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CACmb
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Merge branch 'development' into 'master'

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1.5

See merge request aselimov/cacmb!4
master
Alex Selimov 4 years ago
parent 32ab5a6058 2e7571cfa5
commit 5e56f2da10
27 changed files with 2892 additions and 556 deletions
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74
README.md
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@ -45,16 +45,6 @@ Default orientation is `[100] [010] [001]`. If this keyword is present then the
*Example:* `orient [-112] [110] [-11-1]` *Example:* `orient [-112] [110] [-11-1]`
**Basis**
```
basis num atom_name x y z
```
Default basis has `atom_name = name` with position (0,0,0). If used then the `atom_name x y z` must be include `num` times.
*Example:* `basis 2 Mg 0 0 0 Mg 0.5 0.288675 0.81647`
**Duplicate** **Duplicate**
``` ```
@ -68,7 +58,7 @@ Default duplicate is `1 1 1`. This is used to replicate the element along each d
**Dimensions** **Dimensions**
``` ```
dimensions dimx dimy dimz dim dimx dimy dimz
``` ```
There is no default dimensions as duplicate is the default option. This command assigns a box with user-assigned dimensions and fills it with the desired element. By default atoms fill in the jagged edges at the boundaries if the dimensions command is included. There is no default dimensions as duplicate is the default option. This command assigns a box with user-assigned dimensions and fills it with the desired element. By default atoms fill in the jagged edges at the boundaries if the dimensions command is included.
@ -92,6 +82,13 @@ basis basisnum bname bx by bz
``` ```
This function allows you to define a custom basis. `bname bx by bz` must be repeated `basisnum` times. This function allows you to define a custom basis. `bname bx by bz` must be repeated `basisnum` times.
**efill**
```
efill xyz
```
This command will rerun the creation algorithm with multiple times starting with an esize of `esize` and decreasing it by half on every iteration in an effort to maximize the reduction of degrees of freedom in the system. You must specify which dimensions will be filled. The code accepts `x`, `y`, `z`, `xy`, `yz`, `xz`, and `xyz` specifying which boundaries to fill in.
### Mode Convert ### Mode Convert
``` ```
@ -132,6 +129,11 @@ wrap
This will wrap atomic positions back inside the box. Effectively as if periodic boundary conditions are applied so that atoms which exit from one side of the simulation cell enter back in through the other. This will wrap atomic positions back inside the box. Effectively as if periodic boundary conditions are applied so that atoms which exit from one side of the simulation cell enter back in through the other.
###Mode Metric
```
--metric cmetric nfiles {filepaths}
```
## Options ## Options
Options are additional portions of code which have additional functionality. Options are performed in the order that they appear in the argument list and can be added to any mode. If wanting to use strictly options use `--convert` to specify input and output files. Options are additional portions of code which have additional functionality. Options are performed in the order that they appear in the argument list and can be added to any mode. If wanting to use strictly options use `--convert` to specify input and output files.
@ -188,15 +190,15 @@ This option creates a circular planar vacancy cluster of radius `radius` normal
`-group select_type group_shape shape_arguments additional keywords` `-group select_type group_shape shape_arguments additional keywords`
This option selects a group of either elements, nodes, atoms and applies some transformation to them. This option selects a group of either elements or atoms and applies some transformation to them.
`select_type` - Either `nodes`, `atoms`, `elements`, `nodes/atoms`, `all`. When using the option `nodes` only nodes which are within the group are selected, `elements` selects elements based on whether the element center is within the group, `nodes/atoms` selects both nodes and atoms for the group. `all` selects elements based on the element center and atoms based on their position. `select_type` - Either `atoms`, `elements`, or 'both'. `elements` selects elements based on whether the element center is within the group. `both` selects elements based on the element center and atoms based on their position.
