29 use,
intrinsic :: iso_fortran_env
81 real(real64),
allocatable :: center(:)
82 real(real64) :: radius =
m_zero
83 class(box_t),
pointer :: box => null()
85 integer,
allocatable :: map(:)
86 integer :: num_regions
87 integer,
allocatable :: regions(:)
88 type(accel_mem_t) :: buff_map
89 real(real64),
allocatable :: rel_x(:,:)
90 real(real64),
allocatable :: r(:)
91 type(mesh_t),
pointer :: mesh => null()
94 integer :: np_global = -1
95 real(real64),
allocatable :: rel_x_global(:,:)
96 integer,
allocatable :: part_v(:)
97 integer,
allocatable :: global2local(:)
99 type(mesh_cube_map_t) :: cube_map
116 recursive real(real64) function f_n(dims)
result(fn)
121 else if (dims == 1)
then
130 subroutine submesh_init(this, space, mesh, latt, center, rc)
131 type(submesh_t),
intent(inout) :: this
132 class(space_t),
intent(in) :: space
133 class(mesh_t),
target,
intent(in) :: mesh
134 type(lattice_vectors_t),
intent(in) :: latt
135 real(real64),
intent(in) :: center(1:space%dim)
136 real(real64),
intent(in) :: rc
138 real(real64) :: r2, rc2, xx(space%dim), rc_norm_n
139 real(real64),
allocatable :: center_copies(:,:), xtmp(:, :), rtmp(:)
140 integer :: icell, is, ip, ix, iy, iz
141 integer(int64) :: max_elements_count
142 type(lattice_iterator_t) :: latt_iter
143 integer,
allocatable :: map_inv(:), map_temp(:)
144 integer :: nmax(3), nmin(3)
145 real(real64),
parameter :: tol = 1e-13_real64
151 assert(space%dim <= 3)
155 safe_allocate(this%center(1:space%dim))
156 this%center(:) = center(:)
164 if (.not. space%is_periodic())
then
167 safe_allocate(map_inv(0:this%mesh%np))
168 map_inv(0:this%mesh%np) = 0
174 nmin(1:space%dim) = int((center(1:space%dim) - abs(rc))/mesh%spacing(1:space%dim)) - 1
175 nmax(1:space%dim) = int((center(1:space%dim) + abs(rc))/mesh%spacing(1:space%dim)) + 1
179 nmin(1:space%dim) = max(mesh%idx%nr(1, 1:space%dim), nmin(1:space%dim))
180 nmax(1:space%dim) = min(mesh%idx%nr(2, 1:space%dim), nmax(1:space%dim))
184 do iz = nmin(3), nmax(3)
185 do iy = nmin(2), nmax(2)
186 do ix = nmin(1), nmax(1)
188 if (ip == 0 .or. ip > mesh%np) cycle
189 r2 = sum((mesh%x(:, ip) - center)**2)
201 safe_allocate(this%map(1:this%np))
202 safe_allocate(xtmp(1:space%dim, 1:this%np))
203 safe_allocate(rtmp(1:this%np))
206 do iz = nmin(3), nmax(3)
207 do iy = nmin(2), nmax(2)
208 do ix = nmin(1), nmax(1)
210 if (ip == 0 .or. ip > mesh%np) cycle
214 xtmp(:, is) = mesh%x(:, ip) - center
215 rtmp(is) = norm2(xtmp(:,is))
220 safe_deallocate_a(map_inv)
233 safe_allocate(center_copies(1:space%dim, 1:latt_iter%n_cells))
234 do icell = 1, latt_iter%n_cells
235 center_copies(:, icell) = center + latt_iter%get(icell)
240 rc_norm_n = product(ceiling(rc / mesh%spacing(1:space%dim), int64) +
m_one)
241 if (mesh%use_curvilinear) rc_norm_n = rc_norm_n / mesh%coord_system%min_mesh_scaling_product
242 max_elements_count = 3**space%dim * int(
m_pi**
floor(0.5 * space%dim) * rc_norm_n *
