Merge branch 'development' into 'master'

1.5

See merge request aselimov/cacmb!4

LICENSE

@@ -1,8 +1,674 @@
-The MIT License (MIT)
-Copyright © 2020 <copyright holders>
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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+                            Preamble
 
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+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

src/Makefile

@@ -1,53 +1,49 @@
-FC=gfortran
-
-#Ifort flags
-#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
-
-#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
-
-#gfortran flags
-FFLAGS=-mcmodel=large -O3 -g
-#FFLAGS=-mcmodel=large -O0 -g -fbacktrace -fcheck=all
-
-MODES=mode_create.o mode_merge.o mode_convert.o mode_metric.o mode_calc.o
-OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o opt_deform.o opt_redef_box.o opt_slip_plane.o
-OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o neighbors.o $(MODES) $(OPTIONS) call_option.o sorts.o
-
-.SUFFIXES:
 .SUFFIXES: .c .f .f90 .F90 .o
+.DEFAULT_GOAL := all
 
-cacmb: $(OBJECTS) 
-	$(FC) $(FFLAGS) $(OBJECTS) parameters.o -o $@
+FC=mpif90
+FFLAGS=-Wall -mcmodel=large -O0 -g -fbacktrace -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow,denormal 
+
+OBJDIR=obj
+SRCS := $(wildcard *.f90)
+OBJECTS := $(addprefix $(OBJDIR)/,$(SRCS:%.f90=%.o))
+
+
+
+#----------------- DEPENDENCIES -----------------#
+# GENERATED USING https://github.com/ZedThree/fort_depend.py **requires python3**
+# > pip install fortdepend
+# > fortdepend -o Makefile.dep -i mpi -b obj/
+include Makefile.dep
+
+#----------------- DEFAULTS -----------------#
+all: cacmb
+
+.PHONY: deps
+cacmb: $(OBJECTS) $(OBJDIR)/main.o
+	$(FC) $(FFLAGS) $(OBJECTS) -o $@
+
+$(OBJDIR)/%.o: %.f90
+	@mkdir -p $(@D)
+	$(FC) $(FFLAGS) -c -o $@ $< -J$(OBJDIR)
 
 .f90.o: 
 	$(FC) $(FFLAGS) -c $< 
 
+
+deps:
+	@fortdepend -o Makefile.dep -i mpi -b obj -w
+
+#----------------- CLEAN UP -----------------#
+
 .PHONY: clean
-clean: 
-	$(RM) cacmb  *.o *.mod *genmod*
+clean:
+	$(RM) *.mod *.o
+	$(RM) $(OBJDIR)/*.mod $(OBJDIR)/*.o CAC
+	@$(RM) -rf obj/
 
-testfuncs: testfuncs.o functions.o subroutines.o
-	$(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@
+.PHONY: clean-all
+clean-all: clean 
 
-.PHONY: cleantest
-cleantest:
-	$(RM) testfuncs testfuncs.o
-
-.PHONY: test
-test: testfuncs
-	./testfuncs
-
-.PHONY: install
-install: cacmb
-	cp ./cacmb /usr/local/bin
-
-$(OBJECTS) : parameters.o
-atoms.o subroutines.o testfuncs.o box.o : functions.o
-main.o io.o $(MODES) $(OPTIONS) : elements.o 
-call_mode.o : $(MODES)
-call_option.o : $(OPTIONS)
-elements.o : sorts.o
-$(MODES) $(OPTIONS) subroutines.o io.o : atoms.o box.o
-$(MODES) main.o : io.o
-testfuncs.o elements.o mode_create.o $(OPTIONS) $(MODES): subroutines.o
-opt_delete.o mode_metric.o : neighbors.o
+# DEBUGGING VARIABLE PRINT
+print-%  : ; @echo $* = $($*)

src/Makefile.dep

@@ -0,0 +1,167 @@
+# This file is generated automatically. DO NOT EDIT!
+
+obj/main :  \
+	obj/atoms.o \
+	obj/box.o \
+	obj/caller.o \
+	obj/elements.o \
+	obj/functions.o \
+	obj/io.o \
+	obj/main.o \
+	obj/mode_calc.o \
+	obj/mode_convert.o \
+	obj/mode_create.o \
+	obj/mode_merge.o \
+	obj/mode_metric.o \
+	obj/neighbors.o \
+	obj/opt_deform.o \
+	obj/opt_delete.o \
+	obj/opt_disl.o \
+	obj/opt_group.o \
+	obj/opt_orient.o \
+	obj/opt_redef_box.o \
+	obj/opt_slip_plane.o \
+	obj/parameters.o \
+	obj/sorts.o \
+	obj/str.o \
+	obj/subroutines.o
+
+obj/atoms.o :  \
+	obj/functions.o \
+	obj/parameters.o
+
+obj/box.o :  \
+	obj/functions.o \
+	obj/parameters.o
+
+obj/caller.o :  \
+	obj/box.o \
+	obj/mode_calc.o \
+	obj/mode_convert.o \
+	obj/mode_create.o \
+	obj/mode_merge.o \
+	obj/mode_metric.o \
+	obj/opt_deform.o \
+	obj/opt_delete.o \
+	obj/opt_disl.o \
+	obj/opt_group.o \
+	obj/opt_orient.o \
+	obj/opt_redef_box.o \
+	obj/opt_slip_plane.o \
+	obj/parameters.o
+
+obj/elements.o :  \
+	obj/box.o \
+	obj/functions.o \
+	obj/parameters.o \
+	obj/sorts.o \
+	obj/subroutines.o
+
+obj/functions.o :  \
+	obj/parameters.o
+
+obj/io.o :  \
+	obj/atoms.o \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/str.o
+
+obj/main.o :  \
+	obj/caller.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o
+
+obj/mode_calc.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/mode_convert.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o
+
+obj/mode_create.o :  \
+	obj/atoms.o \
+	obj/box.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/mode_merge.o :  \
+	obj/atoms.o \
+	obj/elements.o \
+	obj/io.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/mode_metric.o :  \
+	obj/elements.o \
+	obj/io.o \
+	obj/neighbors.o \
+	obj/parameters.o
+
+obj/neighbors.o :  \
+	obj/elements.o \
+	obj/functions.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_deform.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_delete.o :  \
+	obj/elements.o \
+	obj/neighbors.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_disl.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_group.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_orient.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/opt_redef_box.o :  \
+	obj/box.o \
+	obj/elements.o \
+	obj/subroutines.o
+
+obj/opt_slip_plane.o :  \
+	obj/elements.o \
+	obj/functions.o \
+	obj/parameters.o \
+	obj/subroutines.o
+
+obj/parameters.o : 
+
+obj/sorts.o :  \
+	obj/parameters.o
+
+obj/str.o : 
+
+obj/subroutines.o :  \
+	obj/box.o \
+	obj/functions.o \
+	obj/parameters.o

