void create_dumbbell_signed_distance( const Vec3d& sphere_a_centre,
const Vec3d& sphere_b_centre,
double sphere_radius,
double handle_width,
double dx,
const Vec3d& domain_low,
const Vec3d& domain_high,
Array3d& phi )
{
phi.resize( (int) ceil( (domain_high[0]-domain_low[0]) / dx), (int) ceil( (domain_high[1]-domain_low[1]) / dx), (int) ceil( (domain_high[2]-domain_low[2]) / dx) );
std::cout << "Generating signed distance function. Grid resolution: " << phi.ni << " x " << phi.nj << " x " << phi.nk << std::endl;
for ( int i = 0; i < phi.ni; ++i )
{
for ( int j = 0; j < phi.nj; ++j )
{
for ( int k = 0; k < phi.nk; ++k )
{
Vec3d pt = domain_low + dx * Vec3d(i,j,k);
phi(i,j,k) = signed_distance_dumbbell( pt, sphere_a_centre, sphere_b_centre, sphere_radius, handle_width );
}
}
}
}
void create_cube_signed_distance( const Vec3d& cube_low,
const Vec3d& cube_high,
double dx,
const Vec3d& domain_low,
const Vec3d& domain_high,
Array3d& phi )
{
phi.resize( (int) ceil( (domain_high[0]-domain_low[0]) / dx), (int) ceil( (domain_high[1]-domain_low[1]) / dx), (int) ceil( (domain_high[2]-domain_low[2]) / dx) );
std::cout << "Generating signed distance function. Grid resolution: " << phi.ni << " x " << phi.nj << " x " << phi.nk << std::endl;
for ( int i = 0; i < phi.ni; ++i )
{
for ( int j = 0; j < phi.nj; ++j )
{
for ( int k = 0; k < phi.nk; ++k )
{
Vec3d pt = domain_low + dx * Vec3d(i,j,k);
double dist_low_x = cube_low[0] - pt[0];
double dist_high_x = pt[0] - cube_high[0];
double dist_low_y = cube_low[1] - pt[1];
double dist_high_y = pt[1] - cube_high[1];
double dist_low_z = cube_low[2] - pt[2];
double dist_high_z = pt[2] - cube_high[2];
phi(i,j,k) = max( dist_low_x, dist_high_x, dist_low_y, dist_high_y, dist_low_z, dist_high_z );
}
}
}
}
void calculateChargesPotential(LSMSCommunication &comm, LSMSSystemParameters &lsms, LocalTypeInfo &local, CrystalParameters &crystal, int chargeSwitch)
{
Real *qsub;
Array3d<Real> rhoTemp;
//qsub = new Real[crystal.num_types];
qsub = (Real*)shmalloc(crystal.num_types*sizeof(Real));
for (int i=0; i<crystal.num_types; i++) qsub[i] = 0.0;
rhoTemp.resize(lsms.global.iprpts+1, 2, local.num_local);
rhoTemp = 0.0;
printf("%d:calculateCharges\n",comm.comm.rank);
calculateCharges(comm, lsms, local, crystal, qsub, rhoTemp, chargeSwitch);
// for (int i=0; i<crystal.num_types; i++) printf("i, qsub = %5d %25.15f\n", i, qsub[i]);
printf("%d:calculatePotential\n",comm.comm.rank);
calculatePotential(comm, lsms, local, crystal, qsub, rhoTemp, chargeSwitch);
printf("%d:end of calculatePotential\n",comm.comm.rank);
//delete[] qsub;
shfree(qsub);
return;
}
void create_capsule_signed_distance( const Vec3d& capsule_end_a,
const Vec3d& capsule_end_b,
double capsule_radius,
double dx,
const Vec3d& domain_low,
const Vec3d& domain_high,
Array3d& phi )