f_n(space%dim), int64)
245 safe_allocate(map_temp(1:max_elements_count))
246 safe_allocate(xtmp(1:space%dim, 1:max_elements_count))
247 safe_allocate(rtmp(1:max_elements_count))
251 do icell = 1, latt_iter%n_cells
252 xx = mesh%x(:,ip) - center_copies(:, icell)
253 if(any(abs(xx)>rc+tol)) cycle
263 assert(is < huge(is))
266 safe_allocate(this%map(1:this%np))
267 this%map(1:this%np) = map_temp(1:this%np)
270 safe_deallocate_a(map_temp)
271 safe_deallocate_a(center_copies)
278 safe_deallocate_a(xtmp)
279 safe_deallocate_a(rtmp)
286 class(
space_t),
intent(in) :: space
287 real(real64),
intent(in) :: xtmp(:, :), rtmp(:)
289 integer :: ip, i_region, offset
290 integer,
allocatable :: order(:), order_new(:)
291 integer,
allocatable :: map_new(:)
292 integer,
allocatable :: np_region(:), tmp_array(:)
299 safe_allocate(order(1:this%np))
300 safe_allocate(this%rel_x(1:space%dim, 1:this%np))
301 safe_allocate(this%r(1:this%np))
308 call sort(this%map, order)
311 this%overlap = .false.
312 do ip = 1, this%np - 1
313 if (this%map(ip) == this%map(ip + 1))
then
315 this%overlap = .
true.
323 if(this%overlap)
then
327 safe_allocate(tmp_array(1:this%np))
328 safe_allocate(order_new(1:this%np))
329 safe_allocate(np_region(1:this%np))
330 safe_allocate(map_new( 1:this%np))
337 if (this%map(ip) == this%map(ip - 1))
then
338 i_region = i_region + 1
339 if (i_region > this%num_regions)
then
340 this%num_regions = i_region
341 np_region(i_region) = 0
346 tmp_array(ip) = i_region
347 np_region(i_region) = np_region(i_region) + 1
350 assert( .not.
allocated(this%regions))
353 safe_allocate(this%regions(1:this%num_regions+1))
357 if(this%num_regions > 1)
then
358 do i_region = 1, this%num_regions
359 this%regions(i_region + 1) = this%regions(i_region) + np_region(i_region)
362 this%regions(2) = this%np + 1
365 np_region(1:this%np) = 0
366 order_new(1:this%np) = -1
367 map_new(1:this%np) = -1
372 i_region = tmp_array(ip)
373 np_region(i_region) = np_region(i_region) + 1
374 offset = this%regions(i_region) - 1
375 map_new( offset + np_region(i_region) ) = this%map(ip)
376 order_new( offset + np_region(i_region) ) = order(ip)
379 order(1:this%np) = order_new(1:this%np)
380 this%map(1:this%np) = map_new(1:this%np)
382 safe_deallocate_a(tmp_array)
383 safe_deallocate_a(order_new)
384 safe_deallocate_a(np_region)
385 safe_deallocate_a(map_new)
390 safe_allocate(this%regions(1:2))
392 this%regions(2) = this%np + 1
397 this%rel_x(:, ip) = xtmp(:, order(ip))
398 this%r(ip) = rtmp(order(ip))
401 safe_deallocate_a(order)
412 class(
space_t),
intent(in) :: space
413 class(
mesh_t),
target,
intent(in) :: mesh
416 real(real64),
optional,
intent(in) :: shift(:)
420 real(real64) :: xx(space%dim), diff_centers(space%dim)
427 safe_allocate(this%center(1:space%dim))
428 this%center(:) = sm1%center(:)
429 this%radius = sm1%radius
433 this%overlap = sm1%overlap .or. sm2%overlap