src/call_mode.f90

@@ -1,34 +0,0 @@
-subroutine call_mode(arg_pos)
-    !This code is used to parse the command line argument for the mode information and calls the required 
-    !mode module.
-
-    use mode_create
-    use mode_convert
-    use mode_merge
-    use mode_metric
-    use mode_calc
-    use parameters
-
-    implicit none    
-
-    integer, intent(out) :: arg_pos
-
-    select case(mode)
-    case('--create')
-        call create(arg_pos)
-    case('--convert')
-        call convert(arg_pos)  
-    case('--merge')
-        call merge(arg_pos) 
-    case('--metric')
-        call metric(arg_pos)
-    case('--calc')
-        call calc(arg_pos)
-    case default
-        print *, "Mode ", trim(adjustl(mode)), " currently not accepted. Please check documentation for ", &
-                 "accepted modes and rerun."
-
-        stop 3
-         
-    end select
-end subroutine call_mode

src/call_option.f90

@@ -1,53 +0,0 @@
-subroutine call_option(option, arg_pos)
-    use parameters
-    use opt_disl
-    use opt_group
-    use opt_orient
-    use opt_deform
-    use opt_delete
-    use opt_redef_box
-    use opt_slip_plane
-    use box
-    implicit none
-
-    integer, intent(inout) :: arg_pos
-    character(len=100), intent(in) :: option
-
-    select case(trim(adjustl(option)))
-    case('-dislgen', '-disloop','-vacancydisloop')
-        call dislocation(option, arg_pos)
-    case('-group')
-        call group(arg_pos)
-    case('-ow')
-        arg_pos = arg_pos + 1
-    case('-wrap')
-        arg_pos = arg_pos + 1
-    case('-orient')
-        call orient(arg_pos)
-    case('-unorient')
-        call unorient
-        arg_pos = arg_pos + 1
-    case('-boundary')
-        arg_pos=arg_pos+1
-        call get_command_argument(arg_pos, box_bc)
-        arg_pos=arg_pos+1
-        bound_called = .true.
-    case('-sbox_ori')
-        call sbox_ori(arg_pos)
-    case('-deform')
-        call deform(arg_pos)
-    case('-delete')
-        call run_delete(arg_pos)
-    case('-set_cac')
-        arg_pos=arg_pos +3
-    case('-set_types')
-        arg_pos = arg_pos + 3 + atom_types
-    case('-redef_box')
-        call redef_box(arg_pos)
-    case('-slip_plane')
-        call run_slip_plane(arg_pos)
-    case default
-        print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
-        stop 3 
-    end select
-end subroutine call_option

src/caller.f90

@@ -0,0 +1,91 @@
+module caller
+    !this module just calls modes and options
+
+    use mode_create
+    use mode_convert
+    use mode_merge
+    use mode_metric
+    use mode_calc
+    use parameters
+    use opt_disl
+    use opt_group
+    use opt_orient
+    use opt_deform
+    use opt_delete
+    use opt_redef_box
+    use opt_slip_plane
+    use box
+
+
+    implicit none
+    public 
+    contains
+    subroutine call_mode(arg_pos)
+        !This code is used to parse the command line argument for the mode information and calls the required 
+        !mode module.
+    
+        integer, intent(out) :: arg_pos
+    
+        select case(mode)
+        case('--create')
+            call create(arg_pos)
+        case('--convert')
+            call convert(arg_pos)  
+        case('--merge')
+            call merge(arg_pos) 
+        case('--metric')
+            call metric(arg_pos)
+        case('--calc')
+            call calc(arg_pos)
+        case default
+            print *, "Mode ", trim(adjustl(mode)), " currently not accepted. Please check documentation for ", &
+                     "accepted modes and rerun."
+    
+            stop 3
+        end select
+    end subroutine call_mode
+
+    subroutine call_option(option, arg_pos)
+        integer, intent(inout) :: arg_pos
+        character(len=100), intent(in) :: option
+    
+        select case(trim(adjustl(option)))
+        case('-disl','-dislgen', '-disloop','-vacancydisloop')
+            call dislocation(option, arg_pos)
+        case('-group')
+            call group(arg_pos)
+        case('-ow')
+            arg_pos = arg_pos + 1
+        case('-wrap')
+            arg_pos = arg_pos + 1
+        case('-orient')
+            call orient_opt(arg_pos)
+        case('-unorient')
+            call unorient
+            arg_pos = arg_pos + 1
+        case('-boundary')
+            arg_pos=arg_pos+1
+            call get_command_argument(arg_pos, box_bc)
+            arg_pos=arg_pos+1
+            bound_called = .true.
+        case('-sbox_ori')
+            call sbox_ori(arg_pos)
+        case('-deform')
+            call deform(arg_pos)
+        case('-delete')
+            call run_delete(arg_pos)
+        case('-set_cac')
+            arg_pos=arg_pos +3
+        case('-set_types')
+            arg_pos = arg_pos + 3 + atom_types
+        case('-redef_box')
+            call redef_box(arg_pos)
+        case('-slip_plane')
+            call run_slip_plane(arg_pos)
+        case default
+            print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
+            stop 3 
+        end select
+    end subroutine call_option
+
+end module caller

