Latest working version of cacmb
This commit is contained in:
Alex Selimov
parent
fbaca5859b
commit
f0fd76f12d
261
src/atoms.f90
261
src/atoms.f90
@ -1162,6 +1162,267 @@ END SELECT
|
||||
!
|
||||
END SUBROUTINE ATOMMASSSPECIES
|
||||
!
|
||||
|
||||
subroutine realatomspecies(smass,species)
|
||||
!
|
||||
IMPLICIT NONE
|
||||
CHARACTER(LEN=2),INTENT(OUT):: species
|
||||
INTEGER:: mass
|
||||
REAL(dp),INTENT(IN):: smass
|
||||
|
||||
if(mass_is_equal(smass,1.008d0)) then
|
||||
species = 'H'
|
||||
else if(mass_is_equal(smass,2.014101777d0)) then
|
||||
species = 'D'
|
||||
else if(mass_is_equal(smass,4.002602d0)) then
|
||||
species = 'He'
|
||||
else if(mass_is_equal(smass,6.94d0)) then
|
||||
species = 'Li'
|
||||
else if(mass_is_equal(smass,9.012182d0)) then
|
||||
species = 'Be'
|
||||
else if(mass_is_equal(smass,10.81d0)) then
|
||||
species = 'B'
|
||||
else if(mass_is_equal(smass,12.011d0)) then
|
||||
species='C'
|
||||
else if(mass_is_equal(smass,14.007d0)) then
|
||||
species='N'
|
||||
else if(mass_is_equal(smass,15.999d0)) then
|
||||
species='O'
|
||||
else if(mass_is_equal(smass,18.9984032d0)) then
|
||||
species='F'
|
||||
else if(mass_is_equal(smass,20.1797d0)) then
|
||||
species='Ne'
|
||||
!
|
||||
! n=3
|
||||
else if(mass_is_equal(smass,22.98976928d0)) then
|
||||
species = 'Na'
|
||||
else if(mass_is_equal(smass,24.305d0)) then
|
||||
species='Mg'
|
||||
else if(mass_is_equal(smass,26.9815386d0)) then
|
||||
species='Al'
|
||||
else if(mass_is_equal(smass,28.085d0)) then
|
||||
species='Si'
|
||||
else if(mass_is_equal(smass,30.973762d0)) then
|
||||
species='P'
|
||||
else if(mass_is_equal(smass,32.06d0)) then
|
||||
species='S'
|
||||
else if(mass_is_equal(smass,35.45d0)) then
|
||||
species='Cl'
|
||||
else if(mass_is_equal(smass,39.948d0)) then
|
||||
species='Ar'
|
||||
!
|
||||
! n=4
|
||||
else if(mass_is_equal(smass,39.0983d0)) then
|
||||
species='K'
|
||||
else if(mass_is_equal(smass,40.078d0)) then
|
||||
species='Ca'
|
||||
else if(mass_is_equal(smass,44.955912d0)) then
|
||||
species='Sc'
|
||||
else if(mass_is_equal(smass,47.867d0)) then
|
||||
species='Ti'
|
||||
else if(mass_is_equal(smass,50.9415d0)) then
|
||||
species='V'
|
||||
else if(mass_is_equal(smass,51.9961d0)) then
|
||||
species='Cr'
|
||||
else if(mass_is_equal(smass,54.938045d0)) then
|
||||
species='Mn'
|
||||
else if(mass_is_equal(smass,55.845d0)) then
|
||||
species='Fe'
|
||||
else if(mass_is_equal(smass,58.933195d0)) then
|
||||
species='Co'
|
||||
else if(mass_is_equal(smass,58.6934d0)) then
|
||||
species='Ni'
|
||||
else if(mass_is_equal(smass,63.546d0)) then
|
||||
species='Cu'
|
||||
else if(mass_is_equal(smass,65.38d0)) then
|
||||
species='Zn'
|
||||
else if(mass_is_equal(smass,69.723d0)) then
|
||||
species='Ga'
|
||||
else if(mass_is_equal(smass,72.63d0)) then
|
||||
species='Ge'
|
||||
else if(mass_is_equal(smass,74.9216d0)) then
|
||||
species='As'
|
||||
else if(mass_is_equal(smass,78.96d0)) then
|
||||
species='Se'
|
||||
else if(mass_is_equal(smass,79.904d0)) then
|
||||
species='Br'
|
||||
else if(mass_is_equal(smass,83.798d0)) then
|
||||
species='Kr'
|
||||
!
