Working read from pycac.out file format
This commit is contained in:
Alex Selimov
parent
dadc1f7a4a
commit
5949f04103
@ -1,7 +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 -heap-arrays
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#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
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MODES=mode_create.o mode_merge.o mode_convert.o
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MODES=mode_create.o mode_merge.o mode_convert.o
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OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o opt_deform.o opt_redef_box.o
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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
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@ -1,4 +1,4 @@
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subroutine call_mode(arg_pos,mode)
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subroutine call_mode(arg_pos)
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!This code is used to parse the command line argument for the mode information and calls the required
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!mode module.
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@ -10,7 +10,6 @@ subroutine call_mode(arg_pos,mode)
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implicit none
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integer, intent(out) :: arg_pos
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character(len=100), intent(in) :: mode
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select case(mode)
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case('--create')
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@ -39,6 +39,8 @@ subroutine call_option(option, arg_pos)
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call run_delete(arg_pos)
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case('-set_cac')
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arg_pos=arg_pos +3
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case('-set_types')
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arg_pos = arg_pos + 3 + atom_types
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case('-redef_box')
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call redef_box(arg_pos)
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case default
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@ -13,6 +13,8 @@ module elements
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character(len=100), allocatable :: type_ele(:) !Element type
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integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:), tag_ele(:) !Element size
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real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
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!Element result data structures
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real(kind=8), allocatable :: force_node(:,:,:,:), virial_node(:,:,:,:), energy_node(:,:,:)
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integer, save :: ele_num !Number of elements
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integer, save :: node_num !Total number of nodes
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@ -22,6 +24,8 @@ module elements
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integer, allocatable :: sbox_atom(:), tag_atom(:)
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real(kind =dp),allocatable :: r_atom(:,:) !atom position
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integer :: atom_num=0 !Number of atoms
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!Atom result data structures information
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real(kind=8), allocatable :: force_atom(:,:), virial_atom(:,:), energy_atom(:)
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!Mapping atom type to provided name
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character(len=2), dimension(10) :: type_to_name
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@ -669,17 +673,17 @@ module elements
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esize = size_ele(ie)
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select case(iface)
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case(1)
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pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, -10.0_dp**-2.0_dp /)
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pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, -10.0_dp**(-2.0_dp) /)
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case(2)
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pos = (/ real(esize-1,dp)/2.0_dp, -10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp /)
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pos = (/ real(esize-1,dp)/2.0_dp, -10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp /)
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case(3)
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pos = (/ (esize-1)+10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
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pos = (/ (esize-1)+10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
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case(4)
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pos = (/ real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp /)
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pos = (/ real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp /)
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case(5)
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pos = (/ -10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
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pos = (/ -10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
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case(6)
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pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**-2.0_dp /)
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pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**(-2.0_dp) /)
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end select
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!Now transform it to real space and adjust it to the position of the element in the first node.
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@ -736,4 +740,57 @@ module elements
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end subroutine lattice_map
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subroutine alloc_dat_arrays(n,m)
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!This subroutine used to provide initial allocation for the atom and element data arrays
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integer, intent(in) :: n,m !n-size of element arrays, m-size of atom arrays
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integer :: allostat
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!Allocate element arrays
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if (n > 0) then
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allocate(force_node(3,max_basisnum, max_ng_node, n), &
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virial_node(6,max_basisnum, max_ng_node, n), &
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energy_node(max_basisnum,max_ng_node,n), &
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stat=allostat)
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if(allostat > 0) then
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print *, "Error allocating element data arrays in mode_metric becaus of:", allostat
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stop
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end if
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end if
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if (m > 0) then
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allocate(force_atom(3, m), &
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virial_atom(6, m), &
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energy_atom(m), &
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stat=allostat)
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if(allostat > 0) then
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print *, "Error allocating atom data arrays in mode_metric becaus of:", allostat
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stop
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end if
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end if
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end subroutine
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subroutine add_atom_data(ia, eng, force, virial)
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!Function which sets the atom data arrays
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integer, intent(in) :: ia
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real(kind=dp), intent(in) :: eng, force(3), virial(6)
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energy_atom(ia) = eng
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force_atom(:,ia) = force(:)
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virial_atom(:,ia) = virial(:)
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return
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end subroutine add_atom_data
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subroutine add_element_data(ie, eng, force, virial)
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!Function which sets the element data arrays
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integer, intent(in) :: ie
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real(kind=dp), intent(in) :: eng(max_basisnum, max_ng_node), &
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force(3,max_basisnum, max_ng_node), &
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virial(6,max_basisnum,max_ng_node)
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energy_node(:,:,ie) = eng
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force_node(:,:,:,ie) = force
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virial_node(:,:,:,ie) = virial
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return
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end subroutine add_element_data
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end module elements
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144
src/io.f90
144
src/io.f90
@ -106,7 +106,7 @@ module io
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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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" is not accepted for writing. Please select from: xyz, lmp, vtk, mb, restart, cac and try again"
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stop
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end select
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@ -599,9 +599,24 @@ module io
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infilenum=infilenum+1
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infiles(infilenum) = temp_infile
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exit
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case('out')
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if(atom_types == 0) then
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print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
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stop 3
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end if
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select case(trim(adjustl(mode)))
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case('--convert','--metric')
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infilenum = infilenum+1
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infiles(infilenum) = temp_infile
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exit
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case default
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print *, "Files of type .out cannot be used with mode ", trim(adjustl(mode))
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stop 3
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end select
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case default
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print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
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"please input a filename with extension from following list: mb, restart."