src/elements.f90

@@ -14,10 +14,11 @@ 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=8), allocatable :: force_node(:,:,:,:), virial_node(:,:,:,:), energy_node(:,:,:)
+    real(kind=dp), allocatable :: force_node(:,:,:,:), virial_node(:,:,:,:), energy_node(:,:,:)
 
     integer, save :: ele_num !Number of elements
     integer, save :: node_num !Total number of nodes
+    integer, save :: node_atoms !Count of all basis atoms at nodes summed over all nodes
 
     !Data structure used to represent atoms 
     integer, allocatable ::  type_atom(:)!atom type 
@@ -120,6 +121,7 @@ module elements
         basisnum(:) = 0
         ng_node(:) = 0
         node_num = 0
+        node_atoms = 0
         ele_num = 0
         atom_num = 0
     end subroutine lattice_init
@@ -288,6 +290,7 @@ module elements
 
         ele_num = ele_num + 1
         node_num = node_num + ng_node(lat)
+        node_atoms = node_atoms + ng_node(lat)*basisnum(lat)
 
         if (tag==0) then
             newtag = ele_num !If we don't assign a tag then pass the tag as the ele_num
@@ -386,7 +389,7 @@ module elements
         end if
     end subroutine
 
-    subroutine interpolate_atoms(type, esize, lat_type, r_in, type_interp, r_interp)
+    subroutine interpolate_atoms(type, esize, lat_type, r_in, type_interp, r_interp, eng, f, v, data_interp)
         !This subroutine returns the interpolated atoms from the elements. 
 
         !Arguments
@@ -396,15 +399,19 @@ module elements
         real(kind=dp), dimension(3,max_basisnum, max_ng_node), intent(in) :: r_in !Nodal positions
         integer, dimension(max_basisnum*max_esize**3), intent(out) :: type_interp !Interpolated atomic positions
         real(kind=dp), dimension(3, max_basisnum*max_esize**3), intent(out) :: r_interp !Interpolated atomic positions
+        real(kind = dp), optional, intent(in) :: eng(max_basisnum, max_ng_node), f(3, max_basisnum, max_ng_node), &
+                                                 v(6, max_basisnum, max_ng_node)
+        real(kind=dp), dimension(10, max_basisnum*max_esize**3), optional,intent(out) :: data_interp !Interpolated atomic positions
 
         !Internal variables
         integer :: it, is, ir, ibasis, inod, ia, bnum, lat_type_temp
-        real(kind=dp), allocatable :: a_shape(:)
+        real(kind=dp) :: a_shape(max_ng_node)
         real(kind=dp) :: t, s, r
         
         !Initialize some variables
         r_interp(:,:) = 0.0_dp
         type_interp(:) = 0
+        if(present(data_interp)) data_interp = 0.0_dp
         ia = 0
 
         !Define bnum based on the input lattice type. If lat_type=0 then we are interpolating lattice points which means
@@ -421,7 +428,6 @@ module elements
 
         select case(trim(adjustl(type)))
         case('fcc','bcc')
-            allocate(a_shape(8))
             !Now loop over all the possible sites
             do it = 1, esize
                 t = (1.0_dp*(it-1)-(esize-1)/2)/(1.0_dp*(esize-1)/2)
@@ -437,6 +443,12 @@ module elements
                                 type_interp(ia) = basis_type(ibasis,lat_type_temp)
                                 r_interp(:,ia) = r_interp(:,ia) + a_shape(inod) * r_in(:,ibasis,inod)
 
+                                if(present(data_interp)) then 
+                                    !If data is present then interpolate data arrays as well
+                                    data_interp(1,ia) = data_interp(1,ia) + eng(ibasis, inod)*a_shape(inod)
+                                    data_interp(2:4,ia) = data_interp(2:4,ia) + f(:, ibasis, inod)*a_shape(inod)
+                                    data_interp(5:10,ia) = data_interp(5:10,ia) + v(:, ibasis, inod)*a_shape(inod)
+                                end if
                             end do
                         end do
 