|
||||
! n=5
|
||||
else if(mass_is_equal(smass,85.4678d0)) then
|
||||
species='Rb'
|
||||
else if(mass_is_equal(smass,87.62d0)) then
|
||||
species='Sr'
|
||||
else if(mass_is_equal(smass,88.90585d0)) then
|
||||
species='Y'
|
||||
else if(mass_is_equal(smass,91.224d0)) then
|
||||
species='Zr'
|
||||
else if(mass_is_equal(smass,92.90638d0)) then
|
||||
species='Nb'
|
||||
else if(mass_is_equal(smass,95.96d0)) then
|
||||
species='Mo'
|
||||
else if(mass_is_equal(smass,98.906d0)) then
|
||||
species='Tc'
|
||||
else if(mass_is_equal(smass,101.07d0)) then
|
||||
species='Ru'
|
||||
else if(mass_is_equal(smass,102.90550d0)) then
|
||||
species='Rh'
|
||||
else if(mass_is_equal(smass,106.42d0)) then
|
||||
species='Pd'
|
||||
else if(mass_is_equal(smass,107.8682d0)) then
|
||||
species='Ag'
|
||||
else if(mass_is_equal(smass,112.411d0)) then
|
||||
species='Cd'
|
||||
else if(mass_is_equal(smass,114.818d0)) then
|
||||
species='In'
|
||||
else if(mass_is_equal(smass,118.71d0)) then
|
||||
species='Sn'
|
||||
else if(mass_is_equal(smass,121.76d0)) then
|
||||
species='Sb'
|
||||
else if(mass_is_equal(smass,127.60d0)) then
|
||||
species='Te'
|
||||
else if(mass_is_equal(smass,126.90447d0)) then
|
||||
species='I'
|
||||
else if(mass_is_equal(smass,131.293d0)) then
|
||||
species='Xe'
|
||||
!
|
||||
! n=6
|
||||
else if(mass_is_equal(smass,132.9054519d0)) then
|
||||
species='Cs'
|
||||
else if(mass_is_equal(smass,137.327d0)) then
|
||||
species='Ba'
|
||||
! Lanthanides
|
||||
else if(mass_is_equal(smass,138.90547d0)) then
|
||||
species='La'
|
||||
else if(mass_is_equal(smass,140.116d0)) then
|
||||
species='Ce'
|
||||
else if(mass_is_equal(smass,140.90765d0)) then
|
||||
species='Pr'
|
||||
else if(mass_is_equal(smass,144.242d0)) then
|
||||
species='Nd'
|
||||
else if(mass_is_equal(smass,144.91d0)) then
|
||||
species='Pm'
|
||||
else if(mass_is_equal(smass,150.36d0)) then
|
||||
species='Sm'
|
||||
else if(mass_is_equal(smass,151.964d0)) then
|
||||
species='Eu'
|
||||
else if(mass_is_equal(smass,157.25d0)) then
|
||||
species='Gd'
|
||||
else if(mass_is_equal(smass,158.92535d0)) then
|
||||
species='Tb'
|
||||
else if(mass_is_equal(smass,162.50d0)) then
|
||||
species='Dy'
|
||||
else if(mass_is_equal(smass,164.93032d0)) then
|
||||
species='Ho'
|
||||
else if(mass_is_equal(smass,167.259d0)) then
|
||||
species='Er'
|
||||
else if(mass_is_equal(smass,168.93421d0)) then
|
||||
species='Tm'
|
||||
else if(mass_is_equal(smass,173.054d0)) then
|
||||
species='Yb'
|
||||
else if(mass_is_equal(smass,174.9668d0)) then
|
||||
species='Lu'
|
||||
! End of Lanthanides
|
||||
else if(mass_is_equal(smass,178.49d0)) then
|
||||
species='Hf'
|
||||
else if(mass_is_equal(smass,180.94788d0)) then
|
||||
species='Ta'
|
||||
else if(mass_is_equal(smass,183.84d0)) then
|
||||
species='W'
|
||||
else if(mass_is_equal(smass,186.207d0)) then
|
||||
species='Re'
|
||||
else if(mass_is_equal(smass,190.23d0)) then
|
||||
species='Os'
|
||||
else if(mass_is_equal(smass,192.217d0)) then
|
||||
species='Ir'
|
||||
else if(mass_is_equal(smass,195.084d0)) then
|
||||
species='Pt'
|
||||
else if(mass_is_equal(smass,196.966569d0)) then
|
||||
species='Au'
|
||||
else if(mass_is_equal(smass,200.59d0)) then
|
||||
species='Hg'
|
||||
else if(mass_is_equal(smass,204.38d0)) then
|
||||
species='Tl'
|
||||
else if(mass_is_equal(smass,207.2d0)) then
|
||||
species='Pb'
|
||||
else if(mass_is_equal(smass,208.9804d0)) then
|
||||
species='Bi'
|
||||
else if(mass_is_equal(smass,209.98d0)) then
|
||||
species='Po'
|
||||
else if(mass_is_equal(smass,209.99d0)) then
|
||||
species='At'
|
||||
else if(mass_is_equal(smass,222.02d0)) then
|
||||
species='Rn'
|
||||
!
