bool compareArraysNeg(
const Array1 &a1, const std::string &a1_name,
const Array2 &a2, const std::string &a2_name,
FancyOStream &out
)
{
bool success = true;
out << "Comparing " << a1_name << " == -(" << a2_name << ") ... ";
const int n = a1.size();
// Compare sizes
if (as<int>(a2.size()) != n) {
out << "\nError, "<<a1_name<<".size() = "<<a1.size()<<" == "
<< a2_name<<".size() = "<<a2.size()<<" : failed!\n";
return false;
}
// Compare elements
for( int i = 0; i < n; ++i ) {
const bool result = ( a1[i] == -a2[i] ); // Tests C::operator[](i) const
if (!result) {
out << "\nError, "<<a1_name<<"["<<i<<"] = "<<a1[i]<<" == -("
<< a2_name<<"["<<i<<"]) = -("<<a2[i]<<"): failed!\n";
success = false;
}
}
if (success) {
out << "passed\n";
}
return success;
}
void SphSystemData2::computeMass() {
Array1<Vector2D> points;
TrianglePointGenerator pointsGenerator;
BoundingBox2D sampleBound(
Vector2D(-1.5*_kernelRadius, -1.5*_kernelRadius),
Vector2D(1.5*_kernelRadius, 1.5*_kernelRadius));
pointsGenerator.generate(sampleBound, _targetSpacing, &points);
double maxNumberDensity = 0.0;
SphStdKernel2 kernel(_kernelRadius);
for (size_t i = 0; i < points.size(); ++i) {
const Vector2D& point = points[i];
double sum = 0.0;
for (size_t j = 0; j < points.size(); ++j) {
const Vector2D& neighborPoint = points[j];
sum += kernel(neighborPoint.distanceTo(point));
}
maxNumberDensity = std::max(maxNumberDensity, sum);
}
JET_ASSERT(maxNumberDensity > 0);
double newMass = _targetDensity / maxNumberDensity;
ParticleSystemData2::setMass(newMass);
}
TEST(PointSimpleListSearcher3, ForEachNearbyPoint) {
Array1<Vector3D> points = {
Vector3D(0, 1, 3),
Vector3D(2, 5, 4),
Vector3D(-1, 3, 0)
};
PointSimpleListSearcher3 searcher;
searcher.build(points.accessor());
int cnt = 0;
searcher.forEachNearbyPoint(
Vector3D(0, 0, 0),
std::sqrt(10.0),
[&](size_t i, const Vector3D& pt) {
EXPECT_TRUE(i == 0 || i == 2);
if (i == 0) {
EXPECT_EQ(points[0], pt);
} else if (i == 2) {
EXPECT_EQ(points[2], pt);
}
++cnt;
});
EXPECT_EQ(2, cnt);
}
TEST(PointParallelHashGridSearcher3, CopyConstructor) {
Array1<Vector3D> points = {
Vector3D(0, 1, 3),
Vector3D(2, 5, 4),
Vector3D(-1, 3, 0)
};
PointParallelHashGridSearcher3 searcher(4, 4, 4, std::sqrt(10));
searcher.build(points.accessor());
PointParallelHashGridSearcher3 searcher2(searcher);
int cnt = 0;
searcher2.forEachNearbyPoint(
Vector3D(0, 0, 0),
std::sqrt(10.0),
[&](size_t i, const Vector3D& pt) {
EXPECT_TRUE(i == 0 || i == 2);
if (i == 0) {
EXPECT_EQ(points[0], pt);
} else if (i == 2) {
EXPECT_EQ(points[2], pt);
}
++cnt;
});
EXPECT_EQ(2, cnt);
}
TEST(PointParallelHashGridSearcher3, Serialization) {
Array1<Vector3D> points = {
Vector3D(0, 1, 3),
Vector3D(2, 5, 4),
Vector3D(-1, 3, 0)
};
PointParallelHashGridSearcher3 searcher(4, 4, 4, std::sqrt(10));
searcher.build(points.accessor());
std::vector<uint8_t> buffer;
searcher.serialize(&buffer);
PointParallelHashGridSearcher3 searcher2(1, 1, 1, 1.0);
searcher2.deserialize(buffer);
int cnt = 0;
searcher2.forEachNearbyPoint(
Vector3D(0, 0, 0),
std::sqrt(10.0),
[&](size_t i, const Vector3D& pt) {
EXPECT_TRUE(i == 0 || i == 2);