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"please input a filename with extension from following list: mb, restart, cac, or out."
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read(*,*) temp_infile
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end select
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@ -624,9 +639,11 @@ module io
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call read_pycac(infiles(i), displace, temp_box_bd)
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case('cac')
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call read_lmpcac(infiles(i), displace, temp_box_bd)
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case('out')
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call read_pycac_out(infiles(i), displace, temp_box_bd)
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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: mb and try again"
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" is not accepted for reading. Please select from: mb,restart,cac,out and try again"
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stop
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end select
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@ -781,7 +798,7 @@ module io
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integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
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atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
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atom_type, stat
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atom_type, stat
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real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
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character(len=100) :: textholder, in_lattype_map(10)
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character(len=2) :: atomic_element
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@ -960,6 +977,102 @@ module io
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end if
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end subroutine read_pycac
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subroutine read_pycac_out(file, displace, temp_box_bd)
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!This subroutine reads in the pyCAC dump file
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!Arguments
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character(len=100), intent(in) :: file
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real(kind=dp), dimension(3), intent(in) :: displace
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real(kind=dp), dimension(6), intent(out) :: temp_box_bd
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!Internal Variables
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integer :: i, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
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id, type_node, ilat, esize, tag, type
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real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), &
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ee(1,8), fe(3,1,8), ve(3,1,8), re(3,1,8)
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character(len=100) :: textholder, fcc
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open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
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!Now initialize some important variables if they aren't defined
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if (max_basisnum==0) max_basisnum = 1
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if (max_ng_node==0) max_ng_node=8
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fcc="fcc"
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!Skip header comment lines
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read(11, *) textholder
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read(11, *) textholder
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!Read atom number and element number and grow element arrays by needed amount
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read(11,*) textholder, in_atoms, textholder, in_eles
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call grow_ele_arrays(in_eles, in_atoms)
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call alloc_dat_arrays(in_eles, in_atoms)
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!Read boundary information
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read(11,*) textholder, box_bc(1:1), box_bc(2:2), box_bc(3:3), temp_box_bd(:)
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do i = 1, 3
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if (abs(displace(i)) > lim_zero) then
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newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
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else
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newdisplace(i)=displace(i)
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end if
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temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
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temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
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end do
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call grow_box(temp_box_bd)
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!Allocate sub_box boundaries
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if (sub_box_num == 0) then
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call alloc_sub_box(1)
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else
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call grow_sub_box(1)
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end if
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!Because orientations and other needed sub_box information isn't really
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!present within the .cac file we just default a lot of it.
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sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
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sub_box_bd(:, sub_box_num+1) = temp_box_bd
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sub_box_num = sub_box_num + 1
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if(in_atoms > 0 ) then
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!Read atom header
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read(11,*) textholder
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do ia = 1, in_atoms
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read(11,*) tag, type, ra(:), ea, fa(:), va(:)
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call add_atom(tag, type, sub_box_num, ra)
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call add_atom_data(atom_num, ea, fa, va)
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end do
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end if
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if(in_eles > 0) then
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!Add the lattice_types based on the atom types
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inbtypes=0
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do i = 1, maxval(type_atom)
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inbtypes(1) = i
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call lattice_map(1, inbtypes, 8 , 1.0_dp, ilat) !Please check documentation on pycac.out formats
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end do
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!Read element and node headers
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read(11,*) textholder
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read(11,*) textholder
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!read element information, currently only 8 node elements with 1 basis
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do ie =1, in_eles
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read(11,*) tag, lat_type, textholder, textholder, esize
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do inod =1, 8
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read(11,*) textholder, textholder, textholder, re(:,1,inod), ee(1,inod), fe(:,1,inod), ve(:,1,inod)
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end do
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call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
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call add_element_data(ele_num, ee, fe, ve)
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end do
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end if
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call set_max_esize
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return
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end subroutine
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subroutine read_lmpcac(file, displace, temp_box_bd)
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!This subroutine is used to read .cac files which are used with the lammpsCAC format
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character(len=100), intent(in) :: file
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@ -980,7 +1093,7 @@ module io
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!Open the file
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open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
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!Now initialiaze some important variables if they aren't defined
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!Now initialize some important variables if they aren't defined
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if (max_basisnum==0) max_basisnum = 10
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if (max_ng_node==0) max_ng_node=8
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@ -1109,4 +1222,25 @@ module io
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print *, in_lattice_type
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end subroutine set_cac
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subroutine set_types(apos)
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!This code
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integer, intent(in) :: apos
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integer :: i, j,arglen, arg_pos, ntypes
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character(len=100) :: textholder
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arg_pos = apos + 1
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call get_command_argument(arg_pos, textholder, arglen)
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if (arglen==0) stop "Missing numtypes in io"
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read(textholder,*) ntypes
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do i=1,ntypes
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder, arglen)
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call add_atom_type(textholder, j)
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end do
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return
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end subroutine set_types
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end module io
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@ -63,6 +63,8 @@ program main
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case('-set_cac')
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call set_cac(i)
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case('-set_types')
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call set_types(i)
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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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@ -71,7 +73,8 @@ program main
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argument = trim(adjustl(argument))
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if (argument(1:2) == '--') then
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call call_mode(end_mode_arg, argument)
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mode = argument
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call call_mode(end_mode_arg)
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end if
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!Check to make sure a mode was called
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@ -12,5 +12,7 @@ module parameters
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!Numeric constants
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real(kind=dp), parameter :: pi = 3.14159265358979323846_dp
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!Mode type that is being called
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character(len=100) :: mode
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end module parameters
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