|
||||
! n=7
|
||||
else if(mass_is_equal(smass,233.d0)) then
|
||||
species='Fr'
|
||||
else if(mass_is_equal(smass,226.d0)) then
|
||||
species='Ra'
|
||||
! Actinides
|
||||
else if(mass_is_equal(smass,227.d0)) then
|
||||
species='Ac'
|
||||
else if(mass_is_equal(smass,232.03806d0)) then
|
||||
species='Th'
|
||||
else if(mass_is_equal(smass,231.03588d0)) then
|
||||
species='Pa'
|
||||
else if(mass_is_equal(smass,238.02891d0)) then
|
||||
species='U'
|
||||
else if(mass_is_equal(smass,237.d0)) then
|
||||
species='Np'
|
||||
else if(mass_is_equal(smass,244.d0)) then
|
||||
species='Pu'
|
||||
else if(mass_is_equal(smass,243.d0)) then
|
||||
species='Am'
|
||||
else if(mass_is_equal(smass,247.d0)) then
|
||||
species='Cm'
|
||||
else if(mass_is_equal(smass,247.d0)) then
|
||||
species='Bk'
|
||||
else if(mass_is_equal(smass,251.d0)) then
|
||||
species='Cf'
|
||||
else if(mass_is_equal(smass,252.d0)) then
|
||||
species='Es'
|
||||
else if(mass_is_equal(smass,257.d0)) then
|
||||
species='Fm'
|
||||
else if(mass_is_equal(smass,258.d0)) then
|
||||
species='Md'
|
||||
else if(mass_is_equal(smass,259.d0)) then
|
||||
species='No'
|
||||
else if(mass_is_equal(smass,262.d0)) then
|
||||
species='Lr'
|
||||
! End of actinides
|
||||
else if(mass_is_equal(smass,265.d0)) then
|
||||
species='Rf'
|
||||
else if(mass_is_equal(smass,268.d0)) then
|
||||
species='Db'
|
||||
else if(mass_is_equal(smass,271.d0)) then
|
||||
species='Sg'
|
||||
else if(mass_is_equal(smass,270.d0)) then
|
||||
species='Bh'
|
||||
else if(mass_is_equal(smass,277.d0)) then
|
||||
species='Hs'
|
||||
else if(mass_is_equal(smass,276.d0)) then
|
||||
species='Mt'
|
||||
else if(mass_is_equal(smass,281.d0)) then
|
||||
species='Ds'
|
||||
else if(mass_is_equal(smass,280.d0)) then
|
||||
species='Rg'
|
||||
else if(mass_is_equal(smass,285.17d0)) then
|
||||
species='Cn'
|
||||
else if(mass_is_equal(smass,284.d0)) then
|
||||
species='Uu'
|
||||
else if(mass_is_equal(smass,289.d0)) then
|
||||
species='Fl'
|
||||
else if(mass_is_equal(smass,288.d0)) then
|
||||
species='Mc'
|
||||
else if(mass_is_equal(smass,293.d0)) then
|
||||
species='Lv'
|
||||
else if(mass_is_equal(smass,294.d0)) then
|
||||
species='Ts'
|
||||
else if(mass_is_equal(smass,294.d0)) then
|
||||
species='Og'
|
||||
!
