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Change implementation to make atom types a bit better

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development
Alex Selimov 3 years ago
parent f9e7f68676
commit 59a0c18779
2 changed files with 19 additions and 20 deletions
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30
src/io.f90
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@ -509,7 +509,7 @@ module io
character(len=100), intent(in) :: file
integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_type(50), unique_num, &
etype
real(kind=dp) :: box_vec(3), masses(10)
real(kind=dp) :: box_vec(3)
1 format('time' / i16, f23.15)
2 format('number of elements' / i16)
@ -548,9 +548,6 @@ module io
write(11,3) node_num
write(11,19) max_ng_node, max_basisnum
write(11,5) atom_num
do i = 1, atom_types
call atommass(type_to_name(i),masses(i))
end do
write(11,*) "masses: "
write(11, *) (masses(i), i = 1, atom_types)
write(11,7) box_bc(1:1), box_bc(2:2), box_bc(3:3)
@ -631,7 +628,7 @@ module io
write(11,*) box_bd(:)
!Write the number of atom types in the current model and all of their names
write(11,*) atom_types, (type_to_name(i)//' ', i=1, atom_types)
write(11,*) atom_types, (masses(i), i=1, atom_types)
!Write the number of lattice_types, basisnum and number of nodes for each lattice type
write(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
!Now for every lattice type write the basis atom types
@ -754,9 +751,8 @@ module io
new_type_to_type(10), new_lattice_types, new_lattice_map(10), btype_map(10,10), bnum_map(10), &
node_map(10)
character(len=100) :: etype
real(kind=dp) :: r(3), newdisplace(3), lapa_map(10)
real(kind=dp) :: r(3), newdisplace(3), lapa_map(10), new_masses(10)
real(kind=dp), allocatable :: r_innode(:,:,:)
character(len = 2) :: new_type_to_name(10)
!First open the file
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
@ -777,11 +773,11 @@ module io
call grow_box(temp_box_bd)
!Read in the number of atom types and all their names
read(11, *) new_atom_types, (new_type_to_name(i), i = 1, new_atom_types)
read(11, *) new_atom_types, (new_masses(i), i = 1, new_atom_types)
!Now fit these into the global list of atom types, after this new_type_to_type is the actual global
!type of the atoms within this file
do i = 1, new_atom_types
call add_atom_type(new_type_to_name(i), new_type_to_type(i), all_new)
call add_atom_type(new_masses(i), new_type_to_type(i), all_new)
end do
!Read the number of lattice types, basisnum, and number of nodes for each lattice type
read(11,*) new_lattice_types, (bnum_map(i), i = 1, new_lattice_types),(node_map(i), i =1, new_lattice_types)
@ -893,8 +889,7 @@ module io
!Read define atom_types by mass
print *, j
do i = 1, j
call realatomspecies(atomic_masses(i), atomic_element)
call add_atom_type(atomic_element, atom_type_map(i), all_new)
call add_atom_type(atomic_masses(i), atom_type_map(i), all_new)
print *, i, atom_type_map(i)
end do
@ -1029,8 +1024,7 @@ module io
!Read define atom_types by mass
do i = 1, j
call realatomspecies(atomic_masses(i), atomic_element)
call add_atom_type(atomic_element, atom_type_map(i), all_new)
call add_atom_type(atomic_masses(i), atom_type_map(i), all_new)
end do
if(in_atoms > 0 ) then
@ -1152,8 +1146,7 @@ module io
!Read atomic masses
do i = 1, type_in
read(11,*) j, mass
call realatomspecies(mass, atom_species)
call add_atom_type(atom_species, type_map(i), all_new)
call add_atom_type(mass, type_map(i), all_new)
end do
!Read useless info
@ -1226,8 +1219,7 @@ module io
!Read atomic masses
do i = 1, type_in
read(11,*) j, mass, textholder
call realatomspecies(mass, atom_species)
call add_atom_type(atom_species, type_map(i), all_new)
call add_atom_type(mass, type_map(i), all_new)
end do
!Read useless info
@ -1311,6 +1303,7 @@ module io
integer :: i, j,arglen, arg_pos, ntypes
character(len=100) :: textholder
real(kind=dp) :: mass
arg_pos = apos + 1
call get_command_argument(arg_pos, textholder, arglen)
@ -1320,7 +1313,8 @@ module io
do i=1,ntypes
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
call add_atom_type(textholder, j)
call atommass(textholder, mass)
call add_atom_type(mass, j)
end do
return

9
src/mode_create.f90
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@ -186,6 +186,7 @@ module mode_create
character(len=100) :: orient_string
character(len=2) :: btype
logical :: isortho, isrighthanded, bool
real(kind=dp) :: mass
!Pull out all required positional arguments
@ -265,7 +266,8 @@ module mode_create
do i = 1, max_basisnum
call get_command_argument(arg_pos, btype)
arg_pos = arg_pos+1
call add_atom_type(btype, basis_type(i,1))
call atommass(btype, mass)
call add_atom_type(mass, basis_type(i,1))
do j = 1, 3
call get_command_argument(arg_pos, textholder)
read(textholder, *) basis_pos(j,i)
@ -334,7 +336,8 @@ module mode_create
if (basisnum(1) == 0) then
max_basisnum = 1
basisnum(1) = 1
call add_atom_type(name, basis_type(1,1)) !If basis command not defined then we use name as the atom_name
call atommass(name, mass)
call add_atom_type(mass, basis_type(1,1)) !If basis command not defined then we use name as the atom_name
basis_pos(:,1) = 0.0_dp
end if
@ -371,6 +374,8 @@ module mode_create
numlatpoints = numlatpoints*(bd_in_lat(2*i)-bd_in_lat(2*i-1))
end do
if(numlatpoints < 0) stop "number of lattice points is negative, this can occur if the model is too big"
!Allocate the correct lat variable
select case(esize)
!Atomistics

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