95 class(box_t),
pointer :: box
96 class(coordinate_system_t),
pointer :: coord_system
98 logical :: use_curvilinear
100 real(real64),
allocatable :: spacing(:)
107 integer(int64) :: np_global
108 integer(int64) :: np_part_global
109 logical :: parallel_in_domains
110 type(mpi_grp_t) :: mpi_grp
111 type(par_vec_t) :: pv
112 type(partition_t) :: partition
114 real(real64),
allocatable :: x(:,:)
115 real(real64),
allocatable :: chi(:,:)
116 real(real64) :: volume_element
117 real(real64),
allocatable :: vol_pp(:)
118 real(real64),
allocatable :: jacobian_inverse(:,:,:)
120 logical :: masked_periodic_boundaries
121 character(len=256) :: periodic_boundary_mask
127 procedure :: dmesh_allreduce_0, zmesh_allreduce_0, imesh_allreduce_0, lmesh_allreduce_0
128 procedure :: dmesh_allreduce_1, zmesh_allreduce_1, imesh_allreduce_1, lmesh_allreduce_1
129 procedure :: dmesh_allreduce_2, zmesh_allreduce_2, imesh_allreduce_2, lmesh_allreduce_2
130 procedure :: dmesh_allreduce_3, zmesh_allreduce_3, imesh_allreduce_3, lmesh_allreduce_3
131 procedure :: dmesh_allreduce_4, zmesh_allreduce_4, imesh_allreduce_4, lmesh_allreduce_4
132 procedure :: dmesh_allreduce_5, zmesh_allreduce_5, imesh_allreduce_5, lmesh_allreduce_5
133 generic :: allreduce => dmesh_allreduce_0, zmesh_allreduce_0, imesh_allreduce_0, lmesh_allreduce_0
134 generic :: allreduce => dmesh_allreduce_1, zmesh_allreduce_1, imesh_allreduce_1, lmesh_allreduce_1
135 generic :: allreduce => dmesh_allreduce_2, zmesh_allreduce_2, imesh_allreduce_2, lmesh_allreduce_2
136 generic :: allreduce => dmesh_allreduce_3, zmesh_allreduce_3, imesh_allreduce_3, lmesh_allreduce_3
137 generic :: allreduce => dmesh_allreduce_4, zmesh_allreduce_4, imesh_allreduce_4, lmesh_allreduce_4
138 generic :: allreduce => dmesh_allreduce_5, zmesh_allreduce_5, imesh_allreduce_5, lmesh_allreduce_5
155 real(real64) :: u(3), v(3)
156 real(real64) :: origin(3)
157 real(real64) :: spacing
158 integer :: nu, mu, nv, mv
168 real(real64) :: origin(2)
169 real(real64) :: spacing
176 class(mesh_t),
intent(inout) :: this
180 call this%set_time_dependent(.false.)
190 real(real64),
intent(in) :: alpha
191 integer,
intent(out) :: db(:)
200 do idir = 1, space%periodic_dim
201 db(idir) = mesh%idx%ll(idir)
203 do idir = space%periodic_dim + 1, space%dim
204 db(idir) = nint(alpha * (mesh%idx%ll(idir) - 1)) + 1
214 integer,
optional,
intent(in) :: iunit
215 type(
namespace_t),
optional,
intent(in) :: namespace
218 real(real64) :: cutoff
223 do ii = 1, this%box%dim
231 write(
message(2),
'(a, i10)')
' # inner mesh = ', this%np_global
232 write(
message(3),
'(a, i10)')
' # total mesh = ', this%np_part_global
244 pure subroutine mesh_r(mesh, ip, rr, origin, coords)
245 class(mesh_t),
intent(in) :: mesh
246 integer,
intent(in) :: ip
247 real(real64),
intent(out) :: rr
248 real(real64),
intent(in),
optional :: origin(:)
249 real(real64),
intent(out),
optional :: coords(:)
251 real(real64) :: xx(1:mesh%box%dim)
254 if (
present(origin)) xx = xx - origin
257 if (
present(coords))
then
265 class(
mesh_t),
intent(in) :: mesh
266 integer(int64),
intent(in) :: ipg
267 real(real64),
intent(out) :: rr