if (i == 0) {
EXPECT_EQ(points[0], pt);
} else if (i == 2) {
EXPECT_EQ(points[2], pt);
}
++cnt;
});
EXPECT_EQ(2, cnt);
}
void Force_fitter::fit_force(Array1 <doublevar> & r,
Array1 <doublevar> & bare_force,
Array1 <doublevar> & fit_force) {
int ndim=bare_force.GetDim(0);
fit_force=bare_force; return;
fit_force.Resize(ndim);
fit_force=0;
if(r(0) < cut) {
for(int d=0; d< ndim; d++) {
doublevar basis=0;
for(int i=0; i< nexp; i++) {
basis+=coeff(i)*pow(r(0),i+m);
}
fit_force(d)=bare_force(d)*basis;
}
}
else {
fit_force=bare_force;
}
}
JET_END_TEST_F
JET_BEGIN_TEST_F(FlipSolver2, Rotation) {
// Build solver
auto solver = FlipSolver2::builder()
.withResolution({10, 10})
.withDomainSizeX(1.0)
.makeShared();
solver->setGravity({0, 0});
solver->setPressureSolver(nullptr);
// Build emitter
auto box = Sphere2::builder()
.withCenter({0.5, 0.5})
.withRadius(0.4)
.makeShared();
auto emitter = VolumeParticleEmitter2::builder()
.withSurface(box)
.withSpacing(1.0 / 20.0)
.withIsOneShot(true)
.makeShared();
solver->setParticleEmitter(emitter);
Array1<double> r;
for (Frame frame; frame.index < 360; ++frame) {
auto x = solver->particleSystemData()->positions();
auto v = solver->particleSystemData()->velocities();
r.resize(x.size());
for (size_t i = 0; i < x.size(); ++i) {
r[i] = (x[i] - Vector2D(0.5, 0.5)).length();
}
solver->update(frame);
if (frame.index == 0) {
x = solver->particleSystemData()->positions();
v = solver->particleSystemData()->velocities();
for (size_t i = 0; i < x.size(); ++i) {
Vector2D rp = x[i] - Vector2D(0.5, 0.5);
v[i].x = rp.y;
v[i].y = -rp.x;
}
} else {
for (size_t i = 0; i < x.size(); ++i) {
Vector2D rp = x[i] - Vector2D(0.5, 0.5);
if (rp.lengthSquared() > 0.0) {
double scale = r[i] / rp.length();
x[i] = scale * rp + Vector2D(0.5, 0.5);
}
}
}
saveParticleDataXy(solver->particleSystemData(), frame.index);
}
}
//----------------------------------------------------------------------
doublevar dot(const Array1 <doublevar> & a, const Array1 <doublevar> & b){
int dim=a.GetSize();
assert(a.GetSize()==b.GetSize());
doublevar sum=0;
for(int i=0;i<dim;i++)
sum+=a(i)*b(i);
return sum;
}
dcomplex dot(const Array1 <dcomplex> & a, const Array1 <dcomplex> & b){
int dim=a.GetSize();
assert(a.GetSize()==b.GetSize());
dcomplex sum(0.0,0.0);
for(int i=0;i<dim;i++)
sum+=a(i)*b(i);
return sum;
}
void copy_array (Array1& source, Array2& dest) {
assert(std::equal(source.shape(),source.shape()+source.num_dimensions(),
dest.shape()));
// Dispatch to the proper function
typedef typename Array1::element element_type;
copy_dispatch<element_type>::
copy_array(source.begin(),source.end(),dest.begin());
}
void SetUp(const ::benchmark::State& state) {
int N = state.range(0);
points.clear();
for (int i = 0; i < N; ++i) {
points.append(makeVec());
}
}
TEST(PointKdTreeSearcher3, ForEachNearbyPointEmpty) {
Array1<Vector3D> points;
PointKdTreeSearcher3 searcher;
searcher.build(points.accessor());
searcher.forEachNearbyPoint(Vector3D(0, 0, 0), std::sqrt(10.0),
[](size_t, const Vector3D&) {});
}
log_value<dcomplex>
TransposeInverseMatrix(const Array2 < complex <doublevar> > & a,
