From a47c384a3f61fb5df80582f3993918f722f38d26 Mon Sep 17 00:00:00 2001 From: Alex Selimov Date: Mon, 29 Jun 2020 18:51:01 -0400 Subject: [PATCH] Added tags to the element and atom arrays --- src/Makefile | 4 ++-- src/elements.f90 | 44 ++++++++++++++++++++++++++++++++++++-------- src/io.f90 | 20 ++++++++++---------- src/mode_create.f90 | 6 +++--- src/opt_group.f90 | 6 +++--- 5 files changed, 54 insertions(+), 26 deletions(-) diff --git a/src/Makefile b/src/Makefile index 642fce5..87f9306 100644 --- a/src/Makefile +++ b/src/Makefile @@ -1,6 +1,6 @@ FC=ifort -#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays -FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays +FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays +#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays MODES=mode_create.o mode_merge.o mode_convert.o OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES) $(OPTIONS) call_option.o sorts.o diff --git a/src/elements.f90 b/src/elements.f90 index 0dffecc..954719f 100644 --- a/src/elements.f90 +++ b/src/elements.f90 @@ -11,7 +11,7 @@ module elements !Data structures used to represent the CAC elements. Each index represents an element character(len=100), allocatable :: type_ele(:) !Element type - integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:) !Element size + integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:), tag_ele(:) !Element size real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array integer, save :: ele_num !Number of elements @@ -19,7 +19,7 @@ module elements !Data structure used to represent atoms integer, allocatable :: type_atom(:)!atom type - integer, allocatable :: sbox_atom(:) + integer, allocatable :: sbox_atom(:), tag_atom(:) real(kind =dp),allocatable :: r_atom(:,:) !atom position integer :: atom_num=0 !Number of atoms @@ -146,7 +146,7 @@ module elements !Allocate element arrays if(n > 0) then - allocate(type_ele(n), size_ele(n), lat_ele(n), sbox_ele(n), r_node(3,max_basisnum, max_ng_node,n), & + allocate(type_ele(n), tag_ele(n), size_ele(n), lat_ele(n), sbox_ele(n), r_node(3,max_basisnum, max_ng_node,n), & stat=allostat) if(allostat > 0) then print *, "Error allocating element arrays in elements.f90 because of: ", allostat @@ -156,7 +156,7 @@ module elements if(m > 0) then !Allocate atom arrays - allocate(type_atom(m), sbox_atom(m), r_atom(3,m), stat=allostat) + allocate(type_atom(m), sbox_atom(m), tag_atom(m), r_atom(3,m), stat=allostat) if(allostat > 0) then print *, "Error allocating atom arrays in elements.f90 because of: ", allostat stop @@ -187,6 +187,11 @@ module elements temp_int(ele_size+1:) = 0 call move_alloc(temp_int, lat_ele) + allocate(temp_int(n+ele_num+buffer_size)) + temp_int(1:ele_size) = tag_ele + temp_int(ele_size+1:) = 0 + call move_alloc(temp_int, tag_ele) + allocate(temp_int(n+ele_num+buffer_size)) temp_int(1:ele_size) = size_ele temp_int(ele_size+1:) = 0 @@ -214,6 +219,11 @@ module elements temp_int(atom_size+1:) = 0 call move_alloc(temp_int, type_atom) + allocate(temp_int(m+atom_num+buffer_size)) + temp_int(1:atom_size) = tag_atom + temp_int(atom_size+1:) = 0 + call move_alloc(temp_int, tag_atom) + allocate(temp_int(m+atom_num+buffer_size)) temp_int(1:atom_size) = sbox_atom temp_int(atom_size+1:) = 0 @@ -226,15 +236,25 @@ module elements end if end subroutine - subroutine add_element(type, size, lat, sbox, r) + subroutine add_element(tag, type, size, lat, sbox, r) !Subroutine which adds an element to the element arrays - integer, intent(in) :: size, lat, sbox + integer, intent(in) :: size, lat, sbox, tag character(len=100), intent(in) :: type real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node) + integer :: newtag + ele_num = ele_num + 1 + + if (tag==0) then + newtag = ele_num !If we don't assign a tag then pass the tag as the ele_num + else + newtag = tag + end if + !Check to see if we need to grow the arrays call grow_ele_arrays(1,0) + tag_ele(ele_num) = newtag type_ele(ele_num) = type size_ele(ele_num) = size lat_ele(ele_num) = lat @@ -245,14 +265,22 @@ module elements end subroutine add_element - subroutine add_atom(type, sbox, r) + subroutine add_atom(tag, type, sbox, r) !Subroutine which adds an atom to the atom arrays - integer, intent(in) :: type, sbox + integer, intent(in) :: type, sbox, tag real(kind=dp), intent(in), dimension(3) :: r + integer :: newtag + atom_num = atom_num+1 + if(tag==0) then + newtag = atom_num !If we don't assign a tag then pass the tag as the atom_num + else + newtag = tag + end if !Check to see if we need to grow the arrays call grow_ele_arrays(0,1) + tag_atom(atom_num) = tag type_atom(atom_num) = type r_atom(:,atom_num) = r(:) sbox_atom(atom_num) = sbox diff --git a/src/io.f90 b/src/io.f90 index cd3e3f6..6aafafc 100644 --- a/src/io.f90 +++ b/src/io.f90 @@ -543,13 +543,13 @@ module io !Write out atoms first do i = 1, atom_num - write(11,*) i, type_atom(i), sbox_atom(i), r_atom(:,i) + write(11,*) tag_atom(i), type_atom(i), sbox_atom(i), r_atom(:,i) end do !Write out the elements, this is written in two stages, one line for the element and then 1 line for !every basis at every node do i = 1, ele_num - write(11, *) i, lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i) + write(11, *) tag_ele(i), lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i) do inod = 1, ng_node(lat_ele(i)) do ibasis =1, basisnum(lat_ele(i)) write(11,*) inod, ibasis, r_node(:, ibasis, inod, i) @@ -738,19 +738,19 @@ module io do i = 1, in_atoms read(11,*) j, type, sbox, r(:) r = r+newdisplace - call add_atom(new_type_to_type(type), sbox+sub_box_num, r) + call add_atom(j, new_type_to_type(type), sbox+sub_box_num, r) end do !Read the elements do i = 1, in_eles - read(11, *) l, type, size, sbox, etype + read(11, *) j, type, size, sbox, etype do inod = 1, ng_node(type) do ibasis =1, basisnum(type) - read(11,*) j, k, r_innode(:, ibasis, inod) + read(11,*) k, l, r_innode(:, ibasis, inod) r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace end do end do - call add_element(etype, size, new_lattice_map(type), sbox+sub_box_num, r_innode) + call add_element(j, etype, size, new_lattice_map(type), sbox+sub_box_num, r_innode) end do !Close the file being read @@ -773,7 +773,7 @@ module io real(kind=dp), dimension(3), intent(in) :: displace real(kind = dp), dimension(6), intent(out) :: temp_box_bd - integer :: i, inod, ibasis, j, k, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, & + integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, & atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), & atom_type real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3) @@ -919,10 +919,10 @@ module io do i = 1, in_eles read(11,*) j, etype, k, lat_type do inod = 1, 8 - read(11, *) j, k, r_in(:,1,inod) + read(11, *) k, l, r_in(:,1,inod) r_in(:,1,inod) = r_in(:,1,inod) + newdisplace end do - call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in) + call add_element(j, in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in) end do end if @@ -937,7 +937,7 @@ module io do i = 1, in_atoms read(11,*) j, k, atom_type, r_in_atom(:) r_in_atom = r_in_atom + newdisplace - call add_atom(atom_type_map(atom_type), sub_box_num + 1, r_in_atom) + call add_atom(j,atom_type_map(atom_type), sub_box_num + 1, r_in_atom) end do !Close file close(11) diff --git a/src/mode_create.f90 b/src/mode_create.f90 index 5c347ab..454fcb7 100644 --- a/src/mode_create.f90 +++ b/src/mode_create.f90 @@ -109,7 +109,7 @@ module mode_create box_bd(2*i) = maxval(r_node_temp(i,:,:))+10.0_dp**-6.0_dp box_bd(2*i-1) = minval(r_node_temp(i,:,:)) - 10.0_dp**-6.0_dp end do - call add_element(element_type, esize, 1, 1, r_node_temp) + call add_element(0,element_type, esize, 1, 1, r_node_temp) end if !If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays @@ -136,7 +136,7 @@ module mode_create if(lat_atom_num > 0) then do i = 1, lat_atom_num do ibasis = 1, basisnum(1) - call add_atom(basis_type(ibasis, 1), 1, (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis)) + call add_atom(0,basis_type(ibasis, 1), 1, (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis)) end do end do deallocate(r_atom_lat) @@ -150,7 +150,7 @@ module mode_create end do end do - call add_element(element_type, elat(i), 1, 1, r_node_temp) + call add_element(0,element_type, elat(i), 1, 1, r_node_temp) end do end if end if diff --git a/src/opt_group.f90 b/src/opt_group.f90 index 281ab28..c24b857 100644 --- a/src/opt_group.f90 +++ b/src/opt_group.f90 @@ -564,7 +564,7 @@ module opt_group !here as well to make sure they are in the box do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3 call apply_periodic(r_interp(:,j)) - call add_atom(type_interp(j), sbox_ele(ie), r_interp(:,j)) + call add_atom(0,type_interp(j), sbox_ele(ie), r_interp(:,j)) end do end do !Once all atoms are added we delete all of the elements @@ -800,7 +800,7 @@ module opt_group !Add the element, for the sbox we just set it to the same sbox that we get the orientation !from. In this case it is from the sbox of the first atom in the group. new_ele = new_ele+1 - call add_element(remesh_ele_type, working_esize, ilat, sbox_atom(atom_index(1)),r_new_node) + call add_element(0,remesh_ele_type, working_esize, ilat, sbox_atom(atom_index(1)),r_new_node) end if end if @@ -821,7 +821,7 @@ module opt_group lat_points(ix,iy,iz) = .false. r = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat) new_atom=new_atom+1 - call add_atom(basis_type(1,ilat), is, r) + call add_atom(0,basis_type(1,ilat), is, r) end if end do end do