268 real(real64),
intent(in),
optional :: origin(:)
269 real(real64),
intent(out),
optional :: coords(:)
271 real(real64) :: xx(1:mesh%box%dim)
274 if (
present(origin)) xx = xx - origin
277 if (
present(coords))
then
289 class(
mesh_t),
intent(in) :: mesh
290 real(real64),
intent(in) :: pos(:)
291 real(real64),
intent(out) :: dmin
292 integer,
intent(out) :: rankmin
303 dd = sum((pos - mesh%x(ip, :))**2)
304 if ((dd < dmin) .or. (ip == 1))
then
311 call mesh%mpi_grp%bcast(imin, 1, mpi_integer, rankmin)
319 class(
mesh_t),
intent(in ) :: mesh
320 real(real64),
intent(inout) ::
values(:, :)
322 integer :: i, ip, ndim
324 real(real64) :: dummy
328 if (mesh%parallel_in_domains)
then
333 if (mesh%mpi_grp%rank == process)
values(:, i) = mesh%x(ip, :)
334 call mesh%mpi_grp%bcast(
values(:, i), ndim, mpi_double_precision, process)
339 values(:, i) = mesh%x(ip, :)
353 class(
mesh_t),
intent(in) :: mesh
356 gmax =
m_pi / (maxval(mesh%spacing))
363 type(
mesh_t),
intent(in) :: mesh
364 character(len=*),
intent(in) :: dir
365 character(len=*),
intent(in) :: filename
366 type(mpi_grp_t),
intent(in) :: mpi_grp
367 type(namespace_t),
intent(in) :: namespace
368 integer,
intent(out) :: ierr
376 iunit = io_open(trim(dir)//
"/"//trim(filename), namespace, action=
'write', &
377 die=.false., grp=mpi_grp)
378 if (iunit == -1)
then
379 message(1) =
"Unable to open file '"//trim(dir)//
"/"//trim(filename)//
"'."
380 call messages_warning(1, namespace=namespace)
383 if (mpi_grp_is_root(mpi_grp))
then
384 write(iunit,
'(a20,i21)')
'np_part_global= ', mesh%np_part_global
385 write(iunit,
'(a20,i21)')
'np_global= ', mesh%np_global
386 write(iunit,
'(a20,i21)')
'algorithm= ', 1
387 write(iunit,
'(a20,i21)')
'checksum= ', mesh%idx%checksum
388 write(iunit,
'(a20,i21)')
'bits= ', mesh%idx%bits
389 write(iunit,
'(a20,i21)')
'dim= ', mesh%idx%dim
390 write(iunit,
'(a20,i21)')
'type= ', mesh%idx%type
391 do ii = 1, mesh%idx%dim
392 write(iunit,
'(a7,i2,a11,i21)')
'offset(',ii,
')= ', mesh%idx%offset(ii)
394 do ii = 1, mesh%idx%dim
395 write(iunit,
'(a7,i2,a11,i21)')
'nn(',ii,
')= ', mesh%idx%nr(2, ii) - mesh%idx%nr(1, ii) + 1
398 call io_close(iunit, grp=mpi_grp)
411 read_np_part, read_np, bits, type, offset, nn, ierr)
412 type(
mesh_t),
intent(in) :: mesh
413 character(len=*),
intent(in) :: dir
414 character(len=*),
intent(in) :: filename
415 type(mpi_grp_t),
intent(in) :: mpi_grp
416 type(namespace_t),
intent(in) :: namespace
417 integer(int64),
intent(out) :: read_np_part
418 integer(int64),
intent(out) :: read_np
419 integer,
intent(out) :: bits
420 integer,
intent(out) :: type
421 integer,
intent(out) :: offset(1:mesh%idx%dim)
422 integer,
intent(out) :: nn(1:mesh%idx%dim)
423 integer,
intent(out) :: ierr
425 character(len=20) :: str
426 character(len=100) :: lines(7)
427 integer :: iunit, algorithm, dim, err, ii
428 integer(int64) :: checksum
434 read_np_part = 0_int64
437 iunit = io_open(trim(dir)//
"/"//trim(filename), namespace, action=
'read', &
438 status=
'old', die=.false., grp=mpi_grp)
439 if (iunit == -1)
then
441 message(1) =
"Unable to open file '"//trim(dir)//
"/"//trim(filename)//
"'."