Array2 < complex <doublevar> > & a1,
const int n)
{
Array2 <complex <doublevar> > temp(n,n);
Array1 <int> indx(n);
doublevar d;
// a(i,j) first index i is row index (convention)
// elements of column vectors are stored contiguous in memory in C style arrays
// a(i) refers to a column vector
// calculate the inverse of the transposed matrix because this
// allows to pass a column vector to lubksb() instead of a row
// put the transposed matrix in temp
//cout << "temp " << endl;
for(int i=0;i<n;++i)
{
for(int j=0;j<n;++j)
{
temp(i,j)=a(i,j);
a1(i,j)=complex <doublevar> (0.0,0.0);
}
a1(i,i)=complex <doublevar> (1.0,0.0);
}
//cout << "ludcmp" << endl;
//if the matrix is singular, the determinant is zero.
if(ludcmp(temp,n,indx,d)==0) {
#ifdef SUPERDEBUG
cout << "log_value<dcomplex>TransposeInverseMatrix:zero determinant " << endl;
#endif
return dcomplex(0.0,0.0);
}
//cout << "lubksb" << endl;
for(int j=0;j<n;++j)
{
// get column vector
Array1 <complex <doublevar> > yy;//(a1(j));
yy.refer(a1(j));
lubksb(temp,n,indx,yy);
}
//complex <doublevar> det(d,0);
log_value<dcomplex> det=dcomplex(d,0);
for(int j=0;j<n;++j) {
det *= temp(j,j);
}
return det;
}
void exportStates(Array1<double>& x, Array1<double>& y) const
{
x.resize(positions.size());
y.resize(positions.size());
for (size_t i = 0; i < positions.size(); ++i)
{
x[i] = positions[i].x;
y[i] = positions[i].y;
}
}
void Properties_final_average::showSummary(ostream & os, Array1 <Average_generator*> avg_gen) {
int nwf=avg.GetDim(1);
if(avg_gen.GetDim(0)%nwf != 0 ) error("Something wrong in the showSummary translation");
int navg=avg_gen.GetDim(0)/nwf;
Array2 <Average_generator*> avg2(nwf,navg);
int count=0;
for(int w=0; w< nwf; w++) {
for(int i=0; i< navg; i++) avg2(w,i)=avg_gen(count++);
}
showSummary(os, avg2);
}
TEST(PointParallelHashGridSearcher3, ForEachNearbyPointEmpty) {
Array1<Vector3D> points;
PointParallelHashGridSearcher3 searcher(4, 4, 4, std::sqrt(10));
searcher.build(points.accessor());
searcher.forEachNearbyPoint(
Vector3D(0, 0, 0),
std::sqrt(10.0),
[](size_t, const Vector3D&) {
});
}
int HEG_system::enforcePbc(Array1 <doublevar> & pos, Array1 <int> & nshifted) {
assert(pos.GetDim(0) >=3);
int shifted=0;
nshifted.Resize(3);
nshifted=0;
int nshift=0;
for(int i=0; i< 3; i++) {
int shouldcontinue=1;
while(shouldcontinue) {
//Whether we're past the origin side
doublevar tooshort=0;
for(int j=0; j<3;j++) tooshort+=normVec(i,j)*(pos(j)-origin(j));
//Whether we're past the lattice vector
doublevar toofar=0;
for(int j=0; j< 3; j++) toofar+=normVec(i,j)*(pos(j)-corners(i,j));
//the 1e-12 seems to help avoid numerical problems, esp
//when integrating over a grid(which tends to hit the edges)
if(tooshort < -1e-12) {
//cout <<"tooshort " << tooshort << endl;
for(int j=0; j< 3; j++) pos(j)+=latVec(i,j);
shifted=1;
nshifted(i)+=1;
nshift++;
}
else if(toofar > 1e-12) {
//cout << "toofar " << toofar << endl;
for(int j=0; j< 3; j++) pos(j)-=latVec(i,j);
shifted=1;
// JK: here was +1, which works fine for real k-points that
// correspond to standing waves. For general (complex) k-points the
// wavefunction is "directional", however.