{
phi.resize( (int) ceil( (domain_high[0]-domain_low[0]) / dx), (int) ceil( (domain_high[1]-domain_low[1]) / dx), (int) ceil( (domain_high[2]-domain_low[2]) / dx) );
std::cout << "Generating signed distance function. Grid resolution: " << phi.ni << " x " << phi.nj << " x " << phi.nk << std::endl;
for ( int i = 0; i < phi.ni; ++i )
{
for ( int j = 0; j < phi.nj; ++j )
{
for ( int k = 0; k < phi.nk; ++k )
{
Vec3d pt = domain_low + dx * Vec3d(i,j,k);
double distance;
Vec3d central_segment(capsule_end_b - capsule_end_a);
double m2=mag2(central_segment);
// find parameter value of closest point on infinite line
double s = dot(capsule_end_b - pt, central_segment)/m2;
if ( s < 0.0 )
{
// dist = distance to the cylinder disc at end b
distance = dist(pt, capsule_end_b);
distance -= capsule_radius;
}
else if ( s > 1.0 )
{
// dist = distance to the cylinder disc at end b
distance = dist(pt, capsule_end_a );
distance -= capsule_radius;
}
else
{
// dist = distance to the cylinder's central axis
distance = dist(pt, s*capsule_end_a + (1-s)*capsule_end_b);
distance -= capsule_radius;
}
phi(i,j,k) = distance;
}
}
}
}
void calculateLocalCharges(LSMSSystemParameters &lsms, LocalTypeInfo &local, int chargeSwitch)
{
Array3d<Real> rhoTemp;
rhoTemp.resize(lsms.global.iprpts+1, 2, local.num_local);
// Compute integrated densities of states and store in xval**
// (from mufind_c.f)
for(int i=0; i<local.num_local; i++)
{
if (lsms.n_spin_cant == 2) // nspin >=3
{
local.atom[i].qvalmt = local.atom[i].dosckint[0];
local.atom[i].qvalws = local.atom[i].dosint[0];
local.atom[i].mvalws = local.atom[i].dosint[1] * local.atom[i].evecNew[0] + \
local.atom[i].dosint[2] * local.atom[i].evecNew[1] + \
local.atom[i].dosint[3] * local.atom[i].evecNew[2];
local.atom[i].mvalmt = local.atom[i].dosckint[1] * local.atom[i].evecNew[0] + \
local.atom[i].dosckint[2] * local.atom[i].evecNew[1] + \
local.atom[i].dosckint[3] * local.atom[i].evecNew[2];
local.atom[i].xvalmt[0] = 0.5 * (local.atom[i].qvalmt + local.atom[i].mvalmt);
local.atom[i].xvalwsNew[0] = 0.5 * (local.atom[i].qvalws + local.atom[i].mvalws);
local.atom[i].xvalmt[1] = 0.5 * (local.atom[i].qvalmt - local.atom[i].mvalmt);
local.atom[i].xvalwsNew[1] = 0.5 * (local.atom[i].qvalws - local.atom[i].mvalws);
}
else if (lsms.n_spin_pola == 2) // nspin = 2
{
local.atom[i].qvalmt = local.atom[i].dosckint[0] + local.atom[i].dosckint[1];
local.atom[i].qvalws = local.atom[i].dosint[0] + local.atom[i].dosint[1];
local.atom[i].mvalmt = local.atom[i].dosckint[0] - local.atom[i].dosckint[1];
local.atom[i].mvalws = local.atom[i].dosint[0] - local.atom[i].dosint[1];
local.atom[i].xvalmt[0] = local.atom[i].dosckint[0];
local.atom[i].xvalwsNew[0] = local.atom[i].dosint[0];
local.atom[i].xvalmt[1] = local.atom[i].dosckint[1];