442 call messages_warning(1, namespace=namespace)
444 call iopar_read(mpi_grp, iunit, lines, 7, err)
448 read(lines(1),
'(a20,i21)') str, read_np_part
449 read(lines(2),
'(a20,i21)') str, read_np
450 read(lines(3),
'(a20,i21)') str, algorithm
451 read(lines(4),
'(a20,i21)') str, checksum
452 read(lines(5),
'(a20,i21)') str, bits
453 read(lines(6),
'(a20,i21)') str, dim
454 read(lines(7),
'(a20,i21)') str,
type
456 if (dim /= mesh%idx%dim)
then
460 call iopar_read(mpi_grp, iunit, lines, dim, err)
465 read(lines(ii),
'(a20,i21)') str, offset(ii)
470 call iopar_read(mpi_grp, iunit, lines, dim, err)
475 read(lines(ii),
'(a20,i21)') str, nn(ii)
480 assert(read_np_part >= read_np)
482 if (read_np_part == mesh%np_part_global &
483 .and. read_np == mesh%np_global &
484 .and. algorithm == 1 &
485 .and. checksum == mesh%idx%checksum)
then
491 call io_close(iunit, grp=mpi_grp)
499 type(
mesh_t),
intent(in) :: mesh
500 character(len=*),
intent(in) :: dir
501 character(len=*),
intent(in) :: filename
502 type(namespace_t),
intent(in) :: namespace
503 type(mpi_grp_t),
intent(in) :: mpi_grp
504 logical,
intent(out) :: grid_changed
505 logical,
intent(out) :: grid_reordered
506 integer(int64),
allocatable,
intent(out) :: map(:)
507 integer,
intent(out) :: ierr
509 integer(int64) :: ipg, ipg_new, read_np_part, read_np
511 integer :: bits,
type, offset(mesh%idx%dim), point(mesh%idx%dim), nn(mesh%idx%dim)
512 integer(int64),
allocatable :: read_indices(:)
513 type(index_t) :: idx_old
519 grid_changed = .false.
520 grid_reordered = .false.
524 bits,
type, offset, nn, err)
527 message(1) =
"Unable to read mesh fingerprint from '"//trim(dir)//
"/"//trim(filename)//
"'."
528 call messages_warning(1, namespace=namespace)
530 else if (read_np > 0)
then
531 if (.not.
associated(mesh%box))
then
536 grid_changed = .
true.
541 grid_reordered = (read_np == mesh%np_global)
544 safe_allocate(read_indices(1:read_np_part))
545 call io_binary_read(trim(io_workpath(dir, namespace))//
"/indices.obf", read_np_part, &
549 message(1) =
"Unable to read index map from '"//trim(dir)//
"'."
550 call messages_warning(1, namespace=namespace)
553 call index_init(idx_old, mesh%idx%dim)
556 idx_old%nr(1, :) = -offset
557 idx_old%nr(2, :) = -offset + nn - 1
558 idx_old%offset = offset
559 idx_old%stride(1) = 1
560 do idir = 2, mesh%idx%dim
561 idx_old%stride(idir) = idx_old%stride(idir-1) * nn(idir-1)
564 safe_allocate(map(1:read_np))
567 call index_spatial_to_point(idx_old, mesh%idx%dim, read_indices(ipg), point)
572 if (map(ipg) > mesh%np_global) map(ipg) = 0
574 if (map(ipg) == 0) grid_reordered = .false.