435 diff_centers = sm1%center - sm2%center
436 if (
present(shift)) diff_centers = diff_centers - shift
443 xx = sm2%rel_x(:, ip) - diff_centers
445 if (sum(xx**2) > sm1%radius**2) is = is + 1
450 safe_allocate(this%map(1:this%np))
451 safe_allocate(this%rel_x(1:space%dim, 1:this%np))
452 safe_allocate(this%r(1:this%np))
453 this%map(1:sm1%np) = sm1%map(1:sm1%np)
454 this%rel_x(:, 1:sm1%np) = sm1%rel_x(:, 1:sm1%np)
455 this%r(1:sm1%np) = sm1%r(1:sm1%np)
460 xx = sm2%rel_x(:, ip) - diff_centers
462 if (r2 > sm1%radius**2)
then
464 this%map(is) = sm2%map(ip)
465 this%r(is) =
sqrt(r2)
466 this%rel_x(:, is) = xx
478 class(
space_t),
intent(in) :: space
479 real(real64),
intent(in) :: newcenter(:)
481 real(real64) :: xx(space%dim), diff_centers(space%dim), oldcenter(space%dim)
487 oldcenter = this%center
488 this%center(:) = newcenter(:)
490 diff_centers = newcenter - oldcenter
493 xx = this%rel_x(:, ip) - diff_centers
494 this%r(ip) = norm2(xx)
495 this%rel_x(:, ip) = xx
506 type(
mesh_t),
target,
intent(in) :: mesh
507 real(real64),
intent(in) :: center(1:space%dim)
508 real(real64),
intent(in) :: radius
509 integer,
intent(in) :: root
512 integer :: nparray(1:3)
517 if (root /= mpi_grp%rank)
then
519 safe_allocate(this%center(1:space%dim))
520 this%center(:) = center(:)
524 if (mpi_grp%size > 1)
then
526 if (root == mpi_grp%rank)
then
528 nparray(2) = this%num_regions
529 if (this%overlap)
then
536 call mpi_grp%bcast(nparray, 3, mpi_integer, root)
538 this%num_regions = nparray(2)
539 this%overlap = (nparray(3) == 1)
541 if (root /= mpi_grp%rank)
then
542 safe_allocate(this%map(1:this%np))
543 safe_allocate(this%rel_x(1:space%dim, 1:this%np))
544 safe_allocate(this%r(1:this%np))
545 safe_allocate(this%regions(1:this%num_regions+1))
548 call mpi_grp%bcast(this%regions(1), this%num_regions+1, mpi_integer, root)
550 if (this%np > 0)
then
551 call mpi_grp%bcast(this%map(1), this%np, mpi_integer, root)
552 call mpi_grp%bcast(this%rel_x(1, 1), this%np*space%dim, mpi_double_precision, root)
553 call mpi_grp%bcast(this%r(1), this%np, mpi_double_precision, root)
565 real(real64),
intent(in) :: radius
566 real(real64),
intent(in) :: center(:)
567 real(real64),
intent(in) :: dx
570 if (
allocated(this%center))
then
573 if (radius <= this%radius+dx*1e-6_real64 .and. all(abs(this%center - center) < 0.25*dx))
then
588 if (this%np /= -1)
then
590 safe_deallocate_a(this%center)
591 safe_deallocate_a(this%map)
592 safe_deallocate_a(this%rel_x)
593 safe_deallocate_a(this%r)
594 safe_deallocate_a(this%regions)
609 class(
space_t),
intent(in) :: space
611 integer :: ii, jj, dd
616 if (.not. space%is_periodic())
then
618 distance = sum((sm1%center - sm2%center)**2)
619 overlap =
distance <= (1.5_real64*(sm1%radius + sm2%radius))**2
622 if (.not. overlap)
return
630 do while(ii <= sm1%np .and. jj <= sm2%np)
631 dd = sm1%map(ii) - sm2%map(jj)
634 else if (dd > 0)
then