local.atom[i].xvalwsNew[1] = local.atom[i].dosint[1];
}
else // nspin = 1
{
local.atom[i].qvalmt = local.atom[i].dosckint[0];
local.atom[i].qvalws = local.atom[i].dosint[0];
local.atom[i].mvalmt = 0.0;
local.atom[i].mvalws = 0.0;
local.atom[i].xvalmt[0] = local.atom[i].dosckint[0];
local.atom[i].xvalwsNew[0] = local.atom[i].dosint[0];
}
if (lsms.global.iprint > 0)
{
printf(" LOCAL WS Int[n(e)] = %18.11f\n", local.atom[i].qvalws);
printf(" LOCAL MT Int[n(e)] = %18.11f\n", local.atom[i].qvalmt);
printf(" LOCAL interstial Q = %18.11f\n", local.atom[i].qvalws - local.atom[i].qvalmt);
if (lsms.n_spin_pola == 2)
{
printf(" LOCAL WS Int[m(e)] = %18.11f\n", local.atom[i].mvalws);
printf(" LOCAL MT Int[m(e)] = %18.11f\n", local.atom[i].mvalmt);
}
printf(" LOCAL interstial M = %18.11f\n", local.atom[i].mvalws - local.atom[i].mvalmt);
printf(" Spin = 1 LOCAL WS Int[n(e)] = %18.11f\n", local.atom[i].xvalwsNew[0]);
printf(" Spin = 2 LOCAL WS Int[n(e)] = %18.11f\n", local.atom[i].xvalwsNew[1]);
printf(" Spin = 1 LOCAL MT Int[n(e)] = %18.11f\n", local.atom[i].xvalmt[0]);
printf(" Spin = 2 LOCAL MT Int[n(e)] = %18.11f\n", local.atom[i].xvalmt[1]);
printf(" Spin = 1 LOCAL interstial Q = %18.11f\n", local.atom[i].xvalwsNew[0] - local.atom[i].xvalmt[0]);
printf(" Spin = 2 LOCAL interstial Q = %18.11f\n", local.atom[i].xvalwsNew[1] - local.atom[i].xvalmt[1]);
printf(" LOCAL Moment orientation = (%18.11f, %18.11f, %18.11f)\n", local.atom[i].evecNew[0], local.atom[i].evecNew[1], local.atom[i].evecNew[2]);
}
// Calculate qtotws and mtotws
switch (chargeSwitch)
{
case 1:
{
local.atom[i].qtotws = local.atom[i].xvalws[0] + \
(lsms.n_spin_pola-1) * local.atom[i].xvalws[lsms.n_spin_pola-1] + \
local.atom[i].zsemss + \
local.atom[i].zcorss;
local.atom[i].mtotws = local.atom[i].xvalws[0] - local.atom[i].xvalws[lsms.n_spin_pola-1];
break;
}
default:
{
local.atom[i].qtotws = local.atom[i].xvalwsNew[0] + \
(lsms.n_spin_pola-1) * local.atom[i].xvalwsNew[lsms.n_spin_pola-1] + \
local.atom[i].zsemss + \
local.atom[i].zcorss;
local.atom[i].mtotws = local.atom[i].xvalwsNew[0] - local.atom[i].xvalwsNew[lsms.n_spin_pola-1];
}
}
// printf("qtotws = %12.8f\n", local.atom[i].qtotws);
// printf("mtotws = %12.8f\n", local.atom[i].mtotws);
// from genpot_c.f
// ================================================================
// calculate qtotmt and mtotmt.....................................
// ----------------------------------------------------------------
Real rSphere;
switch (lsms.mtasa)
{
case 1:
rSphere = local.atom[i].rws;
break;
case 2:
rSphere = local.atom[i].rws;
break;
default:
rSphere = local.atom[i].rInscribed;
}
Real *rTemp;
rTemp = new Real[local.atom[i].jmt+3];
rTemp[0] = 0.0;
for (int j=0; j<local.atom[i].jmt+2; j++)
{
//rTemp's indices need to be shifted by 1 for passing into getqm_mt!