nshifted(i)-=1;
nshift++;
}
else {
shouldcontinue=0;
}
if(nshift > 1000)
error("Did over 1000 shifts and we're still out of the simulation cell."
" There's probably something wrong. Position : ", pos(i));
}
}
return shifted;
}
void Molecular_system::setIonPos(int ion, Array1 <doublevar> & r)
{
assert(r.GetDim(0) >=3);
Array1 <doublevar> temp(r.GetDim(0));
temp=r;
if(use_bounding_box) {
bounding_box.enforcePbc(temp);
}
for(int i=0; i< 3; i++) {
ions.r(i,ion)=temp(i);
}
}
void Center_set::assignBasis(Array1 <CBasis_function *> basisfunc)
{
int totbasis=basisfunc.GetDim(0);
basis.Resize(ncenters, totbasis);
for(int i=0; i< ncenters; i++)
{
int found=0;
for(int j=0; j < totbasis; j++)
{
if(basisfunc(j)->label() == labels[i])
{
appendbasis(j,i);
found=1;
//break;
}
}
if(!found)
{
cout << "\n****WARNING*****\n"
<< "Couldn't find basis for atom " << labels[i]
<< endl;
}
}
}
//----------------------------------------------------------------------
//Keeping this separate from calcLoc for efficiency reasons..
//It's most likely faster to add to a double than fill matrices..
//We also don't need to calculate the ion-ion interaction for this
void Molecular_system::separatedLocal(Sample_point * sample,Array1 <doublevar> & onebody,
Array2 <doublevar> & twobody)
{
int nions=sample->ionSize();
int nelectrons=sample->electronSize();
onebody.Resize(nelectrons);
twobody.Resize(nelectrons,nelectrons);
onebody=0.0; twobody=0.0;
Array1 <doublevar> R(5);
sample->updateEIDist();
sample->updateEEDist();
for(int e=0; e< nelectrons; e++) {
for(int i=0; i < nions; i++) {
sample->getEIDist(e,i, R);
onebody(e)-=sample->getIonCharge(i)/R(0);
}
}
Array1 <doublevar> R2(5);
for(int i=0; i< nelectrons; i++) {
for(int j=i+1; j<nelectrons; j++) {
sample->getEEDist(i,j,R2);
twobody(i,j)+= 1/R2(0);
}
}
Array1 <doublevar> pos(3);
for(int e=0; e< nelectrons; e++) {
sample->getElectronPos(e,pos);
for(int d=0; d< 3; d++)
onebody(e)-=electric_field(d)*pos(d);
}
}
void MO_matrix_blas::writeorb(ostream & os, Array2 <doublevar> & rotation, Array1 <int> &moList) {
int nmo_write=moList.GetDim(0);
assert(rotation.GetDim(0)==nmo_write);
assert(rotation.GetDim(1)==nmo_write);
os.precision(15);
int counter=0;
for(int m=0; m < nmo_write; m++) {
int mo=moList(m);
for(int ion=0; ion<centers.size(); ion++)
{
int f=0;
for(int n=0; n< centers.nbasis(ion); n++)
{
int fnum=centers.basis(ion,n);
int imax=basis(fnum)->nfunc();
for(int i=0; i<imax; i++)
{
os << mo+1 << " " << f+1 << " " << ion+1 << " " << counter+1 << endl;
f++; //keep a total of functions on center
counter++;
} //i
} //n
} //ion
}
os << "COEFFICIENTS\n";
