From 9ebdfff0a137179cb30384e1f20016f4f642ceed Mon Sep 17 00:00:00 2001 From: Alex Selimov Date: Tue, 28 Jan 2020 10:42:30 -0500 Subject: [PATCH 1/2] Added print messages to let user know whats going on --- src/io.f90 | 4 ++++ src/main.f90 | 40 +++++++++++++++++++++++++++------------- src/mode_create.f90 | 7 +++++++ src/mode_merge.f90 | 5 +++++ src/opt_disl.f90 | 7 ++++++- src/opt_group.f90 | 14 +++++++++++++- 6 files changed, 62 insertions(+), 15 deletions(-) diff --git a/src/io.f90 b/src/io.f90 index fdde73d..8fd139b 100644 --- a/src/io.f90 +++ b/src/io.f90 @@ -627,6 +627,7 @@ module io temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i) end do + call grow_box(temp_box_bd) !Read in the number of sub_boxes and allocate the variables read(11, *) n @@ -707,6 +708,9 @@ module io call grow_ele_arrays(in_eles, in_atoms) allocate(r_innode(3,max_basisnum, max_ng_node)) + print *, "Read in ", in_eles, " elements and ", in_atoms, " atoms from ", trim(adjustl(file)) + print *, "New box dimensions are: ", box_bd + !Read the atoms do i = 1, in_atoms read(11,*) j, type, r(:) diff --git a/src/main.f90 b/src/main.f90 index ed34c53..7d24d6d 100644 --- a/src/main.f90 +++ b/src/main.f90 @@ -1,25 +1,39 @@ program main - !**************************** CACmb ******************************* - !* CAC model building toolkit * - ! ____________ * - ! / / * - ! / / * - ! /___________/ * - ! _|_ _|_ _|____________ * - ! / / * - ! / / * - ! /___________/ * - ! * - !******************************************************************* + !**************************** CACmb ******************** + !* CAC model building toolkit * + !* ____________ * + !* / / * + !* / / * + !* /___________/ * + !* _|_ _|_ _|____________ * + !* / / * + !* / / * + !* /___________/ * + !* * + !******************************************************** use parameters use elements use io - + integer :: i, end_mode_arg, arg_num, arg_pos character(len=100) :: argument + !Print introduction text + print *, '*********************** CACmb *********************' + print *, '* CAC model building toolkit *' + print *, '* _______ *' + print *, '* / / *' + print *, '* / / *' + print *, '* /______ / *' + print *, '* _|_ _|_ _|_______ *' + print *, '* / / *' + print *, '* / / *' + print *, '* /______ / *' + print *, '* *' + print *, '****************************************************' + !Call initialization functions call lattice_init call box_init diff --git a/src/mode_create.f90 b/src/mode_create.f90 index 9463e92..c3e6bcc 100644 --- a/src/mode_create.f90 +++ b/src/mode_create.f90 @@ -30,6 +30,8 @@ module mode_create integer :: i, ibasis, inod real(kind=dp), allocatable :: r_node_temp(:,:,:) + print *, '-----------------------Mode Create---------------------------' + !Initialize default parameters orient = reshape((/ 1.0_dp, 0.0_dp, 0.0_dp, 0.0_dp, 1.0_dp, 0.0_dp, 0.0_dp, 0.0_dp, 1.0_dp /), shape(orient)) cell_mat(:,:)=0.0_dp @@ -91,6 +93,8 @@ module mode_create end do else + print *, "Creating 1 element" + call cell_init(lattice_parameter, esize, element_type, orient, cell_mat) !If the user doesn't pass any build instructions than we just put the cell mat into the element_array call alloc_ele_arrays(1,0) @@ -110,6 +114,7 @@ module mode_create !If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays if(dup_flag.or.dim_flag) then + !Call the build function with the correct transformation matrix select case(trim(adjustl(element_type))) case('fcc') @@ -123,6 +128,8 @@ module mode_create !Now that it is built multiply by the lattice parameter box_bd = box_bd*lattice_parameter + print *, "Using mode create, ", lat_ele_num, " elements are created and ", lat_atom_num*basisnum(1), " atoms are created." + !Allocate variables call alloc_ele_arrays(lat_ele_num, lat_atom_num*basisnum(1)) if(lat_atom_num > 0) then diff --git a/src/mode_merge.f90 b/src/mode_merge.f90 index 567b19b..14a015d 100644 --- a/src/mode_merge.f90 +++ b/src/mode_merge.f90 @@ -20,6 +20,8 @@ module mode_merge integer :: i real(kind=dp) :: displace(3), temp_box_bd(6) + print *, '-----------------------Mode Merge---------------------------' + wrap = .false. shift_flag = .false. @@ -34,6 +36,7 @@ module mode_merge !The new starts variable dictate where in the atom and element array each new !file starts. This is used for additional options that can be applied to solely !these new atoms/elements that are read in. + new_starts(1) = atom_num + 1 new_starts(2) = ele_num + 1 @@ -136,6 +139,8 @@ module mode_merge !Calculate the current shift which is the filenum-1 multiplied by the user specified shift current_shift = (filenum-1)*shift_vec + print *, "Atoms/elements from file ", trim(adjustl(infiles(filenum))), " are shifted by ", current_shift + !First shift all the atoms do i = array_start(1), atom_num r_atom(:,i) = r_atom(:,i) + current_shift diff --git a/src/opt_disl.f90 b/src/opt_disl.f90 index 62ceae6..025d680 100644 --- a/src/opt_disl.f90 +++ b/src/opt_disl.f90 @@ -23,12 +23,12 @@ module opt_disl contains subroutine dislocation(option, arg_pos) - !Main calling function for all codes related to dislocations character(len=100), intent(in) :: option integer, intent(inout) :: arg_pos + print *, '--------------------Option Dislocation-----------------------' select case(trim(adjustl(option))) case('-dislgen') @@ -97,6 +97,8 @@ module opt_disl real(kind=dp) :: ss_ori(3,3), ss_inv(3,3), be, bs, slipx(3), disp_transform(3,3), inv_transform(3,3), & actan, r(3), disp(3) + print *, "Dislocation with centroid ", centroid, " is inserted" + !Calculate screw and edge burgers vectors be = sin(char_angle*pi/180.0_dp)*b bs = cos(char_angle*pi/180.0_dp)*b @@ -254,6 +256,9 @@ module opt_disl real(kind = dp) :: perimeter, angle, theta, omega, xA(3), xB(3), xC(3), u(3) real(kind=dp), dimension(:,:), allocatable :: xloop !coordinate of points forming loop + + print *, "Dislocation loop with centroid ", centroid, " is inserted" + if(allocated(xLoop)) deallocate(xLoop) !Define new directions diff --git a/src/opt_group.f90 b/src/opt_group.f90 index 25d8671..6d129f1 100644 --- a/src/opt_group.f90 +++ b/src/opt_group.f90 @@ -22,6 +22,8 @@ module opt_group !Main calling function for the group option integer, intent(inout) :: arg_pos + print *, '-----------------------Option Group-------------------------' + group_ele_num = 0 group_atom_num = 0 remesh_size=0 @@ -117,6 +119,9 @@ module opt_group select case(trim(adjustl(shape))) case('block') + + print *, "Group has block shape with boundaries: ", block_bd + !Allocate variables to arbitrary size allocate(element_index(1024), atom_index(1024)) !Check the type to see whether we need to find the elements within the group @@ -162,6 +167,8 @@ module opt_group end do end select end select + + print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms." end subroutine get_group subroutine displace_group @@ -169,6 +176,8 @@ module opt_group integer :: i, inod, ibasis + print *, "Elements/atoms in group displaced by ", disp_vec + !Displace atoms do i = 1, group_atom_num r_atom(:,atom_index(i)) = r_atom(:,atom_index(i)) + disp_vec @@ -207,7 +216,7 @@ module opt_group subroutine remesh_group !This command is used to remesh the group to a desired element size - integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num + integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3) !Refining