642 if (sm1%mesh%parallel_in_domains)
then
643 call sm1%mesh%mpi_grp%allreduce_inplace(overlap, 1, mpi_logical, mpi_lor)
651 class(
space_t),
intent(in) :: space
653 integer,
allocatable :: part_np(:)
654 integer :: ipart, ind, ip
658 if (.not. this%mesh%parallel_in_domains)
then
659 this%np_global = this%np
664 safe_allocate(part_np(this%mesh%pv%npart))
666 part_np(this%mesh%pv%partno) = this%np
668 call this%mesh%allreduce(part_np)
669 this%np_global = sum(part_np)
671 safe_allocate(this%rel_x_global(1:space%dim, 1:this%np_global))
672 safe_allocate(this%part_v(1:this%np_global))
673 safe_allocate(this%global2local(1:this%np_global))
674 this%rel_x_global(1:space%dim, 1:this%np_global) =
m_zero
675 this%part_v(1:this%np_global) = 0
676 this%global2local(1:this%np_global) = 0
679 do ipart = 1, this%mesh%pv%npart
680 if (ipart == this%mesh%pv%partno)
then
682 this%rel_x_global(:, ind + ip) = this%rel_x(:, ip)
683 this%part_v(ind + ip) = this%mesh%pv%partno
684 this%global2local(ind + ip) = ip
687 ind = ind + part_np(ipart)
690 call this%mesh%allreduce(this%rel_x_global)
691 call this%mesh%allreduce(this%part_v)
692 call this%mesh%allreduce(this%global2local)
694 safe_deallocate_a(part_np)
705 safe_deallocate_a(this%rel_x_global)
707 safe_deallocate_a(this%part_v)
708 safe_deallocate_a(this%global2local)
717 complex(real64),
intent(in) :: sphi(:)
718 complex(real64),
intent(inout) :: phi(:)
719 complex(real64),
optional,
intent(in) :: factor
725 if (
present(factor))
then
729 phi(this%map(ip)) = phi(this%map(ip)) + factor*sphi(ip)
731 if (this%np.ge.4)
then
732 do ip = m+1, this%np, 4
733 phi(this%map(ip)) = phi(this%map(ip)) + factor*sphi(ip)
734 phi(this%map(ip+1)) = phi(this%map(ip+1)) + factor*sphi(ip+1)
735 phi(this%map(ip+2)) = phi(this%map(ip+2)) + factor*sphi(ip+2)
736 phi(this%map(ip+3)) = phi(this%map(ip+3)) + factor*sphi(ip+3)
742 phi(this%map(ip)) = phi(this%map(ip)) + sphi(ip)
744 if (this%np.ge.4)
then
745 do ip = m+1, this%np, 4
746 phi(this%map(ip)) = phi(this%map(ip)) + sphi(ip)
747 phi(this%map(ip+1)) = phi(this%map(ip+1)) + sphi(ip+1)
748 phi(this%map(ip+2)) = phi(this%map(ip+2)) + sphi(ip+2)
749 phi(this%map(ip+3)) = phi(this%map(ip+3)) + sphi(ip+3)
760 complex(real64),
intent(in) :: sphi(:)
761 complex(real64),
intent(in) :: phi(:)
762 logical,
optional,
intent(in) :: reduce
770 if (this%mesh%use_curvilinear)
then
772 dotp = dotp + this%mesh%vol_pp(this%map(is))*phi(this%map(is))*conjg(sphi(is))
777 dotp = dotp + phi(this%map(ip))*conjg(sphi(ip))
779 if (this%np.ge.4)
then
780 do ip = m+1, this%np, 4
781 dotp = dotp + phi(this%map(ip))*conjg(sphi(ip)) &
782 + phi(this%map(ip+1))*conjg(sphi(ip+1)) &
783 + phi(this%map(ip+2))*conjg(sphi(ip+2)) &
784 + phi(this%map(ip+3))*conjg(sphi(ip+3))
787 dotp = dotp*this%mesh%vol_pp(1)
792 call this%mesh%allreduce(dotp)
802 type(
submesh_t),
target,
intent(in) :: sm
803 class(
space_t),
intent(in) :: space