ifstream orbin(orbfile.c_str());
rotate_orb(orbin, os, rotation, moList, totbasis);
orbin.close();
}
void particlesToXml(const Array1<Vector3D>& positions,
const std::string& xmlFilename) {
printInfo(positions.size());
std::ofstream file(xmlFilename.c_str());
if (file) {
printf("Writing %s...\n", xmlFilename.c_str());
file << "<scene version=\"0.5.0\">";
for (const auto& pos : positions) {
file << "<shape type=\"instance\">";
file << "<ref id=\"spheres\"/>";
file << "<transform name=\"toWorld\">";
char buffer[64];
snprintf(buffer, sizeof(buffer),
"<translate x=\"%f\" y=\"%f\" z=\"%f\"/>", pos.x, pos.y,
pos.z);
file << buffer;
file << "</transform>";
file << "</shape>";
}
file << "</scene>";
file.close();
} else {
printf("Cannot write file %s.\n", xmlFilename.c_str());
exit(EXIT_FAILURE);
}
}
int binary_read_checksum(Array1 <doublevar> & a, FILE * f,int nhint) {
int ntry=0;
while(true) {
//First try to read in zeros
ntry++;
if(ntry>1) cout << "WARNING: detected corruption" << endl;
doublevar zero1,zero2;
int ntry_zero=0;
while(true) {
ntry_zero++;
if(!fread(&zero1,sizeof(doublevar),1,f)) return 0;
//cout << "zero1 " << zero1 << endl;
if(zero1==0) {
if(!fread(&zero2,sizeof(doublevar),1,f)) return 0;
if(zero2==0) break;
}
}
if(ntry_zero> 1) cout << "WARNING: possible corruption: had to search " << ntry_zero << endl;
doublevar n_d;
fread(&n_d,sizeof(doublevar),1,f);
int n=int(n_d);
if(n_d-n == 0 and ( nhint<0 or n==nhint)) {
a.Resize(n);
fread(a.v,sizeof(doublevar),n,f);
doublevar check_array=checksum(a);
doublevar check_file=1e99;
fread(&check_file,sizeof(doublevar),1,f);
if(fabs(check_array-check_file) < 1e-10) return ntry;
else {
cout << "WARNING: detected corruption" << endl;
}
if(ferror(f)) return 0;
}
}
}
void recenter(Array2 <doublevar> & pos, Array1 <doublevar> & mass) {
int natoms=pos.GetDim(0);
assert(pos.GetDim(0)==mass.GetDim(0));
assert(pos.GetDim(1)==3);
Array1 <doublevar> center(3,0.0); //center of mass
doublevar tot=0.0;
for(int at=0; at< natoms; at++) {
for(int d=0; d< 3; d++) {
center(d)+=mass(at)*pos(at,d);
}
tot+=mass(at);
}
for(int d=0; d< 3; d++) {
center(d)/=tot;
}
for(int at=0; at< natoms; at++) {
for(int d=0; d< 3; d++) {
pos(at,d)-=center(d);
}
}
}
void particlesToObj(const Array1<Vector3D>& positions, const Size3& resolution,
const Vector3D& gridSpacing, const Vector3D& origin,
double kernelRadius, const std::string& method,
const std::string& objFilename) {
PointsToImplicit3Ptr converter;
if (method == kSpherical) {
converter =
std::make_shared<SphericalPointsToImplicit3>(kernelRadius, false);
} else if (method == kSph) {
converter = std::make_shared<SphPointsToImplicit3>(