to atoms and remeshing to elements are different processes so check which code we need to run @@ -216,6 +225,7 @@ module opt_group !Refining to atoms case(2) if(group_ele_num > 0) then + orig_atom_num = atom_num !Estimate number of atoms we are adding, this doesn't have to be exact add_atom_num = group_ele_num*basisnum(lat_ele(element_index(1)))*size_ele(element_index(1))**3 call grow_ele_arrays(0,add_atom_num) @@ -236,6 +246,8 @@ module opt_group !Once all atoms are added we delete all of the elements call delete_elements(group_ele_num, element_index) + print *, group_ele_num, " elements of group are refined to ", atom_num -orig_atom_num, " atoms." + end if !Remeshing to elements, currently not available case default From a942b8e2a1ccad6cc883cc4355d4afd6c8515357 Mon Sep 17 00:00:00 2001 From: Alex Selimov Date: Tue, 28 Jan 2020 10:59:49 -0500 Subject: [PATCH 2/2] Added -ow option which allows for automatic overwriting --- README.md | 10 +++++++++- src/call_option.f90 | 6 +++++- src/io.f90 | 4 ++-- src/main.f90 | 12 ++++++++++++ 4 files changed, 28 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 1851f36..5d45ef3 100644 --- a/README.md +++ b/README.md @@ -217,4 +217,12 @@ This command wraps atoms back into the simulation cell as though periodic bounda remesh esize ``` -This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics. \ No newline at end of file +This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics. + +### Option overwrite + +``` +-ow +``` + +If this option is passed then all files are automatically overwritten without asking the user. \ No newline at end of file diff --git a/src/call_option.f90 b/src/call_option.f90 index befb46c..60551af 100644 --- a/src/call_option.f90 +++ b/src/call_option.f90 @@ -12,7 +12,11 @@ subroutine call_option(option, arg_pos) call dislocation(option, arg_pos) case('-group') call group(arg_pos) + case('-ow') + arg_pos = arg_pos + 1 + continue case default - print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.' + print *, 'Option ', trim(adjustl(option)), ' is not currently accepted. Skipping to next argument' + arg_pos = arg_pos + 1 end select end subroutine call_option \ No newline at end of file diff --git a/src/io.f90 b/src/io.f90 index 8fd139b..26d4250 100644 --- a/src/io.f90 +++ b/src/io.f90 @@ -9,7 +9,7 @@ module io integer :: outfilenum = 0, infilenum = 0 character(len=100) :: outfiles(10), infiles(10) - + logical :: force_overwrite public contains @@ -38,7 +38,7 @@ module io !Check to see if file exists, if it does then ask user if they would like to overwrite the file inquire(file=trim(temp_outfile), exist=file_exists) - if (file_exists) then + if (file_exists.and.(.not.(force_overwrite))) then if (overwrite == 'r') print *, "File ", trim(temp_outfile), " already exists. Would you like to overwrite? (Y/N)" read(*,*) overwrite if((scan(overwrite, "n") > 0).or.(scan(overwrite, "N") > 0)) then diff --git a/src/main.f90 b/src/main.f90 index 7d24d6d..31f5f58 100644 --- a/src/main.f90 +++ b/src/main.f90 @@ -37,11 +37,23 @@ program main !Call initialization functions call lattice_init call box_init + force_overwrite=.false. + end_mode_arg = 0 ! Command line parsing arg_num = command_argument_count() + !Check to see if overwrite flag is passed + do i = 1, arg_num + call get_command_argument(i,argument) + select case(trim(adjustl(argument))) + + case('-ow') + force_overwrite = .true. + print *, "Overwrite flag passed, output files will be overwritten" + end select + end do !Determine if a mode is being used and what it is. The first argument has to be the mode !if a mode is being used call get_command_argument(1, argument)