|
||||
end if
|
||||
end subroutine realatomspecies
|
||||
END MODULE atoms
|
||||
|
||||
@ -14,7 +14,7 @@ module elements
|
||||
integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:), tag_ele(:) !Element size
|
||||
real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
|
||||
!Element result data structures
|
||||
real(kind=dp), allocatable :: force_node(:,:,:,:), virial_node(:,:,:,:), energy_node(:,:,:)
|
||||
real(kind=dp), allocatable :: force_node(:,:,:,:), virial_node(:,:,:,:), energy_node(:,:,:), vel_node(:,:,:,:)
|
||||
|
||||
integer, save :: ele_num !Number of elements
|
||||
integer, save :: node_num !Total number of nodes
|
||||
@ -26,7 +26,7 @@ module elements
|
||||
real(kind =dp),allocatable :: r_atom(:,:) !atom position
|
||||
integer :: atom_num=0 !Number of atoms
|
||||
!Atom result data structures information
|
||||
real(kind=8), allocatable :: force_atom(:,:), virial_atom(:,:), energy_atom(:)
|
||||
real(kind=8), allocatable :: force_atom(:,:), virial_atom(:,:), energy_atom(:), vel_atom(:,:)
|
||||
|
||||
!Mapping atom type to provided name
|
||||
character(len=2), dimension(10) :: type_to_name
|
||||
@ -42,7 +42,7 @@ module elements
|
||||
integer :: lattice_types = 0
|
||||
integer :: max_ng_node, ng_node(10) !Max number of nodes per element and number of nodes per element for each lattice type
|
||||
integer :: max_esize=0 !Maximum number of atoms per side of element
|
||||
real(kind=dp) :: lapa(10)
|
||||
real(kind=dp) :: lapa(10), masses(10)
|
||||
|
||||
!These variables contain information on the basis, for simplicities sake we limit
|
||||
!the user to the definition of 10 lattice types with 10 basis atoms at each lattice point.
|
||||
@ -919,7 +919,6 @@ do i = 1, atom_num
|
||||
integer, intent(in) :: n,m !n-size of element arrays, m-size of atom arrays
|
||||
integer :: allostat
|
||||
|
||||
print *, max_ng_node
|
||||
!Allocate element arrays
|
||||
if (n > 0) then
|
||||
if (allocated(force_node)) then
|
||||
@ -952,6 +951,38 @@ do i = 1, atom_num
|
||||
|
||||
end subroutine
|
||||
|
||||
subroutine alloc_vel_arrays(n,m)
|
||||
!This subroutine used to provide initial allocation for the atom and element data arrays
|
||||
integer, intent(in) :: n,m !n-size of element arrays, m-size of atom arrays
|
||||
integer :: allostat
|
||||
|
||||
!Allocate element arrays
|
||||
if (n > 0) then
|
||||
if (allocated(vel_node)) then
|
||||
deallocate(vel_node)
|
||||
end if
|
||||
allocate(vel_node(3,max_basisnum,max_ng_node,n), stat=allostat)
|
||||
if(allostat > 0) then
|
||||
print *, "Error allocating element data arrays in mode_metric because of:", allostat
|
||||
stop
|
||||
end if
|
||||
|
||||
end if
|
||||
|
||||
if (m > 0) then
|
||||
if (allocated(vel_atom)) then
|
||||
deallocate(vel_atom)
|
||||
end if
|
||||
allocate(vel_atom(3,m), stat=allostat)
|
||||
if(allostat > 0) then
|
||||
print *, "Error allocating atom data arrays in mode_metric because of:", allostat
|
||||
stop
|
||||
end if
|
||||
end if
|
||||
|
||||
end subroutine alloc_vel_arrays
|
||||
|
||||
|
||||
subroutine add_atom_data(ia, eng, force, virial)
|
||||
!Function which sets the atom data arrays
|
||||
integer, intent(in) :: ia
|
||||
|
||||
@ -254,6 +254,19 @@ END FUNCTION StrDnCase
|
||||
return
|
||||
end function is_equal
|
||||
|
||||
function mass_is_equal(A, B)
|
||||
!This function checks if too numbers are equal within a tolerance
|
||||
real(kind=dp), intent(in) :: A, B
|
||||
logical :: mass_is_equal
|
||||
|
||||
if((A>(B - 10.0_dp**(-2))).and.(A < (B+10.0_dp**(-2)))) then
|
||||
mass_is_equal = .true.
