Compute {
double rcutfac;
double *radelem;
double *wjelem;
class SNA** snaptr;
class SNA* snaptr;
int quadraticflag;
int nthreads;
};
}

16
src/SNAP/openmp_snap.h
View File

@ -1,16 +0,0 @@
#ifndef LMP_OPENMP_SNAP_H
#define LMP_OPENMP_SNAP_H
#if defined(_OPENMP)
#include <omp.h>
#else
enum omp_sched_t {omp_sched_static, omp_sched_dynamic, omp_sched_guided, omp_sched_auto};
inline int omp_get_thread_num() { return 0;}
inline int omp_set_num_threads(int num_threads) {return 1;}
/* inline int __sync_fetch_and_add(int* ptr, int value) {int tmp = *ptr; ptr[0]+=value; return tmp;} */
inline void omp_set_schedule(omp_sched_t schedule,int modifier=1) {}
inline int omp_in_parallel() {return 0;}
#endif
#endif

1321
src/SNAP/pair_snap.cpp
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File diff suppressed because it is too large Load Diff

64
src/SNAP/pair_snap.h
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@ -29,8 +29,6 @@ public:
PairSNAP(class LAMMPS *);
~PairSNAP();
virtual void compute(int, int);
void compute_regular(int, int);
void compute_optimized(int, int);
void settings(int, char **);
virtual void coeff(int, char **);
virtual void init_style();
@ -42,56 +40,14 @@ public:
protected:
int ncoeffq, ncoeffall;
double **bvec, ***dbvec;
class SNA** sna;
int nmax;
int nthreads;
class SNA* snaptr;
virtual void allocate();
void read_files(char *, char *);
inline int equal(double* x,double* y);
inline double dist2(double* x,double* y);
double extra_cutoff();
void load_balance();
void set_sna_to_shared(int snaid,int i);
void build_per_atom_arrays();
int schedule_user;
double schedule_time_guided;
double schedule_time_dynamic;
int ncalls_neigh;
int do_load_balance;
int ilistmask_max;
int* ilistmask;
int ghostinum;
int ghostilist_max;
int* ghostilist;
int ghostnumneigh_max;
int* ghostnumneigh;
int* ghostneighs;
int* ghostfirstneigh;
int ghostneighs_total;
int ghostneighs_max;
int use_optimized;
int use_shared_arrays;
int i_max;
int i_neighmax;
int i_numpairs;
int **i_pairs;
double ***i_rij;
int **i_inside;
double **i_wj;
double **i_rcutij;
int *i_ninside;
double ****i_uarraytot_r, ****i_uarraytot_i;
double ******i_zarray_r, ******i_zarray_i;
#ifdef TIMING_INFO
// timespec starttime, endtime;
double timers[4];
#endif
void compute_beta();
void compute_bispectrum();
double rcutmax; // max cutoff for all elements
int nelements; // # of unique elements
@ -99,10 +55,13 @@ protected:
double *radelem; // element radii
double *wjelem; // elements weights
double **coeffelem; // element bispectrum coefficients
double** beta; // betas for all atoms in list
double** bispectrum; // bispectrum components for all atoms in list
int *map; // mapping from atom types to elements
int twojmax, diagonalstyle, switchflag, bzeroflag;
int twojmax, switchflag, bzeroflag;
double rfac0, rmin0, wj1, wj2;
int rcutfacflag, twojmaxflag; // flags for required parameters
int beta_max; // length of beta
};
}
@ -124,15 +83,6 @@ Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Must set number of threads via package omp command
Because you are using the USER-OMP package, set the number of threads
via its settings, not by the pair_style snap nthreads setting.
W: Communication cutoff is too small for SNAP micro load balancing, increased to %lf
Self-explanatory.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.