576 call index_end(idx_old)
579 safe_deallocate_a(read_indices)
589 class(
mesh_t),
intent(inout) :: this
594 call lmpi_destroy_shared_memory_window(this%idx%window_grid_to_spatial)
595 call lmpi_destroy_shared_memory_window(this%idx%window_spatial_to_grid)
596 nullify(this%idx%grid_to_spatial_global)
597 nullify(this%idx%spatial_to_grid_global)
599 safe_deallocate_p(this%idx%grid_to_spatial_global)
600 safe_deallocate_p(this%idx%spatial_to_grid_global)
603 safe_deallocate_a(this%x)
604 safe_deallocate_a(this%chi)
605 safe_deallocate_a(this%vol_pp)
606 safe_deallocate_a(this%jacobian_inverse)
608 if (this%parallel_in_domains)
then
609 call par_vec_end(this%pv)
610 call partition_end(this%partition)
613 call index_end(this%idx)
614 safe_deallocate_a(this%spacing)
627 class(
mesh_t),
intent(in) :: mesh
628 class(space_t),
intent(in) :: space
629 integer,
intent(in) :: ip
631 integer :: ix(space%dim), nr(2, space%dim), idim
632 real(real64) :: xx(space%dim), rr, ufn_re, ufn_im
637 nr(1, :) = mesh%idx%nr(1, :) + mesh%idx%enlarge(:)
638 nr(2, :) = mesh%idx%nr(2, :) - mesh%idx%enlarge(:)
640 do idim = 1, space%periodic_dim
641 if (ix(idim) < nr(1, idim)) ix(idim) = ix(idim) + mesh%idx%ll(idim)
642 if (ix(idim) > nr(2, idim)) ix(idim) = ix(idim) - mesh%idx%ll(idim)
648 if (mesh%masked_periodic_boundaries)
then
649 call mesh_r(mesh, ip, rr, coords = xx)
650 call parse_expression(ufn_re, ufn_im, space%dim, xx, rr, m_zero, mesh%periodic_boundary_mask)
657 class(
mesh_t),
intent(in) :: mesh
658 class(space_t),
intent(in) :: space
659 integer(int64),
intent(in) :: ipg_in
661 integer :: ix(space%dim), nr(2, space%dim), idim
662 real(real64) :: xx(space%dim), rr, ufn_re, ufn_im
667 nr(1, :) = mesh%idx%nr(1, :) + mesh%idx%enlarge(:)
668 nr(2, :) = mesh%idx%nr(2, :) - mesh%idx%enlarge(:)
670 do idim = 1, space%periodic_dim
671 if (ix(idim) < nr(1, idim)) ix(idim) = ix(idim) + mesh%idx%ll(idim)
672 if (ix(idim) > nr(2, idim)) ix(idim) = ix(idim) - mesh%idx%ll(idim)
678 if (mesh%masked_periodic_boundaries)
then
680 call parse_expression(ufn_re, ufn_im, space%dim, xx, rr, m_zero, mesh%periodic_boundary_mask)
681 if (int(ufn_re) == 0) ipg = ipg_in
690 use iso_c_binding,
only: c_sizeof, c_long_long
691 class(
mesh_t),
intent(in) :: mesh
694 memory = c_sizeof(c_long_long) * real(mesh%np_part_global, real64) * 2
701 use iso_c_binding,
only: c_sizeof, c_long_long
702 class(
mesh_t),
intent(in) :: mesh
707 memory = memory + real64 * real(mesh%np_part, real64) * mesh%idx%dim
709 memory = memory + c_sizeof(c_long_long) * real(mesh%np_part, real64) * 2
715 class(
mesh_t),
intent(in) :: mesh
716 integer(int64),
intent(in) :: ipg
717 real(real64) :: xx(1:mesh%box%dim)
719 real(real64) :: chi(1:mesh%box%dim)
720 integer :: ix(1:mesh%box%dim)
725 chi = ix * mesh%spacing
726 xx = mesh%coord_system%to_cartesian(chi)
733 type(
mesh_t),
intent(in) :: mesh
735 cb = .not. mesh%use_curvilinear .and. &
736 .not. mesh%parallel_in_domains
743 class(
mesh_t),
intent(in) :: mesh
744 type(symmetries_t),
intent(in) :: symm
745 integer,
intent(in) :: periodic_dim
747 integer :: iop, ip, idim, nops, ix(1:3)
748 real(real64) :: destpoint(1:3), srcpoint(1:3), lsize(1:3), offset(1:3)