`group_shape` - Specifies what shape the group takes and dictates which options must be passed. Each shape requires different arguments and these arguments are represented by the placeholder `shape_arguments`. The accepted group shapes and arguments are below: `group_shape` - Specifies what shape the group takes and dictates which options must be passed. Each shape requires different arguments and these arguments are represented by the placeholder `shape_arguments`. The accepted group shapes and arguments are below:
*Block:* *Block:*
`-group nodes block xlo xhi ylo yhi zlo zhi` `-group atoms block xlo xhi ylo yhi zlo zhi`
This selects a group residing in a block with edges perpendicular to the simulation cell. The block boundaries are given by `xlo xhi ylo yhi zlo zhi`. This selects a group residing in a block with edges perpendicular to the simulation cell. The block boundaries are given by `xlo xhi ylo yhi zlo zhi`.
@ -204,7 +206,7 @@ This selects a group residing in a block with edges perpendicular to the simulat
*Wedge:* *Wedge:*
`-group nodes wedge dim1 dim2 bx by bz bw` `-group atoms wedge dim1 dim2 bx by bz bw`
This selects a group which are within a wedge shape. The options are given as follows: This selects a group which are within a wedge shape. The options are given as follows:
`dim1` - The dimension containing the plane normal of the wedge base. `dim1` - The dimension containing the plane normal of the wedge base.
`dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2. `dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2.
@ -213,7 +215,7 @@ This selects a group which are within a wedge shape. The options are given as fo
*Notch:* *Notch:*
`-group nodes notch dim1 dim2 bx by bz bw tr` `-group atoms notch dim1 dim2 bx by bz bw tr`
This shape is similar to a wedge shape except instead of becoming atomically sharp, it finishes in a rounded tip with tip radius `tr`. Options are as follows. This shape is similar to a wedge shape except instead of becoming atomically sharp, it finishes in a rounded tip with tip radius `tr`. Options are as follows.
`dim1` - The dimension containing the plane normal of the wedge base. `dim1` - The dimension containing the plane normal of the wedge base.
`dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2. `dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2.
@ -221,6 +223,11 @@ This shape is similar to a wedge shape except instead of becoming atomically sha
`bw` - Base width `bw` - Base width
`tr` - Tip radius `tr` - Tip radius
*Sphere*
`-group atoms sphere x y z r`
This shape selects all atoms within a sphere centered at `(x,y,z)` with radius `r`.
**Displace:** **Displace:**
``` ```
@ -240,10 +247,10 @@ This command wraps atoms back into the simulation cell as though periodic bounda
**Remesh** **Remesh**
``` ```
remesh esize lattice_parameter lattice_type 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. When remeshing to atomistics the group can contain any orientations of elements but when remeshing to different finite elements, the group must contain all atoms/elements with the same orientation. `lattice_parameter` is the lattice parameter for the elements within the group and `lattice_type` is the lattice type (integer) that these new elements will be assigned to. This command remeshes the atoms/elements within the group to the new element size `esize`.
**Max** **Max**
@ -261,6 +268,29 @@ delete
This command deletes all selected atoms and elements within the group. This command deletes all selected atoms and elements within the group.
**Random**
```
random n
```
This command selects `n` random atoms and `n` random elements within your group bounds. If using group type `atoms` or `elements` then only `n` random atoms or elements are selected. This random atoms/elements then form the new group.
**Nodes**
```
nodes
```
This keyword changes the selection criteria when using `elements` or `both` to element nodes instead of element centroids.
**Flip**
```
flip
```
This keyword changes the group selection criteria from the atoms/elements inside a region to the atoms/elements outside the group.
### Option overwrite ### Option overwrite
``` ```
@ -303,8 +333,14 @@ This command will delete all overlapping atoms within a specific cutoff radius `
This option is primarily used when reading data from non .mb formats. This code simply sets the orientation variable for the specified sub box `sbox`. This option is primarily used when reading data from non .mb formats. This code simply sets the orientation variable for the specified sub box `sbox`.
### Option redef_box
```
-redef_box redef_dim {xlo xhi} {ylo yhi} {zlo zhi}
```
This option allows for the user to redefine box boundaries deleting atoms/elements outside of the new box boundaries. Elements are refined to atmoistics if they intersect the newly defined box boundaries.