804 integer,
intent(out) :: db(1:space%dim)
807 real(real64) :: chi(space%dim), max_chi(space%dim)
808 integer :: db_red(1:space%dim)
809 real(real64),
parameter :: tol=1.0e-10_real64
815 chi = sm%mesh%coord_system%from_cartesian(sm%rel_x(:, ip))
816 do idir = 1, space%dim
817 max_chi(idir) = max(max_chi(idir), abs(chi(idir))/sm%mesh%spacing(idir))
821 do idir = 1, space%dim
822 db(idir) = nint(max_chi(idir)-tol)
825 if(sm%mesh%parallel_in_domains)
then
826 call sm%mesh%mpi_grp%allreduce(db(1), db_red(1), space%dim, mpi_integer, mpi_max)
827 db(1:space%dim) = db_red(1:space%dim)
837 type(
submesh_t),
target,
intent(inout) :: sm
838 class(
space_t),
intent(in) :: space
842 real(real64) :: chi(space%dim), shift(space%dim)
846 sm%cube_map%nmap = sm%np
848 safe_allocate(sm%cube_map%map(1:space%dim, 1:sm%cube_map%nmap))
852 chi = sm%mesh%coord_system%from_cartesian(sm%center)
853 do idir = 1, space%dim
854 shift(idir) = nint(chi(idir)/sm%mesh%spacing(idir))*sm%mesh%spacing(idir)
856 shift = sm%mesh%coord_system%to_cartesian(shift)
857 shift = shift - sm%center
859 do ip = 1, sm%cube_map%nmap
860 chi = sm%mesh%coord_system%from_cartesian(sm%rel_x(:,ip) - shift)
861 do idir = 1, space%dim
862 sm%cube_map%map(idir, ip) = nint(chi(idir)/sm%mesh%spacing(idir))
868 call accel_write_buffer(sm%cube_map%map_buffer, space%dim, sm%cube_map%nmap, sm%cube_map%map)
893 class(
batch_t),
intent(in) :: ss
894 class(
batch_t),
intent(inout) :: mm
896 integer :: ist, idim, jdim, is
900 assert(.not. mm%is_packed())
903 assert(ss%nst_linear == mm%nst_linear)
904 assert(ss%status() == mm%status())
905 assert(ss%dim == mm%dim)
907 assert(mm%nst == ss%nst)
912 jdim = min(idim, ss%dim)
915 mm%zff(this%map(is), idim, ist) = &
916 mm%zff(this%map(is), idim, ist) + ss%dff(is, jdim, ist)
929#include "submesh_inc.F90"
932#include "complex.F90"
933#include "submesh_inc.F90"
This is the common interface to a sorting routine. It performs the shell algorithm,...
double sqrt(double __x) __attribute__((__nothrow__
double floor(double __x) __attribute__((__nothrow__
double fn(const gsl_vector *v, void *params)
subroutine, public accel_free_buffer(this, async)
pure logical function, public accel_is_enabled()
integer, parameter, public accel_mem_read_only
This module implements batches of mesh functions.
Module implementing boundary conditions in Octopus.
real(real64), parameter, public m_two
real(real64), parameter, public m_zero
real(real64), parameter, public m_pi
some mathematical constants
complex(real64), parameter, public m_z0
real(real64), parameter, public m_one
This module implements the index, used for the mesh points.
subroutine, public mesh_cube_map_end(this)
This module defines the meshes, which are used in Octopus.
integer function, public mesh_local_index_from_coords(mesh, ix)
This function returns the local index of the point for a given vector of integer coordinates.