|
||||
else
|
||||
mass_is_equal = .false.
|
||||
end if
|
||||
return
|
||||
end function mass_is_equal
|
||||
|
||||
pure function unitvec(n,vec)
|
||||
integer, intent(in) :: n
|
||||
real(kind=dp), intent(in) :: vec(n)
|
||||
|
||||
130
src/io.f90
130
src/io.f90
@ -520,6 +520,8 @@ module io
|
||||
12 format('coarse-grained domain')
|
||||
13 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z')
|
||||
14 format('atomistic domain' / 'ia type_atom x y z')
|
||||
15 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z velx vely velz')
|
||||
16 format('atomistic domain' / 'ia type_atom x y z velx vely velz')
|
||||
19 format('max nodes per element and basis per nodes' / 2i16)
|
||||
20 format('max interpo per element' / i16)
|
||||
21 format('atom types to elements')
|
||||
@ -562,7 +564,11 @@ module io
|
||||
if(ele_num > 0) then
|
||||
write(11,12)
|
||||
ip = 0
|
||||
write(11,13)
|
||||
if(allocated(vel_node)) then
|
||||
write(11,15)
|
||||
else
|
||||
write(11,13)
|
||||
end if
|
||||
do i = 1, ele_num
|
||||
select case(type_ele(i))
|
||||
case('fcc','bcc')
|
||||
@ -570,21 +576,38 @@ module io
|
||||
case('20fcc')
|
||||
write(11, '(4i16)') i, basisnum(lat_ele(i)), 3, (size_ele(i)-1)
|
||||
end select
|
||||
do inod = 1, ng_node(lat_ele(i))
|
||||
do ibasis = 1, basisnum(lat_ele(i))
|
||||
ip = ip + 1
|
||||
write(11, '(3i16, 3f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i)
|
||||
if(allocated(vel_node)) then
|
||||
do inod = 1, ng_node(lat_ele(i))
|
||||
do ibasis = 1, basisnum(lat_ele(i))
|
||||
ip = ip + 1
|
||||
write(11, '(3i16, 6f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i), &
|
||||
vel_node(:,ibasis,inod,i)
|
||||
end do
|
||||
end do
|
||||
end do
|
||||
else
|
||||
do inod = 1, ng_node(lat_ele(i))
|
||||
do ibasis = 1, basisnum(lat_ele(i))
|
||||
ip = ip + 1
|
||||
write(11, '(3i16, 3f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i)
|
||||
end do
|
||||
end do
|
||||
end if
|
||||
end do
|
||||
end if
|
||||
|
||||
!Now write the atomic information
|
||||
if(atom_num /= 0) then
|
||||
write(11,14)
|
||||
do i = 1, atom_num
|
||||
write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
|
||||
end do
|
||||
if(allocated(vel_atom)) then
|
||||
write(11, 16)
|
||||
do i = 1, atom_num
|
||||
write(11, '(2i16, 6f23.15)') i, type_atom(i), r_atom(:,i), vel_atom(:, i)
|
||||
end do
|
||||
else
|
||||
write(11,14)
|
||||
do i = 1, atom_num
|
||||
write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
|
||||
end do
|
||||
end if
|
||||
end if
|
||||
|
||||
close(11)
|
||||
@ -730,9 +753,10 @@ module io
|
||||
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
|
||||
|
||||
integer :: i, j, k, l, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
|
||||
new_type_to_type(10), new_lattice_types, sbox, new_lattice_map(10)
|
||||
new_type_to_type(10), new_lattice_types, sbox, 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)
|
||||
real(kind=dp) :: r(3), newdisplace(3), lapa_map(10)
|
||||
real(kind=dp), allocatable :: r_innode(:,:,:)
|
||||
character(len = 2) :: new_type_to_name(10)
|
||||
!First open the file
|
||||
@ -782,45 +806,29 @@ module io
|
||||
call add_atom_type(new_type_to_name(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, (basisnum(i), i = lattice_types+1, lattice_types+new_lattice_types), &
|
||||
(ng_node(i), i = lattice_types+1, lattice_types+new_lattice_types)
