Merge pull request #6 from aselimov/ft-write-lammpscac
Ft write lammpscac
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aselimov
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889edfd314
@ -1,6 +1,7 @@
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FC=ifort
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#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
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FFLAGS=-mcmodel=large -Ofast
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FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
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#FFLAGS=-mcmodel=large -Ofast
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MODES=mode_create.o mode_merge.o mode_convert.o
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OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES)
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@ -8,7 +9,7 @@ OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box
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.SUFFIXES: .c .f .f90 .F90 .o
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cacmb: $(OBJECTS)
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$(FC) $(FFLAGS) $(OBJECTS) -o $@
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$(FC) $(FFLAGS) $(OBJECTS) parameters.o -o $@
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.f90.o:
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$(FC) $(FFLAGS) -c $<
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@ -30,4 +31,4 @@ main.o io.o build_subroutines.o: elements.o
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call_mode.o : $(MODES)
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$(MODES) io.o: atoms.o box.o
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$(MODES) main.o : io.o
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testfuncs.o elements.o mode_create.o: subroutines.o
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testfuncs.o elements.o mode_create.o: subroutines.o
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@ -101,10 +101,28 @@ module elements
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real(kind=dp), dimension(3,max_ng_node), intent(out) :: cell_mat
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integer :: inod, i
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real(kind=dp), dimension(3,max_ng_node) :: adjustVar
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adjustVar(:,:) = 0.0_dp
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select case(trim(ele_type))
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case('fcc')
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cell_mat(:,1:8) = lapa * ((esize-1)*matmul(orient_mat, fcc_cell))
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if(lmpcac) then
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do inod = 1, 8
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do i = 1,3
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if(is_equal(cubic_cell(i, inod),0.0_dp)) then
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adjustVar(i,inod) = -0.5_dp
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else
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adjustVar(i, inod) = 0.5_dp
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end if
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end do
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end do
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adjustVar(:,1:8) = matmul(fcc_mat, adjustVar(:,1:8))
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end if
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cell_mat(:, 1:8) = fcc_cell + adjustVar(:,1:8)
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cell_mat(:,1:8) = lapa * ((esize-1)*matmul(orient_mat, cell_mat(:,1:8)))
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case default
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print *, "Element type ", trim(ele_type), " currently not accepted"
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stop
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82
src/io.f90
82
src/io.f90
@ -9,6 +9,7 @@ module io
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integer :: outfilenum = 0, infilenum = 0
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character(len=100) :: outfiles(10), infiles(10)
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public
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contains
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@ -62,9 +63,14 @@ module io
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outfilenum=outfilenum+1
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outfiles(outfilenum) = temp_outfile
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exit
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case('cac')
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lmpcac = .true.
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outfilenum=outfilenum+1
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outfiles(outfilenum) = temp_outfile
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exit
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case default
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print *, "File type: ", trim(temp_outfile(scan(temp_outfile,'.',.true.):)), "not currently accepted. ", &
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"please input a filename with extension from following list: xyz, lmp, vtk."
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print *, "File type: ", trim(temp_outfile(scan(temp_outfile,'.',.true.):)), " not currently accepted. ", &
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"please input a filename with extension from following list: xyz, lmp, vtk, cac."
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read(*,*) temp_outfile
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end select
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@ -72,7 +78,6 @@ module io
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end subroutine get_out_file
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subroutine write_out
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!This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
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@ -94,6 +99,8 @@ module io
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call write_mb(outfiles(i))
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case('restart')
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call write_pycac(outfiles(i))
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case('cac')
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call write_lmpcac(outfiles(i))
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case default
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print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
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" is not accepted for writing. Please select from: xyz and try again"
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@ -193,6 +200,71 @@ module io
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end do
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end subroutine write_lmp
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subroutine write_lmpcac(file)
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!This subroutine writes out a .lmp style dump file
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character(len=100), intent(in) :: file
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integer :: write_num, i, inod, ibasis
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real(kind=dp) :: mass
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1 format(i16, ' Eight_Node', 4i16)
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2 format(i16, ' Atom', 4i16)
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3 format(3i16,3f23.15)
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open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
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!Comment line
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write(11, '(a)') '# CAC input file made with cacmb'
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write(11, '(a)')
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!Calculate total atom number
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write_num = atom_num + ele_num
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!Write total number of atoms + elements
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write(11, '(i16, a)') write_num, ' cac elements'
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!Write number of atom types
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write(11, '(i16, a)') atom_types, ' atom types'
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write(11,'(a)') ' '
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!Write box bd
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write(11, '(2f23.15, a)') box_bd(1:2), ' xlo xhi'
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write(11, '(2f23.15, a)') box_bd(3:4), ' ylo yhi'
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write(11, '(2f23.15, a)') box_bd(5:6), ' zlo zhi'
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!Masses
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write(11, '(a)') 'Masses'
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write(11, '(a)') ' '
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do i =1, atom_types
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call atommass(type_to_name(i),mass)
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write(11, '(i16, f23.15, 2a)') i, mass, ' # ', type_to_name(i)
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end do
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write(11, '(a)') ' '
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write(11, '(a)') 'CAC Elements'
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write(11, '(a)') ' '
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!Write element nodal positions
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do i = 1, ele_num