@@ -455,7 +467,7 @@ module elements
     subroutine rhombshape(r,s,t, shape_fun)
         !Shape function for rhombohedral elements
         real(kind=8), intent(in) :: r, s, t
-        real(kind=8), intent(out) :: shape_fun(8)
+        real(kind=8), intent(out) :: shape_fun(:)
 
         shape_fun(1) =  (1.0-r)*(1.0-s)*(1.0-t)/8.0
         shape_fun(2) =  (1.0+r)*(1.0-s)*(1.0-t)/8.0

src/io.f90

@@ -4,6 +4,7 @@ module io
     use parameters
     use atoms
     use box
+    use str
 
     implicit none
 
@@ -59,7 +60,7 @@ module io
                 cycle
             end if
             select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
-            case('xyz', 'lmp', 'vtk', 'mb', 'restart')
+            case('xyz', 'lmp', 'vtk', 'mb', 'restart', 'dump')
                 outfilenum=outfilenum+1
                 outfiles(outfilenum) =  temp_outfile
                 exit
@@ -104,6 +105,8 @@ module io
                 call write_pycac(outfiles(i))
             case('cac')
                 call write_lmpcac(outfiles(i))
+            case('dump')
+                call write_ldump(outfiles(i))
             case default
                 print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
                          " is not accepted for writing. Please select from: xyz, lmp, vtk, mb, restart, cac and try again"
@@ -124,7 +127,7 @@ module io
         open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
 
         !Write total number of atoms + elements
-        write(11, '(i16)') node_num+atom_num
+        write(11, '(i16)') node_atoms+atom_num
          
         !Write comment line
         write(11, '(a)') "#Node + atom file created using cacmb"
@@ -140,8 +143,8 @@ module io
             end do 
         end do 
 
-        if(outn /= node_num) then 
-            print *, "outn", outn, " doesn't equal node_num ", node_num
+        if(outn /= node_atoms) then 
+            print *, "outn", outn, " doesn't equal node_atoms ", node_atoms
         end if
 
         !Write atom positions
@@ -150,8 +153,8 @@ module io
             outn = outn + 1
         end do
 
-        if((outn-atom_num) /= atom_num) then 
-            print *, "outn", (outn-node_num), " doesn't equal atom_num ", atom_num
+        if((outn-node_atoms) /= atom_num) then 
+            print *, "outn", (outn-node_atoms), " doesn't equal atom_num ", atom_num
         end if
 
         !Finish writing 
@@ -219,6 +222,88 @@ module io
         end do
     end subroutine write_lmp
 
+    subroutine write_ldump(file)
+        !This subroutine will only work if element data is defined
+        character(len = *), intent(in) :: file
+        integer :: write_num, i, iatom
+        logical :: write_dat
+        integer :: type_interp(max_basisnum*max_esize**3), interp_num
+        real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), data_interp(10, max_basisnum*max_esize**3)
+
+
+
+1 format('ITEM: TIMESTEP'/i16)
+2 format('ITEM: NUMBER OF ATOMS' /i16)
+3  format('ITEM: BOX BOUNDS ', 2a1, ' ', 2a1, ' ', 2a1 / &
+                               2f23.15 / 2f23.15 / 2f23.15)
+4  format('ITEM: ATOMS id type x y z energy fx fy fz s11 s22 s33 s23 s13 s12')
+5  format('ITEM: ATOMS id type x y z')
+
+        open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
+        
+        print *, max_basisnum, max_esize
+        !Write header information 
+        write(11,1) timestep
+
+        !Calculate total atom number
+        write_num = atom_num
+        do i = 1,ele_num
+            if(type_ele(i) == 'fcc') write_num = write_num + size_ele(i)**3
+            if(type_ele(i) == 'bcc') write_num = write_num + size_ele(i)**3
+        end do
+        !Write total number of atoms
+        write(11,2) write_num
+        !Write box information
+        write(11,3) box_bc(1:1), box_bc(1:1), box_bc(2:2), box_bc(2:2), box_bc(3:3), box_bc(3:3), box_bd(:)
+
+        !Now pick if we are interpolating data or not
+        if(allocated(force_node).or.allocated(force_atom)) then 
+            write(11, 4)
+            write_dat = .true.
+        else 
+            write(11, 5)
+            write_dat = .false.
+        end if
+        
+        if (write_dat) then 
+            do i = 1, atom_num
+                write(11, '(2i16, 13f23.15)') i, type_atom(i), r_atom(:,i), energy_atom(i), force_atom(:,i), virial_atom(:,i)
+            end do
+        else
+            do i = 1, atom_num
+                write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
+            end do
+        end if
+
+        !Write refined element atomic positions
+        interp_num = 0
+        do i = 1, ele_num
+            if(write_dat) then 
+                call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp, &
+                                       energy_node(:,:,i), force_node(:,:,:,i), virial_node(:,:,:,i),  data_interp)
+            else
+                call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
+            end if
+            select case(trim(adjustl(type_ele(i))))
+            case('fcc','bcc')
+                if(write_dat) then 
+                    do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
+                        interp_num = interp_num+1
+                        call apply_periodic(r_interp(:,iatom))
+                        write(11, '(2i16, 13f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom), &
+                                                      data_interp(:,iatom)
+                    end do
+                else
+                    do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
+                        interp_num = interp_num+1
+                        call apply_periodic(r_interp(:,iatom))
+                        write(11, '(2i16, 3f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
+                    end do
+                end if
+            end select
+        end do
+    end subroutine write_ldump
+
     subroutine write_lmpcac(file)
         !This subroutine writes out a .lmp style dump file
         character(len=100), intent(in) :: file
@@ -392,54 +477,30 @@ module io
         character(len=100), intent(in) :: file
         integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_type(50), unique_num, &
                    etype
-        real(kind=dp) :: box_vec(3)
+        real(kind=dp) :: box_vec(3), masses(10)
 