|
||||
!Define max_ng_node and max_basis_num
|
||||
max_basisnum = maxval(basisnum)
|
||||
max_ng_node = maxval(ng_node)
|
||||
read(11,*) new_lattice_types, (bnum_map(i), i = 1, new_lattice_types),(node_map(i), i =1, new_lattice_types)
|
||||
!Read the basis atom types for every lattice
|
||||
read(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = lattice_types+1, lattice_types+new_lattice_types)
|
||||
read(11,*) ((btype_map(i,j), i = 1, bnum_map(j)), j = 1, new_lattice_types)
|
||||
!Convert the basis_atom types
|
||||
do j = lattice_types+1, lattice_types+new_lattice_types
|
||||
do i = 1, basisnum(j)
|
||||
basis_type(i,j) = new_type_to_type(basis_type(i,j))
|
||||
do j =1, new_lattice_types
|
||||
do i = 1, bnum_map(j)
|
||||
btype_map(i,j) = new_type_to_type(btype_map(i,j))
|
||||
end do
|
||||
end do
|
||||
!Read the lattice parameters for every lattice type
|
||||
read(11,*) (lapa(i), i = lattice_types+1, lattice_types+new_lattice_types)
|
||||
read(11,*) (lapa_map(i), i = 1, new_lattice_types)
|
||||
|
||||
!Now we loop over all new lattice types and check to see if they are exactly the same as any old lattice types
|
||||
!If they are then we map the new type to the old type.
|
||||
k = lattice_types + 1
|
||||
new_lattice_map(:) = 0
|
||||
new_loop:do i = 1, new_lattice_types
|
||||
old_loop:do j = 1, lattice_types
|
||||
!First check all the lattice level variables
|
||||
if ((basisnum(lattice_types + i) == basisnum(j)).and. &
|
||||
(ng_node(lattice_types + i) == ng_node(j))) then
|
||||
!Now check the basis level variables
|
||||
do ibasis =1, basisnum(i)
|
||||
if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then
|
||||
cycle old_loop
|
||||
end if
|
||||
end do
|
||||
new_lattice_map(i) = j
|
||||
cycle new_loop
|
||||
end if
|
||||
end do old_loop
|
||||
new_lattice_map(i) = k
|
||||
k = k+1
|
||||
call lattice_map(bnum_map(i), btype_map(:,i), node_map(i), lapa_map(i), new_lattice_map(i))
|
||||
end do new_loop
|
||||
|
||||
!Define max_ng_node and max_basis_num
|
||||
max_basisnum = maxval(basisnum)
|
||||
max_ng_node = maxval(ng_node)
|
||||
|
||||
!Read number of elements and atoms and allocate arrays
|
||||
read(11, *) in_atoms, in_eles
|
||||
call grow_ele_arrays(in_eles, in_atoms)
|
||||
@ -909,7 +917,7 @@ module io
|
||||
!Read define atom_types by mass
|
||||
print *, j
|
||||
do i = 1, j
|
||||
call atommassspecies(atomic_masses(i), atomic_element)
|
||||
call realatomspecies(atomic_masses(i), atomic_element)
|
||||
call add_atom_type(atomic_element, atom_type_map(i), all_new)
|
||||
print *, i, atom_type_map(i)
|
||||
end do
|
||||
@ -1009,13 +1017,15 @@ module io
|
||||
!Internal Variables
|
||||
integer :: i, j, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
|
||||
id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip, atom_type_map(100)
|
||||
real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), &
|
||||
ee(10,20), fe(3,10,20), ve(6,10,20), re(3,10,20), atomic_masses(10)
|
||||
real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), vela(3),&
|
||||
ee(10,20), fe(3,10,20), ve(6,10,20), re(3,10,20), vele(3,10,20), atomic_masses(10)
|
||||
character(len=100) :: textholder, fcc
|
||||
character(len=1000) :: line
|
||||
character(len=2) :: atomic_element
|
||||
logical :: read_vel
|
||||
|
||||
|
||||
read_vel =.false.