749 real(real64),
parameter :: tol_spacing = 1e-12_real64
757 if (mesh%idx%ll(1) == mesh%idx%ll(2) .and. &
758 mesh%idx%ll(2) == mesh%idx%ll(3) .and. &
759 abs(mesh%spacing(1) - mesh%spacing(2)) < tol_spacing .and. &
760 abs(mesh%spacing(2) - mesh%spacing(3)) < tol_spacing)
return
764 message(1) =
"Checking if the real-space grid is symmetric"
765 call messages_info(1)
767 lsize(1:3) = real(mesh%idx%ll(1:3), real64)
768 offset(1:3) = real(mesh%idx%nr(1, 1:3) + mesh%idx%enlarge(1:3), real64)
770 nops = symmetries_number(symm)
777 destpoint(1:3) = real(ix(1:3), real64) - offset(1:3)
779 assert(all(destpoint >= 0))
780 assert(all(destpoint < lsize))
783 destpoint = destpoint - real(int(lsize)/2, real64)
787 destpoint(idim) = destpoint(idim)/lsize(idim)
792 srcpoint = symm_op_apply_red(symm%ops(iop), destpoint)
796 srcpoint(idim) = srcpoint(idim)*lsize(idim)
800 srcpoint = srcpoint + real(int(lsize)/2, real64)
803 do idim = 1, periodic_dim
804 if (nint(srcpoint(idim)) < 0 .or. nint(srcpoint(idim)) >= lsize(idim))
then
805 srcpoint(idim) = modulo(srcpoint(idim)+m_half*symprec, lsize(idim))
808 assert(all(srcpoint >= -symprec))
809 assert(all(srcpoint < lsize))
811 srcpoint(1:3) = srcpoint(1:3) + offset(1:3)
813 if (any(srcpoint-anint(srcpoint)> symprec*m_two))
then
814 message(1) =
"The real-space grid breaks at least one of the symmetries of the system."
815 message(2) =
"Change your spacing or use SymmetrizeDensity=no."
816 call messages_fatal(2)
827 class(
mesh_t),
intent(in) :: mesh
828 integer,
intent(in) :: ix(:)
830 index = index_from_coords(mesh%idx, ix)
836 type(
mesh_t),
intent(in) :: mesh
837 integer(int64),
intent(in) :: ipg
838 integer,
intent(out) :: ix(:)
840 call index_to_coords(mesh%idx, ipg, ix)
846 type(
mesh_t),
intent(in) :: mesh
847 integer,
intent(in) :: ix(:)
849 integer(int64) :: ipg
851 ipg = index_from_coords(mesh%idx, ix)
858 type(
mesh_t),
intent(in) :: mesh
859 integer,
intent(in) :: ip
860 integer,
intent(out) :: ix(:)
862 integer(int64) :: ipg
865 call index_to_coords(mesh%idx, ipg, ix)
870 type(
mesh_t),
intent(in) :: mesh
871 integer,
intent(in) :: ip
873 ipg = par_vec_local2global(mesh%pv, ip)
880 type(
mesh_t),
intent(in) :: mesh
881 integer(int64),
intent(in) :: ipg
883 ip = par_vec_global2local(mesh%pv, ipg)
889 type(
mesh_t),
intent(in) :: mesh
890 real(real64),
intent(inout) :: min_or_max
891 integer,
intent(out) :: rank_min_or_max
892 type(mpi_op),
intent(in) :: op
894 real(real64) :: loc_in(2), loc_out(2)
898 assert(op == mpi_minloc .or. op == mpi_maxloc)
901 if (mesh%parallel_in_domains)
then
902 loc_in(1) = min_or_max
903 loc_in(2) = mesh%mpi_grp%rank
904 call mesh%mpi_grp%allreduce(loc_in, loc_out, 1, mpi_2double_precision, op)
905 min_or_max = loc_out(1)
906 rank_min_or_max = nint(loc_out(2))
915#include "mesh_inc.F90"
918#include "complex.F90"
919#include "mesh_inc.F90"
922#include "integer.F90"
923#include "mesh_inc.F90"
926#include "integer8.F90"
927#include "mesh_inc.F90"
real(real64), parameter, public m_two
real(real64), parameter, public m_zero
real(real64), parameter, public m_pi
some mathematical constants
This module implements a simple hash table for non-negative integer keys and integer values.