rTemp[j+1] = std::sqrt(local.atom[i].r_mesh[j]);
}
switch (chargeSwitch)
{
case 1:
{
if (local.atom[i].rhotot(local.atom[i].jmt,0) == 0.0)
local.atom[i].rhotot(local.atom[i].jmt,0) = local.atom[i].rhotot(local.atom[i].jmt-1,0);
if (local.atom[i].rhotot(local.atom[i].jmt+1,0) == 0.0)
local.atom[i].rhotot(local.atom[i].jmt+1,0) = local.atom[i].rhotot(local.atom[i].jmt-1,0);
if (local.atom[i].rhotot(local.atom[i].jmt,lsms.n_spin_pola-1) == 0.0)
local.atom[i].rhotot(local.atom[i].jmt,lsms.n_spin_pola-1) = local.atom[i].rhotot(local.atom[i].jmt-1,lsms.n_spin_pola-1);
if (local.atom[i].rhotot(local.atom[i].jmt+1,lsms.n_spin_pola-1) == 0.0)
local.atom[i].rhotot(local.atom[i].jmt+1,lsms.n_spin_pola-1) = local.atom[i].rhotot(local.atom[i].jmt-1,lsms.n_spin_pola-1);
if (lsms.global.iprint > 0)
{
printf("Spin = 1 rhotot[jmt-1], [jmt], [jmt+1] = %20.16f %20.16f %20.16f\n", local.atom[i].rhotot(local.atom[i].jmt-1,0), local.atom[i].rhotot(local.atom[i].jmt,0), local.atom[i].rhotot(local.atom[i].jmt+1,0));
printf("Spin = 2 rhotot[jmt-1], [jmt], [jmt+1] = %20.16f %20.16f %20.16f\n", local.atom[i].rhotot(local.atom[i].jmt-1,lsms.n_spin_pola-1), local.atom[i].rhotot(local.atom[i].jmt,lsms.n_spin_pola-1), local.atom[i].rhotot(local.atom[i].jmt+1,lsms.n_spin_pola-1));
}
getqm_mt_(&lsms.n_spin_pola, &local.atom[i].jmt, &local.atom[i].rInscribed, rTemp, &local.atom[i].rhotot(0,0), &lsms.global.iprpts, &rhoTemp(0,0,i), &lsms.mtasa, &local.atom[i].qtotmt, &local.atom[i].mtotmt, &rSphere, &lsms.global.iprint);
break;
}
default:
{
if (local.atom[i].rhoNew(local.atom[i].jmt,0) == 0.0)
local.atom[i].rhoNew(local.atom[i].jmt,0) = local.atom[i].rhoNew(local.atom[i].jmt-1,0);
if (local.atom[i].rhoNew(local.atom[i].jmt+1,0) == 0.0)
local.atom[i].rhoNew(local.atom[i].jmt+1,0) = local.atom[i].rhoNew(local.atom[i].jmt-1,0);
if (local.atom[i].rhoNew(local.atom[i].jmt,lsms.n_spin_pola-1) == 0.0)
local.atom[i].rhoNew(local.atom[i].jmt,lsms.n_spin_pola-1) = local.atom[i].rhoNew(local.atom[i].jmt-1,lsms.n_spin_pola-1);
if (local.atom[i].rhoNew(local.atom[i].jmt+1,lsms.n_spin_pola-1) == 0.0)
local.atom[i].rhoNew(local.atom[i].jmt+1,lsms.n_spin_pola-1) = local.atom[i].rhoNew(local.atom[i].jmt-1,lsms.n_spin_pola-1);
if (lsms.global.iprint > 0)
{
printf("Spin = 1 rhoNew[jmt-1], [jmt], [jmt+1] = %20.16f %20.16f %20.16f\n", local.atom[i].rhoNew(local.atom[i].jmt-1,0), local.atom[i].rhoNew(local.atom[i].jmt,0), local.atom[i].rhoNew(local.atom[i].jmt+1,0));
printf("Spin = 2 rhoNew[jmt-1], [jmt], [jmt+1] = %20.16f %20.16f %20.16f\n", local.atom[i].rhoNew(local.atom[i].jmt-1,lsms.n_spin_pola-1), local.atom[i].rhoNew(local.atom[i].jmt,lsms.n_spin_pola-1), local.atom[i].rhoNew(local.atom[i].jmt+1,lsms.n_spin_pola-1));
}
getqm_mt_(&lsms.n_spin_pola, &local.atom[i].jmt, &local.atom[i].rInscribed, rTemp, &local.atom[i].rhoNew(0,0), &lsms.global.iprpts, &rhoTemp(0,0,i), &lsms.mtasa, &local.atom[i].qtotmt, &local.atom[i].mtotmt, &rSphere, &lsms.global.iprint);
}
}
if (lsms.global.iprint >= 0)
{
printf("\n");
printf(" GENPOT / calculateLocalCharges: \n");
printf(" Total charge and moment in W-S cell:\n");
printf(" qtotws = %18.11f\n", local.atom[i].qtotws);
printf(" mtotws = %18.11f\n", local.atom[i].mtotws);
}
delete[] rTemp;
}
}
void make_level_set3(const std::vector<Vec3ui> &tri, const std::vector<Vec3d> &x,