|
||||
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
|
||||
|
||||
!Now initialize some important variables if they aren't defined
|
||||
@ -1063,7 +1073,7 @@ module io
|
||||
|
||||
!Read define atom_types by mass
|
||||
do i = 1, j
|
||||
call atommassspecies(atomic_masses(i), atomic_element)
|
||||
call realatomspecies(atomic_masses(i), atomic_element)
|
||||
call add_atom_type(atomic_element, atom_type_map(i), all_new)
|
||||
end do
|
||||
|
||||
@ -1077,12 +1087,22 @@ module io
|
||||
|
||||
if(in_atoms > 0 ) then
|
||||
!Read atom header
|
||||
read(11,*) textholder
|
||||
read(11,'(a)') line
|
||||
read(line, *) (textholder, i=1, 18)
|
||||
if(textholder=="velx") then
|
||||
call alloc_vel_arrays(in_eles, in_atoms)
|
||||
read_vel = .true.
|
||||
end if
|
||||
do ia = 1, in_atoms
|
||||
read(11,'(a)') line(:)
|
||||
read(line,*) tag, type, ra(:), ea, fa(:), va(:)
|
||||
if(read_vel) then
|
||||
read(line,*) tag, type, ra(:), ea, fa(:), va(:), vela(:)
|
||||
else
|
||||
read(line,*) tag, type, ra(:), ea, fa(:), va(:)
|
||||
end if
|
||||
call add_atom(tag, atom_type_map(type), sub_box_num, ra)
|
||||
call add_atom_data(atom_num, ea, fa, va)
|
||||
if(read_vel) vel_atom(:,atom_num) = vela
|
||||
end do
|
||||
|
||||
end if
|
||||
@ -1096,9 +1116,16 @@ module io
|
||||
do ie =1, in_eles
|
||||
read(11,*) tag, n, bnum, esize
|
||||
inbtypes(:) = 0
|
||||
do inod =1, n*bnum
|
||||
read(11,*) ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), ve(:,ibasis,ip)
|
||||
end do
|
||||
if(read_vel) then
|
||||
do inod =1, n*bnum
|
||||
read(11,*) ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), &
|
||||
ve(:,ibasis,ip), vele(:,ibasis,ip)
|
||||
end do
|
||||
else
|
||||
do inod =1, n*bnum
|
||||
read(11,*) ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), ve(:,ibasis,ip)
|
||||
end do
|
||||
end if
|
||||
do i = 1, bnum
|
||||
inbtypes(ibasis) = atom_type_map(inbtypes(ibasis))
|
||||
end do
|
||||
@ -1110,11 +1137,12 @@ module io
|
||||
end if
|
||||
call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
|
||||
call add_element_data(ele_num, ee, fe, ve)
|
||||
if(read_vel) vel_node(:, :, :, ele_num) = vele(:,1:max_basisnum, 1:max_ng_node)
|
||||
end do
|
||||
end if
|
||||
call set_max_esize
|
||||
return
|
||||
end subroutine
|
||||
end subroutine read_pycac_out
|
||||
|
||||
subroutine read_lmp(file, displace, temp_box_bd)
|
||||
!This subroutine is used to read .cac files which are used with the lammpsCAC format
|
||||
@ -1184,7 +1212,7 @@ module io
|
||||
!Read atomic masses
|
||||
do i = 1, type_in
|
||||
read(11,*) j, mass
|
||||
call ATOMMASSSPECIES(mass, atom_species)
|
||||
call realatomspecies(mass, atom_species)
|
||||
call add_atom_type(atom_species, type_map(i), all_new)
|
||||
end do
|
||||
|
||||
@ -1272,7 +1300,7 @@ module io
|
||||
!Read atomic masses
|
||||
do i = 1, type_in
|
||||
read(11,*) j, mass, textholder
|
||||
call ATOMMASSSPECIES(mass, atom_species)
|
||||
call realatomspecies(mass, atom_species)
|
||||
call add_atom_type(atom_species, type_map(i), all_new)
|
||||
end do
|
||||
|
||||
|
||||
@ -402,7 +402,7 @@ module opt_group
|
||||
|
||||
!Choose what to based on what the option string is
|
||||
select case(trim(textholder))
|
||||
case('displace')
|
||||
case('shift')
|
||||
displace = .true.
|
||||
do i = 1,3
|
||||
arg_pos = arg_pos + 1
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user