The arguments are described below:
`redef_dim` - The dimensions to be redefined. Can be any permutation of `x`, `y`, `z`, `xy`, `yz`, `xz`, `xyz`. The order of the dimensions dictates the order that the new dimensions must be defined
**** ****
## Position Specification ## Position Specification
Specifying positions in cacmb can be done through a variety of ways. Examples of each format is shown below. Specifying positions in cacmb can be done through a variety of ways. Examples of each format is shown below.

79
src/Makefile
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@ -1,44 +1,49 @@
FC=ifort
#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
MODES=mode_create.o mode_merge.o mode_convert.o
OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o
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
.SUFFIXES:
.SUFFIXES: .c .f .f90 .F90 .o .SUFFIXES: .c .f .f90 .F90 .o
.DEFAULT_GOAL := all
cacmb: $(OBJECTS) FC=mpif90
$(FC) $(FFLAGS) $(OBJECTS) parameters.o -o $@ 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: .f90.o:
$(FC) $(FFLAGS) -c $< $(FC) $(FFLAGS) -c $<
deps:
@fortdepend -o Makefile.dep -i mpi -b obj -w
#----------------- CLEAN UP -----------------#
.PHONY: clean .PHONY: clean
clean: clean:
$(RM) cacmb *.o $(RM) *.mod *.o
$(RM) $(OBJDIR)/*.mod $(OBJDIR)/*.o CAC
testfuncs: testfuncs.o functions.o subroutines.o @$(RM) -rf obj/
$(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@
.PHONY: clean-all
.PHONY: cleantest clean-all: clean
cleantest:
$(RM) testfuncs testfuncs.o # DEBUGGING VARIABLE PRINT
print-% : ; @echo $* = $($*)
.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

167
src/Makefile.dep
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@ -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

29
src/box.f90
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@ -14,7 +14,6 @@ module box
real(kind=dp), allocatable :: sub_box_ori(:,:,:)!Orientations for each of the subboxes real(kind=dp), allocatable :: sub_box_ori(:,:,:)!Orientations for each of the subboxes
real(kind=dp), allocatable :: sub_box_bd(:,:)!Boundaries for each of the sub_boxes real(kind=dp), allocatable :: sub_box_bd(:,:)!Boundaries for each of the sub_boxes
!Below are some simulation parameters which may be adjusted if reading in restart files !Below are some simulation parameters which may be adjusted if reading in restart files
integer :: timestep=0 integer :: timestep=0
real(kind=dp) :: total_time=0.0_dp real(kind=dp) :: total_time=0.0_dp
@ -74,10 +73,15 @@ module box
integer :: i integer :: i
do i = 1, 3 if(all(abs(box_bd) < lim_zero)) then
if(temp_box_bd(2*i-1) < box_bd(2*i-1)) box_bd(2*i-1) = temp_box_bd(2*i-1) box_bd = temp_box_bd
if(temp_box_bd(2*i) > box_bd(2*i)) box_bd(2*i) = temp_box_bd(2*i) else
end do do i = 1, 3
if(temp_box_bd(2*i-1) < box_bd(2*i-1)) box_bd(2*i-1) = temp_box_bd(2*i-1)
if(temp_box_bd(2*i) > box_bd(2*i)) box_bd(2*i) = temp_box_bd(2*i)
end do
end if
return return
end subroutine grow_box end subroutine grow_box
@ -98,4 +102,17 @@ module box
end do end do
return return
end subroutine in_sub_box end subroutine in_sub_box
end module box
subroutine reset_box
!This subroutine just resets the box boundary and position
box_bc = "ppp"
box_bd(:) = 0
end subroutine reset_box
pure function box_volume()
real(kind = dp) :: box_volume
box_volume = (box_bd(2) - box_bd(1)) * (box_bd(4) - box_bd(3))*(box_bd(6) - box_bd(5))
return
end function
end module box

29
src/call_mode.f90
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@ -1,29 +0,0 @@
subroutine call_mode(arg_pos,mode)
!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 parameters
implicit none
integer, intent(out) :: arg_pos
character(len=100), intent(in) :: mode
select case(mode)
case('--create')
call create(arg_pos)