1758
src/SNAP/sna.cpp
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File diff suppressed because it is too large Load Diff

75
src/SNAP/sna.h
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@ -18,20 +18,22 @@
#ifndef LMP_SNA_H
#define LMP_SNA_H
#include <complex>
#include "pointers.h"
#include <ctime>
namespace LAMMPS_NS {
struct SNA_LOOPINDICES {
struct SNA_ZINDICES {
int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju;
};
struct SNA_BINDICES {
int j1, j2, j;
};
class SNA : protected Pointers {
public:
SNA(LAMMPS*, double, int, int, int, double, int, int);
SNA(LAMMPS*, double, int, double, int, int);
SNA(LAMMPS* lmp) : Pointers(lmp) {};
~SNA();
@ -44,31 +46,21 @@ public:
// functions for bispectrum coefficients
void compute_ui(int);
void compute_ui_omp(int, int);
void compute_zi();
void compute_zi_omp(int);
void compute_yi(const double*);
void compute_yterm(int, int, int, const double*);
void compute_bi();
void copy_bi2bvec();
// functions for derivatives
void compute_duidrj(double*, double, double);
void compute_dbidrj();
void compute_dbidrj_nonsymm();
void copy_dbi2dbvec();
void compute_deidrj(double*);
double compute_sfac(double, double);
double compute_dsfac(double, double);
#ifdef TIMING_INFO
double* timers;
timespec starttime, endtime;
int print;
int counter;
#endif
//per sna class instance for OMP use
double* bvec, ** dbvec;
double* blist;
double** dblist;
double** rij;
int* inside;
double* wj;
@ -77,29 +69,32 @@ public:
void grow_rij(int);
int twojmax, diagonalstyle;
double*** uarraytot_r, *** uarraytot_i;
double***** zarray_r, ***** zarray_i;
double*** uarraytot_r_b, *** uarraytot_i_b;
double***** zarray_r_b, ***** zarray_i_b;
double*** uarray_r, *** uarray_i;
int twojmax;
private:
double rmin0, rfac0;
//use indexlist instead of loops, constructor generates these
SNA_LOOPINDICES* idxj;
int idxj_max;
// data for bispectrum coefficients
double***** cgarray;
SNA_ZINDICES* idxz;
SNA_BINDICES* idxb;
int idxcg_max, idxu_max, idxz_max, idxb_max;
double** rootpqarray;
double*** barray;
double* cglist;
int*** idxcg_block;
// derivatives of data
double* ulisttot_r, * ulisttot_i;
double* ulist_r, * ulist_i;
int* idxu_block;
double**** duarray_r, **** duarray_i;
double**** dbarray;
double* zlist_r, * zlist_i;
int*** idxz_block;
int*** idxb_block;
double** dulist_r, ** dulist_i;
double* ylist_r, * ylist_i;
static const int nmaxfactorial = 167;
static const double nfac_table[];
@ -109,28 +104,16 @@ private:
void destroy_twojmax_arrays();
void init_clebsch_gordan();
void init_rootpqarray();
void jtostr(char*, int);
void mtostr(char*, int, int);
void print_clebsch_gordan(FILE*);
void zero_uarraytot();
void addself_uarraytot(double);
void add_uarraytot(double, double, double);
void add_uarraytot_omp(double, double, double);
void compute_uarray(double, double, double,
double, double);
void compute_uarray_omp(double, double, double,
double, double, int);
double deltacg(int, int, int);
int compute_ncoeff();
void compute_duarray(double, double, double,
double, double, double, double, double);
// if number of atoms are small use per atom arrays
// for twojmax arrays, rij, inside, bvec
// this will increase the memory footprint considerably,
// but allows parallel filling and reuse of these arrays
int use_shared_arrays;
// Sets the style for the switching function
// 0 = none
// 1 = cosine
@ -140,7 +123,7 @@ private:
double wself;
int bzero_flag; // 1 if bzero subtracted from barray
double *bzero; // array of B values for isolated atoms
double* bzero; // array of B values for isolated atoms
};
}