kernelRadius, sSphCutOffDensity, false);
} else if (method == kZhuBridson) {
converter = std::make_shared<ZhuBridsonPointsToImplicit3>(
kernelRadius, sZhuBridsonCutOffThreshold, false);
} else {
converter = std::make_shared<AnisotropicPointsToImplicit3>(
kernelRadius, sAnisoCutOffDensity, sAnisoPositionSmoothingFactor,
sAnisoMinNumNeighbors, false);
}
VertexCenteredScalarGrid3 sdf(resolution, gridSpacing, origin);
printInfo(resolution, sdf.boundingBox(), gridSpacing, positions.size(),
method);
converter->convert(positions, &sdf);
triangulateAndSave(sdf, objFilename);
}
void match_walkers(Array1<double> & weights, Array1 <int> & branch) {
const double split_threshold=1.8;
branch=-1;
int totwalkers=weights.GetDim(0);
Array1<weight_obj> walkers(totwalkers);
for(int i=0; i< totwalkers; i++) {
walkers(i).w=weights(i);
walkers(i).i=i;
}
sort(walkers.v,walkers.v+totwalkers);
int currsmallest=0;
for(int i=totwalkers-1; i > 1; i--) {
if(walkers(i).w < split_threshold) break;
int w=walkers(i).i;
int smallest=walkers(currsmallest).i;
double weight1=weights(w)/(weights(w)+weights(smallest));
if(weight1+rng.ulec() >= 1.0) {
branch(w)=2;
branch(smallest)=0;
weights(w)+=weights(smallest);
weights(w)/=2.0;
}
else {
branch(w)=0;
branch(smallest)=2;
weights(smallest)+=weights(w);
weights(smallest)/=2.0;
}
currsmallest++;
}
//for(int i=0; i< totwalkers; i++) {
// cout << walkers(i).w << endl;
//}
}
void Cutoff_cusp::calcLap(
const Array1 <doublevar> & r,
Array2 <doublevar> & symvals,
const int startfill
)
{
assert(r.GetDim(0) >=5);
assert(symvals.GetDim(0) >= 1+startfill);
assert(symvals.GetDim(1) >= 5);
if(r(0) < rcut) {
doublevar zz=r(0)*rcutinv;
doublevar zz2=zz*zz;
doublevar pp=zz-zz2+zz*zz2/3;
doublevar pade=1./(1+gamma*pp);
symvals(startfill,0)=cusp*rcut*(pp*pade-pade0);
doublevar pade2=pade*pade;
doublevar ppd=1.-2.*zz+zz2;
doublevar ppdd=-2.+2.*zz;
doublevar dadr=ppd*pade2/r(0);
doublevar dadr2=ppdd*pade2*rcutinv
-2.*gamma*ppd*ppd*pade2*pade*rcutinv
+2.*dadr;
for(int i=1; i< 4; i++) {
symvals(startfill, i)=cusp*dadr*r(i+1);
}
symvals(startfill, 4)=cusp*dadr2;
}
else {
for(int i=0; i< 5; i++)
symvals(startfill, i)=0;
}
}
doublevar norm_i(Array1 <doublevar> & a)
{
int m=a.GetSize();
double norm=0.0;
for (int k=0;k<m;k++)
norm+=a(k)*a(k);
return norm;
}
void Cutoff_cusp::setVarParms(Array1 <doublevar> & parms) {
assert(parms.GetDim(0)==1);
gamma=exp(parms(0));
pade0=1./(3+gamma);
//cout << "parms in " << parms(0) << endl;
}
void normalize(Array1 <doublevar> & a)
{
int m=a.GetSize();
double norm;
norm=norm_i(a);
for (int k=0;k<m;k++)
a(k)=a(k)/sqrt(norm);
}