 1  format('time' / i16, f23.15)
 2  format('number of elements' / i16)
 3  format('number of nodes' / i16)
-4  format('element types' / i16)
 5  format('number of atoms' / i16)
-6  format('number of grains' / i16)
 7  format('boundary ' / 3a1)
 8  format('box bound' / 6f23.15)
 9  format('box length' / 3f23.15)
 10 format('box matrix')
 11 format(3f23.15)
 12 format('coarse-grained domain')
-13 format('ie ele_type grain_ele lat_type_ele'/ 'ip ibasis x y z')
-14 format('atomistic domain' / 'ia grain_atom type_atom x y z')
-15 format('maximum lattice periodicity length' / 3f23.15)
-16 format('Number of lattice types and atom types '/ 2i16)
-17 format('lattice type IDs')
-18 format('lattice types for grains')
-19 format('max nodes per element' / i16)
+13 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z')
+14 format('atomistic domain' / 'ia type_atom x y z')
+19 format('max nodes per element and basis per nodes' / 2i16)
 20 format('max interpo per element' / i16)
 21 format('atom types to elements')
 
         open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
 
+        !Below writes the header information for the restart file
         write(11,1) timestep, total_time
         write(11,2) ele_num
 
-        !Below writes the header information for the restart file
-
-
-            !First figure out all of the unique element types
-            unique_num = 0
-            unique_index(:) = 0
-            eleloop:do i = 1, ele_num
-                do j =1 , unique_num
-                    if ( ( size_ele(i) == size_ele( unique_index(j) ) ).and. &
-                        ( lat_ele(i) == lat_ele(unique_index(j)) ) ) then
-                        cycle eleloop
-                    end if
-                end do
-                unique_num = unique_num + 1
-                unique_index(unique_num) = i
-                unique_size(unique_num) = size_ele(i)
-                unique_type(unique_num) = lat_ele(i)
-            end do eleloop
-
         !Calculate the max number of atoms per element
         select case(max_ng_node)
         case(8)
@@ -447,31 +508,19 @@ module io
         case default
             interp_max = 0
         end select
+
         write(11,20) interp_max
+        !Write 
         write(11,3) node_num
-        write(11,19) max_ng_node
-        write(11,4) unique_num
+        write(11,19) max_ng_node, max_basisnum
         write(11,5) atom_num
-        write(11,6) 1 !Grain_num is ignored 
-        write(11,16) lattice_types, atom_types
-        write(11,21)
         do i = 1, atom_types
-            write(11,*) i, type_to_name(i)
+            call atommass(type_to_name(i),masses(i))
         end do
+        write(11,*) "masses: " 
+        write(11, *) (masses(i), i = 1, atom_types)
         write(11,7) box_bc(1:1), box_bc(2:2), box_bc(3:3)
-        write(11,18)
-        write(11,'(2i16)') 1,1 !This is another throwaway line that is meaningless
-        write(11,17)
-        !This may have to be updated in the future but currently the only 8 node element is fcc
-        do i = 1, lattice_types
-            select case(ng_node(i))
-            case(8)
-                write(11, *) i, 'fcc'
-            end select
-        end do
-        write(11,15) 1.0_dp, 1.0_dp, 1.0_dp !Another throwaway line that isn't needed
         write(11,8) box_bd
-        write(11,9) box_bd(2)-box_bd(1), box_bd(4) - box_bd(3), box_bd(6)-box_bd(5)
         write(11,10)
         !Current boxes are limited to being rectangular 
         do i = 1,3 
@@ -479,35 +528,18 @@ module io
             box_vec(i) = box_bd(2*i) - box_bd(2*i-1)
             write(11,11) box_vec
         end do
-        !We write this as box_mat ori and box_mat current
-        do i = 1,3 
-            box_vec(:) = 0.0_dp
-            box_vec(i) = box_bd(2*i) - box_bd(2*i-1)
-            write(11,11) box_vec
-        end do
 
         !write the element information
         if(ele_num > 0) then
             write(11,12)
-           
-            do i = 1, unique_num
-                write(11,'(3i16)') i, size_ele(unique_index(i))-1, basis_type(1,lat_ele(unique_index(i)))
-            end do
             ip = 0
             write(11,13)
             do i = 1, ele_num
-                !Figure out the ele type
-                do j = 1, unique_num
-                    if ( (unique_size(j) == size_ele(i)).and.(unique_type(j) == lat_ele(i))) then
-                        etype = j
-                        exit
-                    endif
-                end do
-                write(11, '(4i16)') i, etype, 1, basis_type(1,lat_ele(i))
+                write(11, '(4i16)') i, basisnum(lat_ele(i)), 2, (size_ele(i)-1)
                 do inod = 1, ng_node(lat_ele(i))
                     do ibasis = 1, basisnum(lat_ele(i))
                         ip = ip + 1
-                        write(11, '(2i16, 3f23.15)') ip, ibasis, r_node(:, ibasis, inod, i)
+                        write(11, '(3i16, 3f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i)
                     end do
                 end do
             end do 
@@ -517,7 +549,7 @@ module io
         if(atom_num /= 0) then 
             write(11,14)
             do i = 1, atom_num
-                write(11, '(3i16, 3f23.15)') i, 1, type_atom(i), r_atom(:,i)
+                write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
             end do
         end if
 
@@ -803,7 +835,7 @@ module io
         integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
                    atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
                    atom_type, stat 
-        real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
+        real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), atomic_masses(10)
         character(len=100) :: textholder, in_lattype_map(10) 
         character(len=2) :: atomic_element
         !First open the file
@@ -817,31 +849,25 @@ module io
         read(11,*) textholder
         read(11,*) in_eles 
 