case('--convert')
call convert(arg_pos)
case('--merge')
call merge(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

40
src/call_option.f90
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@ -1,40 +0,0 @@
subroutine call_option(option, arg_pos)
use parameters
use opt_disl
use opt_group
use opt_orient
use opt_delete
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('-delete')
call run_delete(arg_pos)
case default
print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
stop 3
end select
end subroutine call_option

91
src/caller.f90
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@ -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

362
src/elements.f90
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@ -11,24 +11,29 @@ module elements
!Data structures used to represent the CAC elements. Each index represents an element !Data structures used to represent the CAC elements. Each index represents an element
character(len=100), allocatable :: type_ele(:) !Element type character(len=100), allocatable :: type_ele(:) !Element type
integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:) !Element size integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:), tag_ele(:) !Element size
real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
!Element result data structures
real(kind=dp), allocatable :: force_node(:,:,:,:), virial_node(:,:,:,:), energy_node(:,:,:)
integer, save :: ele_num !Number of elements integer, save :: ele_num !Number of elements
integer, save :: node_num !Total number of nodes 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 !Data structure used to represent atoms
integer, allocatable :: type_atom(:)!atom type integer, allocatable :: type_atom(:)!atom type
integer, allocatable :: sbox_atom(:) integer, allocatable :: sbox_atom(:), tag_atom(:)
real(kind =dp),allocatable :: r_atom(:,:) !atom position real(kind =dp),allocatable :: r_atom(:,:) !atom position
integer :: atom_num=0 !Number of atoms integer :: atom_num=0 !Number of atoms
!Atom result data structures information
real(kind=8), allocatable :: force_atom(:,:), virial_atom(:,:), energy_atom(:)
!Mapping atom type to provided name !Mapping atom type to provided name
character(len=2), dimension(10) :: type_to_name character(len=2), dimension(10) :: type_to_name
integer :: atom_types = 0 integer :: atom_types = 0
!Variables for creating elements based on primitive cells !Variables for creating elements based on primitive cells
real(kind=dp) :: cubic_cell(3,8), fcc_cell(3,8), fcc_mat(3,3), fcc_inv(3,3) real(kind=dp) :: cubic_cell(3,8), fcc_cell(3,8), fcc_mat(3,3), fcc_inv(3,3), bcc_cell(3,8), bcc_mat(3,3), bcc_inv(3,3)
integer :: cubic_faces(4,6) integer :: cubic_faces(4,6)
!Below are lattice type arrays which provide information on the general form of the elements. !Below are lattice type arrays which provide information on the general form of the elements.
@ -36,16 +41,19 @@ module elements
integer :: lattice_types = 0 integer :: lattice_types = 0
integer :: max_ng_node, ng_node(10) !Max number of nodes per element and number of nodes per element for each lattice type integer :: max_ng_node, ng_node(10) !Max number of nodes per element and number of nodes per element for each lattice type
integer :: max_esize=0 !Maximum number of atoms per side of element integer :: max_esize=0 !Maximum number of atoms per side of element
real(kind=dp) :: lapa(10)
!These variables contain information on the basis, for simplicities sake we limit !These variables contain information on the basis, for simplicities sake we limit
!the user to the definition of 10 lattice types with 10 basis atoms at each lattice point. !the user to the definition of 10 lattice types with 10 basis atoms at each lattice point.
