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https://github.com/TREX-CoE/fparser.git
synced 2024-11-03 20:54:11 +01:00
inline reading of molecule coordinates works
This commit is contained in:
Ravindra Shinde
parent
07e5166d14
commit
dafa315545
209
src/iochamp.f90
209
src/iochamp.f90
@ -81,6 +81,9 @@ PROGRAM iochamp
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phonon_energy = fdf_physical('phonon-energy', 0.01d0, 'eV')
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write(6,fmt=real_format) 'Phonon Energy:', phonon_energy
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write(6,'(A)')
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write(6,*) '------------------------------------------------------'
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! block containing other key-value pairs (currently not working)
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@ -115,6 +118,9 @@ PROGRAM iochamp
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enddo
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endif
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write(6,'(A)')
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write(6,*) '------------------------------------------------------'
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@ -131,39 +137,47 @@ PROGRAM iochamp
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write(6,*) 'outside optimize_orbitals:', doit
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max_iter = fdf_integer('max_iteration', 100)
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write(6,*) 'Examples: maximum_iter =', max_iter
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if (fdf_defined('molecule')) then
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write(6,*) "molecule block has been defined :: molecule's geometry in angstrom units"
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! molecule_name = fdf_string('molecule', 'h2o.xyz')
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! write(6,*) 'Name of xyz file:', molecule_name
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na = 24 ! debug
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if (fdf_block('molecule', bfdf)) then
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ia = 1
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do while(fdf_bline(bfdf, pline))
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! na = fdf_bintegers(pline, 1)
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! write(*,*) na
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symbol(ia) = fdf_bnames(pline, 1)
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do i= 1, 3
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xa(i,ia) = fdf_breals(pline, i)
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enddo
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ia = ia + 1
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enddo
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na = ia - 1
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endif
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endif
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write(6,*) 'Coordinates from an external file:'
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do ia = 1, 24
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write(6,'(A, 4x, 3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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enddo
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write(6,'(A)')
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write(6,*) '------------------------------------------------------'
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! if (fdf_defined('molecule')) then
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! write(6,*) "molecule block has been defined :: molecule's geometry in angstrom units"
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! ! molecule_name = fdf_string('molecule', 'h2o.xyz')
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! ! write(6,*) 'Name of xyz file:', molecule_name
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! na = 24 ! debug
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! if (fdf_block('molecule', bfdf)) then
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! ia = 1
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! do while(fdf_bline(bfdf, pline))
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! ! na = fdf_bintegers(pline, 1)
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! ! write(*,*) na
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! symbol(ia) = fdf_bnames(pline, 1)
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! do i= 1, 3
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! xa(i,ia) = fdf_breals(pline, i)
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! enddo
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! ia = ia + 1
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! enddo
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! na = ia - 1
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! endif
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! endif
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! write(6,*) 'Coordinates from an external file:'
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! do ia = 1, 24
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! write(6,'(A, 4x, 3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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! enddo
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write(6,'(A)')
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write(6,*) '------------------------------------------------------'
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! Molecule coordinate block begins here
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@ -185,10 +199,14 @@ PROGRAM iochamp
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enddo
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! Molecule coordinate block ends here
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write(6,*) '------------------------------------------------------'
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write(6,'(A)')
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write(6,*) '------------------------------------------------------'
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if (fdf_block('Other-Block', bfdf)) then
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if (fdf_block('inline_xyz', bfdf)) then
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! Forward reading
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write(6,*) 'beginning of other block '
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ia = 1
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@ -200,7 +218,13 @@ PROGRAM iochamp
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number_of_atoms = fdf_bintegers(pline, 1)
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write(*,*) "number of atoms", number_of_atoms
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endif
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na = 3
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na = number_of_atoms
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if (pline%ntokens == 1) then
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molecule_name = fdf_string('', 'Unknown molecule')
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write(*,*) "Comment from the XYZ coordinate file", molecule_name
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endif
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if (pline%ntokens == 4) then
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symbol(ia) = fdf_bnames(pline, 1)
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do i= 1, na
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@ -210,73 +234,78 @@ PROGRAM iochamp
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endif
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enddo
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write(6,*) 'Other-Block (Forward):'
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do ia= 1, na
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write(6,'(A4,3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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enddo
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! Backward reading
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ia = 1
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do while((fdf_bbackspace(bfdf, pline)) .and. (ia .le. na))
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symbol(ia) = fdf_bnames(pline, 1)
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do i= 1, na
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xa(i,ia) = fdf_breals(pline, i)
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enddo
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ia = ia + 1
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enddo
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write(6,*) 'Other-Block (Backward):'
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do ia= 1, na
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write(6,'(A4,3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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enddo
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! Forward reading
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ia = 1
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do while((fdf_bline(bfdf, pline)) .and. (ia .le. na))
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symbol(ia) = fdf_bnames(pline, 1)
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do i= 1, na