-        !Discard info and read ng_max_node
-        do i = 1, 5 
+        !Discard info and read ng_max_node and max_basisnum
+        do i = 1, 5
             read(11,*) textholder
         end do 
-        read(11,*) max_ng_node
-
-        !Read element types (only needed inside this subroutine)
-        read(11,*) textholder
-        read(11,*) ele_types
+        read(11,*) max_ng_node, max_basisnum
 
         !Read in atom num
         read(11,*) textholder
         read(11,*) in_atoms
 
-        !read in lattice_types and atom types
-        do i = 1,3 
-            read(11,*) textholder
-        end do
-        read(11,*) in_lat_num, in_atom_types
+        !read in atom masses
+        read(11, *) textholder
+        read(11, '(a)') textholder
+        j = tok_count(textholder)
+        read(textholder, *) (atomic_masses(i), i=1, j)
 
-
-        !Read define atom_types by name
-        read(11,*) textholder
+        !Read define atom_types by mass
         do i = 1, in_atom_types
-            read(11,*) j, atomic_element
+            call atommassspecies(atomic_masses(i), atomic_element)
             call add_atom_type(atomic_element, atom_type_map(i))
         end do 
 
@@ -849,22 +875,6 @@ module io
         read(11,*) textholder
         read(11,*) box_bc
 
-        !Disregard useless info
-        do i = 1, 3
-            read(11,*) textholder
-        end do 
-
-        !Read in lat_type map
-        do i = 1, in_lat_num
-            read(11,*) j, in_lattype_map(i)
-            ng_node(lattice_types+i) = 8 !Only cubic elements are currently supported in pyCAC
-        end do 
-
-        !Disregard useless info
-        do i =1 , 3 
-            read(11,*) textholder
-        end do 
-
         !Read box boundaries and displace them if necessary 
         read(11,*) temp_box_bd(:)
         do i = 1, 3
@@ -892,56 +902,13 @@ module io
         sub_box_bd(:, sub_box_num+1) = temp_box_bd
 
         !Read in more useless info
-        do i = 1, 10
+        do i = 1, 9
             read(11,*) textholder
         end do  
 
-        !Now read the ele_type to size and lat map
-        do i = 1, ele_types
-            read(11,*) j, etype_map(i)
-            etype_map(i) = etype_map(i) + 1
-        end do 
-
-
-        !Now set up the lattice types. In this code it assumes that lattice_type 1 maps to 
-        !atom type 1 because it only allows 1 atom per basis in pyCAC at the moment.
-        do i = 1, in_lat_num
-            basisnum(lattice_types+i) = 1
-            basis_type(1,lattice_types+i) = atom_type_map(i)
-        end do 
-
-        !Figure out the lattice type maps in case we have repeated lattice_types
-        k = lattice_types + 1
-        new_lattice_map(:) = 0
-        new_loop:do i = 1, in_lat_num
-            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
-        end do new_loop
-
-        !Read more useless data
-        read(11,*) textholder
-
-        !set max values and allocate variables 
-        max_basisnum = maxval(basisnum)
-        max_ng_node = maxval(ng_node)
-        call grow_ele_arrays(in_eles, in_atoms)
-
         !Now start reading the elements 
         if(in_eles > 0) then
+            read(11,*) textholder
             read(11,*) textholder
             do i = 1, in_eles 
                 read(11,*) j, etype, k, lat_type 
@@ -992,9 +959,9 @@ module io
 
         !Internal Variables
         integer :: i, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
-            id, type_node, ilat, esize, tag, type
+            id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip
         real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), &
-                         ee(1,8), fe(3,1,8), ve(3,1,8), re(3,1,8)
+                         ee(10,8), fe(3,10,8), ve(6,10,8), re(3,10,8)
         character(len=100) :: textholder, fcc
         character(len=1000) :: line
 
@@ -1002,7 +969,7 @@ module io
         open(unit=11, file=trim(adjustl(file)), action='read',position='rewind') 
 
         !Now initialize some important variables if they aren't defined
-        if (max_basisnum==0) max_basisnum = 1
+        if (max_basisnum==0) max_basisnum = 10
         if (max_ng_node==0) max_ng_node=8
         fcc="fcc"
 
@@ -1010,6 +977,9 @@ module io
         read(11, *) textholder
         read(11, *) textholder
 
+        !Read the timestep
+        read(11, *) textholder, timestep
+
         !Read atom number and element number and grow element arrays by needed amount
         read(11,*) textholder, in_atoms, textholder, in_eles
         call grow_ele_arrays(in_eles, in_atoms)
@@ -1055,30 +1025,28 @@ module io
         end if
 
         if(in_eles > 0) then 
-            !Add the lattice_types based on the atom types
-            inbtypes=0
-            do i = 1, maxval(type_atom)
-                inbtypes(1) = i 
-                call lattice_map(1, inbtypes,  8 , 1.0_dp, ilat) !Please check documentation on pycac.out formats
-            end do 
             !Read element and node headers
             read(11,*) textholder
             read(11,*) textholder
 
             !read element information, currently only 8 node elements with 1 basis
             do ie =1, in_eles
-                    read(11,*)  tag, lat_type, textholder, textholder, esize
-                do inod =1, 8
-                    read(11,*)  textholder, textholder, textholder, re(:,1,inod), ee(1,inod), fe(:,1,inod), ve(:,1,inod)
+                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
+                call lattice_map(bnum, inbtypes, n, 1.0_dp, lat_type)
                 call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
                 call add_element_data(ele_num, ee, fe, ve)
             end do
         end if
         call set_max_esize
         return
-  end subroutine
+    end subroutine
 