const Vec3d &origin, double dx, int ni, int nj, int nk,
Array3d &phi, Array3i& closest_tri, const int exact_band )
{
phi.resize(ni, nj, nk);
phi.assign((ni+nj+nk)*dx); // upper bound on distance
closest_tri.clear();
closest_tri.resize(ni, nj, nk, -1);
Array3i intersection_count(ni, nj, nk, 0); // intersection_count(i,j,k) is # of tri intersections in (i-1,i]x{j}x{k}
// we begin by initializing distances near the mesh, and figuring out intersection counts
Vec3d ijkmin, ijkmax;
for(unsigned int t=0; t<tri.size(); ++t){
unsigned int p, q, r; assign(tri[t], p, q, r);
// coordinates in grid to high precision
double fip=((double)x[p][0]-origin[0])/dx, fjp=((double)x[p][1]-origin[1])/dx, fkp=((double)x[p][2]-origin[2])/dx;
double fiq=((double)x[q][0]-origin[0])/dx, fjq=((double)x[q][1]-origin[1])/dx, fkq=((double)x[q][2]-origin[2])/dx;
double fir=((double)x[r][0]-origin[0])/dx, fjr=((double)x[r][1]-origin[1])/dx, fkr=((double)x[r][2]-origin[2])/dx;
// do distances nearby
int i0=clamp(int(min(fip,fiq,fir))-exact_band, 0, ni-1), i1=clamp(int(max(fip,fiq,fir))+exact_band+1, 0, ni-1);
int j0=clamp(int(min(fjp,fjq,fjr))-exact_band, 0, nj-1), j1=clamp(int(max(fjp,fjq,fjr))+exact_band+1, 0, nj-1);
int k0=clamp(int(min(fkp,fkq,fkr))-exact_band, 0, nk-1), k1=clamp(int(max(fkp,fkq,fkr))+exact_band+1, 0, nk-1);
for(int k=k0; k<=k1; ++k) for(int j=j0; j<=j1; ++j) for(int i=i0; i<=i1; ++i){
Vec3d gx(i*dx+origin[0], j*dx+origin[1], k*dx+origin[2]);
double d=point_triangle_distance(gx, x[p], x[q], x[r]);
if(d<phi(i,j,k)){
phi(i,j,k)=d;
closest_tri(i,j,k)=t;
}
}
// and do intersection counts
j0=clamp((int)std::ceil(min(fjp,fjq,fjr)), 0, nj-1);
j1=clamp((int)std::floor(max(fjp,fjq,fjr)), 0, nj-1);
k0=clamp((int)std::ceil(min(fkp,fkq,fkr)), 0, nk-1);
k1=clamp((int)std::floor(max(fkp,fkq,fkr)), 0, nk-1);
for(int k=k0; k<=k1; ++k) for(int j=j0; j<=j1; ++j){
double a, b, c;
if(point_in_triangle_2d(j, k, fjp, fkp, fjq, fkq, fjr, fkr, a, b, c)){
double fi=a*fip+b*fiq+c*fir; // intersection i coordinate
int i_interval=int(std::ceil(fi)); // intersection is in (i_interval-1,i_interval]
if(i_interval<0) ++intersection_count(0, j, k); // we enlarge the first interval to include everything to the -x direction
else if(i_interval<ni) ++intersection_count(i_interval,j,k);
// we ignore intersections that are beyond the +x side of the grid
}
}
}
// and now we fill in the rest of the distances with fast sweeping
for(unsigned int pass=0; pass<2; ++pass){
sweep(tri, x, phi, closest_tri, origin, dx, +1, +1, +1);
sweep(tri, x, phi, closest_tri, origin, dx, -1, -1, -1);
sweep(tri, x, phi, closest_tri, origin, dx, +1, +1, -1);
sweep(tri, x, phi, closest_tri, origin, dx, -1, -1, +1);
sweep(tri, x, phi, closest_tri, origin, dx, +1, -1, +1);
sweep(tri, x, phi, closest_tri, origin, dx, -1, +1, -1);
sweep(tri, x, phi, closest_tri, origin, dx, +1, -1, -1);
sweep(tri, x, phi, closest_tri, origin, dx, -1, +1, +1);
}
// then figure out signs (inside/outside) from intersection counts
for(int k=0; k<nk; ++k) for(int j=0; j<nj; ++j){
int total_count=0;
for(int i=0; i<ni; ++i){
total_count+=intersection_count(i,j,k);
if(total_count%2==1){ // if parity of intersections so far is odd,
phi(i,j,k)=-phi(i,j,k); // we are inside the mesh
}
}
}
}