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xa(i,ia) = fdf_breals(pline, i)
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enddo
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ia = ia + 1
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enddo
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write(6,*) 'Other-Block (Forward):'
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do ia= 1, na
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write(6,'(A4,3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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enddo
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! Forward reading with rewind
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call fdf_brewind(bfdf)
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ia = 1
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do while((fdf_bline(bfdf, pline)) .and. (ia .le. na))
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symbol(ia) = fdf_bnames(pline, 1)
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do i= 1, na
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xa(i,ia) = fdf_breals(pline, i)
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enddo
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ia = ia + 1
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enddo
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write(6,*) 'Other-Block (Forward-with-rewind):'
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write(6,*) 'Inline XYZ Coordinates block:'
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do ia= 1, na
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write(6,'(A4,3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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enddo
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endif
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if ( fdf_block('ListBlock',bfdf) ) then
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i = 0
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do while ( fdf_bline(bfdf,pline) )
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i = i + 1
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na = fdf_bnlists(pline)
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write(*,'(2(a,i0),a)') 'Listblock line: ',i,' has ',na,' lists'
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do ia = 1 , na
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j = -1
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call fdf_bilists(pline,ia,j,isa)
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write(*,'(tr5,2(a,i0),a)') 'list ',ia,' has ',j,' entries'
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call fdf_bilists(pline,ia,j,isa)
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write(*,'(tr5,a,1000(tr1,i0))') 'list: ',isa(1:j)
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end do
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end do
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end if
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! ! Backward reading
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! ia = 1
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! do while((fdf_bbackspace(bfdf, pline)) .and. (ia .le. na))
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! symbol(ia) = fdf_bnames(pline, 1)
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! do i= 1, na
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! xa(i,ia) = fdf_breals(pline, i)
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! enddo
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! ia = ia + 1
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! enddo
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! write(6,*) 'Other-Block (Backward):'
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! do ia= 1, na
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! write(6,'(A4,3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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! enddo
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! ! Forward reading
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! ia = 1
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! do while((fdf_bline(bfdf, pline)) .and. (ia .le. na))
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! symbol(ia) = fdf_bnames(pline, 1)
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! do i= 1, na
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! xa(i,ia) = fdf_breals(pline, i)
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! enddo
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! ia = ia + 1
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! enddo
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! write(6,*) 'Other-Block (Forward):'
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! do ia= 1, na
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! write(6,'(A4,3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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! enddo
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! ! Forward reading with rewind
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! call fdf_brewind(bfdf)
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! ia = 1
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! do while((fdf_bline(bfdf, pline)) .and. (ia .le. na))
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! symbol(ia) = fdf_bnames(pline, 1)
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! do i= 1, na
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! xa(i,ia) = fdf_breals(pline, i)
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! enddo
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! ia = ia + 1
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! enddo
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! write(6,*) 'Other-Block (Forward-with-rewind):'
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! do ia= 1, na
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! write(6,'(A4,3F10.6)') symbol(ia), (xa(i,ia),i=1,3)
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! enddo
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! if ( fdf_block('ListBlock',bfdf) ) then
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! i = 0
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! do while ( fdf_bline(bfdf,pline) )
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! i = i + 1
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! na = fdf_bnlists(pline)
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! write(*,'(2(a,i0),a)') 'Listblock line: ',i,' has ',na,' lists'
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! do ia = 1 , na
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! j = -1
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! call fdf_bilists(pline,ia,j,isa)
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! write(*,'(tr5,2(a,i0),a)') 'list ',ia,' has ',j,' entries'
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! call fdf_bilists(pline,ia,j,isa)
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! write(*,'(tr5,a,1000(tr1,i0))') 'list: ',isa(1:j)
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! end do
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! end do
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! end if
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! Check lists
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if ( fdf_islinteger('MyList') .and. fdf_islist('MyList') &
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@ -33,20 +33,6 @@ energy_tol 0.004
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%endblock
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# Read molecule's geometry directly from the xyz file
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%block molecule < "caffeine.xyz"
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%block Other-Block
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99
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Nh 1.500000 1.108000 -3.000000
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Ox 0.333000 0.000000 45.000000
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Pd -1.431000 -1.108000 20.000000
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%endblock Other-Block
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# An alternative way to provide coordinates
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%block Coordinates
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@ -66,14 +52,18 @@ energy_tol 0.004
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# %include pool/BFD-T.bfinfo
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%block inline_xyz
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3
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molecule name unknown
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Nh 1.50 1.108000 -3.
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Ox 0.333000 0. 45.
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Pd -1.431000 -1.108000 20.
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%endblock inline_xyz
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### To be implemented (large file reading support, possibly hdf5 files)
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#%include TZ_1M_500.det
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#%include jastrow_good_b3lyp.0
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### Read molecule's geometry directly from the xyz file
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### %block molecule < "caffeine.xyz"
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