+
+    
     subroutine read_lmpcac(file, displace, temp_box_bd)
         !This subroutine is used to read .cac files which are used with the lammpsCAC format
         character(len=100), intent(in) :: file

src/main.f90

@@ -15,6 +15,7 @@ program main
     use parameters
     use elements
     use io
+    use caller
     
  
     integer ::  i, end_mode_arg, arg_num, arg_pos

src/mode_metric.f90

@@ -46,7 +46,7 @@ module mode_metric
         case('def_grad')
             allocate(met(9, np))
         case('microrotation')
-            allocate(met(3,np))
+            allocate(met(4,np))
         end select
 
         !Now set the reference positions
@@ -174,6 +174,7 @@ module mode_metric
                                     end do
                                 end do
                             end do
+                            met(4,ip) = norm2(met(1:3,ip))
                         end if
                     end if
             end select
@@ -222,14 +223,14 @@ module mode_metric
         
         select case(metric_type)
         case('def_grad')
-            write(11,*) "type x y z F11 F12 F13 F21 F22 F23 F31 F32 F33"
+            write(11,*) "type element x y z F11 F12 F13 F21 F22 F23 F31 F32 F33"
         case('microrotation')
-            write(11,*) "type x y z micro1 micro2 micro3"
+            write(11,*) "type element x y z micro1 micro2 micro3 norm2(micro)"
         end select
 
         if(atom_num > 0) then 
             do i = 1, atom_num
-                write(11,*) 0, type_atom(i), r_atom(:,i), met(:,tag_atom(i))
+                write(11,*) type_atom(i), 0, r_atom(:,i), met(:,tag_atom(i))
             end do
         end if
 
@@ -237,7 +238,7 @@ module mode_metric
             do i = 1, ele_num
                 do inod = 1, ng_node(lat_ele(i))
                     do ibasis = 1, basisnum(lat_ele(i))
-                        write(11,*) 1, basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i), &
+                        write(11,*) basis_type(ibasis,lat_ele(i)), 1, r_node(:,ibasis,inod,i), &
                                     met(:, atom_num+(tag_ele(i)-1)*max_ng_node*max_basisnum + (inod-1)*max_basisnum + ibasis) 
                     end do
                 end do

src/opt_disl.f90

@@ -9,6 +9,7 @@ module opt_disl
     implicit none
 
     integer :: vloop_size ! Number of atoms to remove in planar vacancy cluster
+    integer :: iline, islip_plane
     real(kind=dp), dimension(3) :: line, slip_plane, centroid!dislocation line, slip plane vectors, centroid,
     real(kind=dp) ::  burgers(3)  !burgers vector of loop
     real(kind=dp) :: poisson, char_angle, lattice_parameter!Poisson ratio and character angle, lattice_parameter for burgers vector
@@ -31,6 +32,9 @@ module opt_disl
         print *, '--------------------Option Dislocation-----------------------'
 
         select case(trim(adjustl(option)))
+        case('-disl')
+            call parse_disl(arg_pos)
+            call disl
         case('-dislgen')
             call parse_dislgen(arg_pos)
             call dislgen
@@ -43,6 +47,146 @@ module opt_disl
         end select
     end subroutine dislocation
 