!This can be easily increased with no change to efficiency !This can be easily increased with no change to efficiency
integer :: max_basisnum, basisnum(10) !Max basis atom number, number of basis atoms in each lattice type integer :: max_basisnum, basisnum(10) !Max basis atom number, number of basis atoms in each lattice type
integer :: basis_type(10,10) integer :: basis_type(10,10)
real(kind=dp) :: lapa(10)
!Additional module level variables we need !Additional module level variables we need
logical :: wrap_flag logical :: wrap_flag
!flags for data variables
logical :: vflag
public public
contains contains
@ -87,12 +95,33 @@ module elements
0.0_dp, 0.5_dp, 0.5_dp, & 0.0_dp, 0.5_dp, 0.5_dp, &
0.5_dp, 0.0_dp, 0.5_dp /), & 0.5_dp, 0.0_dp, 0.5_dp /), &
shape(fcc_mat)) shape(fcc_mat))
!Initialize the bcc primitive cell
bcc_cell = reshape((/ 0.0_dp, 0.0_dp, 0.0_dp, &
0.5_dp, -0.5_dp, 0.5_dp, &
1.0_dp, 0.0_dp, 1.0_dp, &
0.5_dp, 0.5_dp, 0.5_dp, &
-0.5_dp, 0.5_dp, 0.5_dp, &
0.0_dp, 0.0_dp, 1.0_dp, &
0.5_dp, 0.5_dp, 1.5_dp, &
0.0_dp, 1.0_dp, 1.0_dp /), &
shape(bcc_cell))
bcc_mat = reshape((/ 0.5_dp, -0.5_dp, 0.5_dp, &
0.5_dp, 0.5_dp, 0.5_dp, &
-0.5_dp, 0.5_dp, 0.5_dp /), &
shape(bcc_mat))
call matrix_inverse(fcc_mat,3,fcc_inv) call matrix_inverse(fcc_mat,3,fcc_inv)
call matrix_inverse(bcc_mat,3,bcc_inv)
max_basisnum = 0 max_basisnum = 0
basisnum(:) = 0 basisnum(:) = 0
ng_node(:) = 0 ng_node(:) = 0
node_num = 0 node_num = 0
node_atoms = 0
ele_num = 0 ele_num = 0
atom_num = 0 atom_num = 0
end subroutine lattice_init end subroutine lattice_init
@ -112,6 +141,7 @@ module elements
real(kind=dp), dimension(3,max_ng_node) :: adjustVar real(kind=dp), dimension(3,max_ng_node) :: adjustVar
adjustVar(:,:) = 0.0_dp adjustVar(:,:) = 0.0_dp
vflag = .false.
select case(trim(ele_type)) select case(trim(ele_type))
@ -130,6 +160,9 @@ module elements
end if end if
cell_mat(:, 1:8) = fcc_cell + adjustVar(:,1:8) cell_mat(:, 1:8) = fcc_cell + adjustVar(:,1:8)
cell_mat(:,1:8) = lapa * ((esize-1)*matmul(orient_mat, cell_mat(:,1:8))) cell_mat(:,1:8) = lapa * ((esize-1)*matmul(orient_mat, cell_mat(:,1:8)))
case('bcc')
cell_mat(:,1:8) = bcc_cell
cell_mat(:,1:8) = lapa* ((esize-1)*matmul(orient_mat, cell_mat(:,1:8)))
case default case default
print *, "Element type ", trim(ele_type), " currently not accepted" print *, "Element type ", trim(ele_type), " currently not accepted"
stop stop
@ -146,7 +179,7 @@ module elements
!Allocate element arrays !Allocate element arrays
if(n > 0) then if(n > 0) then
allocate(type_ele(n), size_ele(n), lat_ele(n), sbox_ele(n), r_node(3,max_basisnum, max_ng_node,n), & allocate(type_ele(n), tag_ele(n), size_ele(n), lat_ele(n), sbox_ele(n), r_node(3,max_basisnum, max_ng_node,n), &
stat=allostat) stat=allostat)
if(allostat > 0) then if(allostat > 0) then
print *, "Error allocating element arrays in elements.f90 because of: ", allostat print *, "Error allocating element arrays in elements.f90 because of: ", allostat
@ -156,7 +189,7 @@ module elements
if(m > 0) then if(m > 0) then
!Allocate atom arrays !Allocate atom arrays
allocate(type_atom(m), sbox_atom(m), r_atom(3,m), stat=allostat) allocate(type_atom(m), sbox_atom(m), tag_atom(m), r_atom(3,m), stat=allostat)