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select case(trim(adjustl(type_ele(i))))
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case('fcc')
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!The first entry is the element specifier
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write(11,1) i, basisnum(lat_ele(i)), size_ele(i), size_ele(i), size_ele(i)
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do ibasis = 1, basisnum(lat_ele(i))
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do inod = 1, 8
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!Nodal information for every node
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write(11,3) inod, ibasis, basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i)
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end do
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end do
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end select
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end do
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do i = 1, atom_num
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!Element specifier dictating that it is an atom
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write(11,2) ele_num+i, 1, 1, 1, 1
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!Write the atomic information
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write(11,3) 1, 1, type_atom(i), r_atom(:,i)
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end do
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end subroutine write_lmpcac
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subroutine write_vtk(file)
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!This subroutine writes out a vtk style dump file
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integer :: i, j, inod, ibasis
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@ -249,7 +321,7 @@ module io
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do i = 1, ele_num
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do inod=1, ng_node(lat_ele(i))
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do ibasis = 1, basisnum(lat_ele(i))
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write(11, '(3f23.1)') sum(r_node(:,:,inod,i),2)/basisnum(lat_ele(i))
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write(11, '(3f23.15)') sum(r_node(:,:,inod,i),2)/basisnum(lat_ele(i))
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end do
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end do
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end do
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@ -601,4 +673,4 @@ module io
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!just overwrite the arrays
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if(in_eles > 0) lattice_types = lattice_types + new_lattice_types
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end subroutine read_mb
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end module io
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end module io
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11
src/main.f90
11
src/main.f90
@ -27,6 +27,17 @@ program main
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! Command line parsing
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arg_num = command_argument_count()
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!First check if we are writing out to lammpscac format by looping over all arguments
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do i = 1, arg_num
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call get_command_argument(i, argument)
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select case(argument(scan(argument,'.',.true.)+1:))
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case('cac')
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lmpcac = .true.
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case default
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continue
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end select
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end do
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!Determine if a mode is being used and what it is. The first argument has to be the mode
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!if a mode is being used
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call get_command_argument(1, argument)
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@ -12,7 +12,7 @@ module mode_create
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character(len=100) :: name, element_type
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real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
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orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3)
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orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3), adjustVar(3,8)
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integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
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basis_pos(3,10)
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logical :: dup_flag, dim_flag
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@ -299,7 +299,7 @@ module mode_create
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!Internal variables
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integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), &
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vlat(3), temp_lat(3,8), m, n, o
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real(kind=dp) :: v(3), temp_nodes(3,1,8)
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real(kind=dp) :: v(3), temp_nodes(3,1,8), adjustVar(3,8)
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real(kind=dp), allocatable :: resize_lat_array(:,:)
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logical, allocatable :: lat_points(:,:,:)
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logical :: node_in_bd(8)
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@ -307,6 +307,23 @@ module mode_create
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!Do some value initialization
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max_esize = esize
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!If we are writing out to lammpscac format then we have to adjust the nodal positions
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if(lmpcac) then
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do inod = 1, 8
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do i = 1,3
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if(is_equal(cubic_cell(i, inod),0.0_dp)) then
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adjustVar(i,inod) = -0.5_dp
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else
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adjustVar(i, inod) = 0.5_dp
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end if
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end do
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end do
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adjustVar(:,1:8) = matmul(orient,matmul(fcc_mat,adjustVar(:,1:8)))
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else
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adjustVar(:,:)=0.0_dp
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end if
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!First find the bounding lattice points (min and max points for the box in each dimension)
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numlatpoints = 1
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do i = 1, 3
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@ -324,7 +341,6 @@ module mode_create
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continue
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end select
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!Loop over all of lattice points within the boundary, we choose between two loops. One for the atomistic case
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!and one for the regular case
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if (esize==2) then
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@ -437,9 +453,11 @@ module mode_create
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end do
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if(all(node_in_bd)) then
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lat_ele_num = lat_ele_num+1
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r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
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lat_ele_num = lat_ele_num+1
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do inod = 1, 8
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r_lat(:,inod,lat_ele_num) = temp_nodes(:,1,inod) + adjustVar(:,inod)
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end do
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!Now set all the lattice points contained within an element to false
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do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
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do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))
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@ -505,4 +523,4 @@ module mode_create
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end subroutine error_message
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end module mode_create
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end module mode_create
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@ -5,4 +5,6 @@ module parameters
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integer, parameter :: dp= selected_real_kind(15,307)
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real(kind=dp), parameter :: lim_zero = epsilon(1.0_dp), &
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lim_large = huge(1.0_dp)
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logical, save :: lmpcac
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end module parameters
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