+    subroutine parse_disl(arg_pos)
+
+        !Parse disl command
+
+        integer, intent(inout) :: arg_pos
+
+        integer :: i,arglen
+        character(len=100) :: textholder
+        character(len=1) :: parse_dim
+
+        !Parse all of the commands
+        arg_pos = arg_pos + 1
+        line(:) = 0.0_dp
+
+        call get_command_argument(arg_pos, parse_dim, arglen)
+        if (arglen==0) STOP "Missing line dim in disl command"
+        select case(parse_dim)
+        case('x','X')
+            iline=1
+        case('y','Y')
+            iline=2
+        case('z','Z')
+            iline=3
+        end select
+
+        arg_pos=arg_pos + 1
+        call get_command_argument(arg_pos, parse_dim, arglen)
+        if (arglen==0) STOP "Missing plane dim in disl command"
+        select case(parse_dim)
+        case('x','X')
+            islip_plane=1
+        case('y','Y')
+            islip_plane=2
+        case('z','Z')
+            islip_plane=3
+        end select
+        do i = 1, 3
+            arg_pos = arg_pos + 1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if (arglen==0) STOP "Missing centroid in disl command"
+            call parse_pos(i, textholder, centroid(i))           
+        end do
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, textholder, arglen)
+        if (arglen==0) STOP "Missing parameter in disl command"
+        read(textholder, *) b 
+
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, textholder, arglen)
+        if (arglen==0) STOP "Missing character angle in disl command"
+        read(textholder, *) char_angle
+
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, textholder, arglen)
+        if (arglen==0) STOP "Missing poisson in disl command"
+        read(textholder, *) poisson
+
+        arg_pos = arg_pos + 1
+    end subroutine parse_disl
+
+    subroutine disl
+        !This subroutine creates the actual dislocation
+
+        integer :: i, sub_box, inod, ibasis, ix, iy, iz
+        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
+        
+        !Map box dimensions to dislocation dimensions, iz is along the dislocation line and iy is along the slip plane
+        iz = iline
+        iy = islip_plane
+        do i = 1, 3
+            if ((i /= iy).and.(i /=iz)) then 
+                ix = i
+                exit
+            end if
+        end do
+
+        if(atom_num > 0) then 
+            do i = 1, atom_num
+                r=r_atom(:,i) - centroid
+                if (r(ix) == 0) then 
+                    actan=pi/2
+                else
+                    actan = datan2(r(iy),r(ix))
+                end if
+
+                if ((r(ix)**2 + r(iy)**2) == 0) cycle
+
+                !This is the elastic displacement field for dislocation according to Hirth and Lowe
+                disp(ix) = be/(2.0_dp*pi) * (actan + (r(ix)*r(iy))/(2.0_dp*(1.0_dp-poisson)*(r(ix)**2.0_dp + r(iy)**2.0_dp)))
+                disp(iy) = -be/(2.0_dp*pi)*((1.0_dp-2.0_dp*poisson)/(4.0_dp-4.0_dp*poisson) * &
+                                            log(r(ix)**2.0_dp + r(iy)**2.0_dp) &
+                                            + (r(ix)**2.0_dp - r(iy)**2.0_dp)/(4.0_dp*(1.0_dp-poisson)&
+                                            *(r(ix)**2.0_dp+r(iy)**2.0_dp)))
+                disp(iz) = bs/(2.0_dp*pi) * actan
+                
+                r_atom(:,i) = r_atom(:,i) + disp
+            end do
+        end if
+
+        if(ele_num > 0) then 
+            do i = 1, ele_num
+                do inod=1, ng_node(lat_ele(i))
+                    do ibasis = 1, basisnum(lat_ele(i))
+                        r = r_node(:,ibasis,inod,i)-centroid
+                        if (r(ix) == 0) then 
+                            actan = pi/2
+                        else
+                            actan = datan2(r(iy),r(ix))
+                        end if
+
+                        if ((r(ix)**2 + r(iy)**2) == 0) cycle
+                
+                        !This is the elastic displacement field for dislocation according to Hirth and Lowe
+                        disp(ix) = be/(2.0_dp*pi)*(actan + (r(ix)*r(iy))/(2.0_dp*(1.0_dp-poisson)*(r(ix)**2.0_dp + r(iy)**2.0_dp)))
+                        disp(iy) = -be/(2.0_dp*pi)*((1.0_dp-2.0_dp*poisson)/(4.0_dp-4.0_dp*poisson) * &
+                                                    log(r(ix)**2.0_dp + r(iy)**2.0_dp) &
+                                                    + (r(ix)**2.0_dp - r(iy)**2.0_dp)/(4.0_dp*(1.0_dp-poisson)&
+                                                    *(r(ix)**2.0_dp+r(iy)**2.0_dp)))
+                        disp(iz) = bs/(2.0_dp*pi) * actan
+
+
+                        r_node(:,ibasis,inod,i) = r_node(:,ibasis,inod,i) + disp
+                    end do
+                end do
+            end do
+        end if
+
+
+    end subroutine disl
+
     subroutine parse_dislgen(arg_pos)
 
         !Parse dislgen command
@@ -123,6 +267,7 @@ module opt_disl
         call matrix_inverse(ss_ori, 3, ss_inv)
 
         !Apply the rotation
+        print *, ss_inv
         disp_transform = matmul(sub_box_ori(:,:,i), ss_inv)
         call matrix_inverse(disp_transform,3,inv_transform)
 
@@ -183,8 +328,6 @@ module opt_disl
             end do
         end if
 
-        !Now make sure all atoms are wrapped back into the simulation cell
-        call wrap_atoms
 
     end subroutine dislgen
 
@@ -398,8 +541,6 @@ module opt_disl
         end do
         return
 
-        !Now make sure all atoms are wrapped back into the simulation cell
-        call wrap_atoms
     end subroutine
 
     !********************************************************

src/opt_orient.f90

@@ -16,7 +16,7 @@ module opt_orient
     public 
     contains
 
-    subroutine orient(arg_pos)
+    subroutine orient_opt(arg_pos)
 
         integer, intent(inout) :: arg_pos
 
@@ -82,7 +82,7 @@ module opt_orient
         end do
 
             call def_new_box
-    end subroutine orient
+    end subroutine orient_opt
 
     subroutine parse_orient(arg_pos)
         !This parses the orient option 

src/opt_redef_box.f90

@@ -78,7 +78,7 @@ module opt_redef_box
 
     end subroutine redef_box
 
-    subroutine parse_redef_box(arg_pos)
+        subroutine parse_redef_box(arg_pos)
         !Parse the command
         integer, intent(inout) :: arg_pos
 

src/str.f90

@@ -0,0 +1,33 @@
+module str
+
+    !this module has some string manipulation commands 
+    public
+    contains
+
+    pure function tok_count(text)
+        !counts number of tokens in a string
+        character(len =  *), intent(in) ::  text
+        integer :: tok_count
+        integer :: i, j
+        logical :: in_tok
+
+        j = len(trim(adjustl(text)))
+        in_tok = .false.
+        tok_count = 0
+        do i = 1, j
+            !This checks if it is a white space character which is the delimiter
+            if(trim(adjustl(text(i:i))) == ' ') then 
+                !If previously we were in token and the current character is the delimiter 
+                !Then we are no longer in the token
+                if(in_tok) in_tok = .false.
+
+            !If the character isn't a white space character and we previously weren't in the token then set in_tok 
+            !to true and increment token count
+            else if(.not.in_tok) then 
+                in_tok = .true.
+                tok_count = tok_count + 1
+            end if
+        end do
+        return
+    end function tok_count
+end module str