This module implements the index, used for the mesh points.
This module defines the meshes, which are used in Octopus.
integer(int64) function, public mesh_periodic_point(mesh, space, ip)
This function returns the point inside the grid corresponding to a boundary point when PBCs are used....
subroutine, public mesh_global_index_to_coords(mesh, ipg, ix)
Given a global point index, this function returns the set of integer coordinates of the point.
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.
subroutine, public mesh_double_box(space, mesh, alpha, db)
finds the dimension of a box doubled in the non-periodic dimensions
integer(int64) function, public mesh_global_index_from_coords(mesh, ix)
This function returns the true global index of the point for a given vector of integer coordinates.
subroutine, public mesh_check_symmetries(mesh, symm, periodic_dim)
subroutine, public mesh_write_info(this, iunit, namespace)
subroutine, public mesh_local_index_to_coords(mesh, ip, ix)
Given a local point index, this function returns the set of integer coordinates of the point.
subroutine, public mesh_discretize_values_to_mesh(mesh, values)
Assign a set of values to their nearest discrete points on the mesh.
integer function, public mesh_nearest_point(mesh, pos, dmin, rankmin)
Returns the index of the point which is nearest to a given vector position pos.
integer(int64) function, public mesh_periodic_point_global(mesh, space, ipg_in)
real(real64) pure function, public mesh_global_memory(mesh)
subroutine, public mesh_read_fingerprint(mesh, dir, filename, mpi_grp, namespace, read_np_part, read_np, bits, type, offset, nn, ierr)
This function reads the fingerprint of a mesh written in filename. If the meshes are equal (same fing...
pure subroutine, public mesh_r(mesh, ip, rr, origin, coords)
return the distance to the origin for a given grid point
subroutine, public mesh_check_dump_compatibility(mesh, dir, filename, namespace, mpi_grp, grid_changed, grid_reordered, map, ierr)
real(real64) function, public mesh_gcutoff(mesh)
mesh_gcutoff returns the "natural" band limitation of the grid mesh, in terms of the maximum G vector...
subroutine, public mesh_minmaxloc(mesh, min_or_max, rank_min_or_max, op)
Given a local min/max this returns the global min/max and the rank where this is located.
integer function, public mesh_global2local(mesh, ipg)
This function returns the local mesh index for a given global index.
recursive subroutine, public mesh_end(this)
logical pure function, public mesh_compact_boundaries(mesh)
real(real64) pure function, public mesh_local_memory(mesh)
integer(int64) function, public mesh_local2global(mesh, ip)
This function returns the global mesh index for a given local index.
real(real64) function, dimension(1:mesh%box%dim), public mesh_x_global(mesh, ipg)
subroutine mesh_r_global(mesh, ipg, rr, origin, coords)
return the distance to the origin for a given grid point
subroutine, public mesh_write_fingerprint(mesh, dir, filename, mpi_grp, namespace, ierr)
subroutine mesh_init(this)
character(len=256), dimension(max_lines), public message
to be output by fatal, warning
subroutine, public messages_info(no_lines, iunit, debug_only, stress, all_nodes, namespace)
This module contains some common usage patterns of MPI routines.
Some general things and nomenclature:
brief This module defines the class unit_t which is used by the unit_systems_oct_m module.
character(len=20) pure function, public units_abbrev(this)
This module defines the unit system, used for input and output.
type(unit_system_t), public units_out
abstract class for basis sets
This data type defines a line, and a regular grid defined on this line (or rather,...
define a grid on a plane.
Describes mesh distribution to nodes.
real(real64) function values(xx)