Some general things and nomenclature:
subroutine, public profiling_out(label)
Increment out counter and sum up difference between entry and exit time.
subroutine, public profiling_in(label, exclude)
Increment in counter and save entry time.
This module is intended to contain "only mathematical" functions and procedures.
real(real64) function, public dsm_integrate_frommesh(mesh, sm, ff, reduce)
subroutine zdsubmesh_add_to_mesh(this, sphi, phi, factor)
subroutine, public submesh_init_cube_map(sm, space)
logical function, public submesh_overlap(sm1, sm2, space)
subroutine, public zsubmesh_batch_dotp_matrix(this, mm, ss, dot, reduce)
real(real64) function, public dsm_nrm2(sm, ff, reduce)
this function returns the the norm of a vector
subroutine zzsubmesh_add_to_mesh(this, sphi, phi, factor)
subroutine, public submesh_end_global(this)
subroutine, public zsubmesh_copy_from_mesh(this, phi, sphi, conjugate)
subroutine submesh_reorder_points(this, space, xtmp, rtmp)
complex(real64) function, public zsm_integrate(mesh, sm, ff, reduce)
subroutine, public submesh_shift_center(this, space, newcenter)
complex(real64) function zzsubmesh_to_mesh_dotp(this, sphi, phi, reduce)
real(real64) function, public dsm_integrate(mesh, sm, ff, reduce)
subroutine, public dsubmesh_batch_add_matrix(this, factor, ss, mm)
The following functions takes a batch of functions defined in submesh (ss) and adds all of them to ea...
recursive real(real64) function f_n(dims)
subroutine, public dsubmesh_copy_from_mesh(this, phi, sphi, conjugate)
real(real64) function ddsubmesh_to_mesh_dotp(this, sphi, phi, reduce)
subroutine, public submesh_merge(this, space, mesh, sm1, sm2, shift)
subroutine, public dzsubmesh_batch_add(this, ss, mm)
The following function takes a batch of functions defined in submesh (ss) and adds one of them to eac...
subroutine, public zsubmesh_batch_add(this, ss, mm)
The following function takes a batch of functions defined in submesh (ss) and adds one of them to eac...
real(real64) function, public zsm_nrm2(sm, ff, reduce)
this function returns the the norm of a vector
subroutine, public zsubmesh_batch_add_matrix(this, factor, ss, mm)
The following functions takes a batch of functions defined in submesh (ss) and adds all of them to ea...
subroutine, public submesh_end_cube_map(sm)
subroutine, public submesh_end(this)
subroutine ddsubmesh_add_to_mesh(this, sphi, phi, factor)
subroutine, public submesh_get_cube_dim(sm, space, db)
finds the dimension of a box containing the submesh
subroutine, public dsubmesh_batch_dotp_matrix(this, mm, ss, dot, reduce)
complex(real64) function, public zsm_integrate_frommesh(mesh, sm, ff, reduce)
logical function, public submesh_compatible(this, radius, center, dx)
subroutine, public submesh_build_global(this, space)
subroutine, public submesh_broadcast(this, space, mesh, center, radius, root, mpi_grp)
subroutine, public dsubmesh_batch_add(this, ss, mm)
The following function takes a batch of functions defined in submesh (ss) and adds one of them to eac...
subroutine, public submesh_init(this, space, mesh, latt, center, rc)
complex(real64) function zdsubmesh_to_mesh_dotp(this, sphi, phi, reduce)
type(type_t), parameter, public type_cmplx
type(type_t), parameter, public type_integer
type(type_t), parameter, public type_float
Class defining batches of mesh functions.
The following class implements a lattice iterator. It allows one to loop over all cells that are with...
Describes mesh distribution to nodes.
This is defined even when running serial.
A submesh is a type of mesh, used for the projectors in the pseudopotentials It contains points on a ...
void distance(const int iatom, const int jatom, const double coordinates[], double *rr, double *rr2, double *rr6, double *rr7)