if(allostat > 0) then if(allostat > 0) then
print *, "Error allocating atom arrays in elements.f90 because of: ", allostat print *, "Error allocating atom arrays in elements.f90 because of: ", allostat
stop stop
@ -175,84 +208,124 @@ module elements
!The default size we grow the !The default size we grow the
buffer_size = 1024 buffer_size = 1024
!Figure out the size of the atom and element arrays
ele_size = size(size_ele) !First check to make sure if it is allocated
atom_size = size(type_atom) if (allocated(size_ele)) then
!Check if we need to grow the ele_size, if so grow all the variables !Figure out the size of the atom and element arrays
if ( n+ele_num > size(size_ele)) then ele_size = size(size_ele)
allocate(temp_int(n+ele_num+buffer_size)) !Check if we need to grow the ele_size, if so grow all the variables
temp_int(1:ele_size) = lat_ele if ( n+ele_num > size(size_ele)) then
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, lat_ele) allocate(temp_int(n+ele_size+buffer_size))
temp_int(1:ele_size) = lat_ele(1:ele_size)
allocate(temp_int(n+ele_num+buffer_size)) temp_int(ele_size+1:) = 0
temp_int(1:ele_size) = size_ele call move_alloc(temp_int, lat_ele)
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, size_ele) allocate(temp_int(n+ele_size+buffer_size))
temp_int(1:ele_size) = tag_ele(1:ele_size)
allocate(temp_int(n+ele_num+buffer_size)) temp_int(ele_size+1:) = 0
temp_int(1:ele_size) = lat_ele call move_alloc(temp_int, tag_ele)
temp_int(ele_size+1:) = 0
call move_alloc(temp_int, sbox_ele) allocate(temp_int(n+ele_size+buffer_size))
temp_int(1:ele_size) = size_ele(1:ele_size)
allocate(char_temp(n+ele_num+buffer_size)) temp_int(ele_size+1:) = 0
char_temp(1:ele_size) = type_ele call move_alloc(temp_int, size_ele)
call move_alloc(char_temp, type_ele)
allocate(temp_int(n+ele_size+buffer_size))
allocate(temp_ele_real(3, max_basisnum, max_ng_node, n+ele_num+buffer_size)) temp_int(1:ele_size) = sbox_ele(1:ele_size)
temp_ele_real(:,:,:,1:ele_size) = r_node temp_int(ele_size+1:) = 0
temp_ele_real(:,:,:,ele_size+1:) = 0.0_dp call move_alloc(temp_int, sbox_ele)
call move_alloc(temp_ele_real, r_node)
allocate(char_temp(n+ele_size+buffer_size))
char_temp(1:ele_size) = type_ele(1:ele_size)
call move_alloc(char_temp, type_ele)
allocate(temp_ele_real(3, max_basisnum, max_ng_node, n+ele_size+buffer_size))
temp_ele_real(:,:,:,1:ele_size) = r_node(:,:,:,1:ele_size)
temp_ele_real(:,:,:,ele_size+1:) = 0.0_dp
call move_alloc(temp_ele_real, r_node)
end if
else
call alloc_ele_arrays(n,0)
end if end if
!Now grow atom arrays if needed !Now grow atom arrays if needed
if (m+atom_num > atom_size) then if (allocated(type_atom)) then
allocate(temp_int(m+atom_num+buffer_size)) atom_size = size(type_atom)
temp_int(1:atom_size) = type_atom if (m+atom_num > atom_size) then
temp_int(atom_size+1:) = 0 allocate(temp_int(m+atom_size+buffer_size))
call move_alloc(temp_int, type_atom) temp_int(1:atom_size) = type_atom
temp_int(atom_size+1:) = 0
allocate(temp_int(m+atom_num+buffer_size)) call move_alloc(temp_int, type_atom)
temp_int(1:atom_size) = sbox_atom
temp_int(atom_size+1:) = 0 allocate(temp_int(m+atom_size+buffer_size))
call move_alloc(temp_int, sbox_atom) temp_int(1:atom_size) = tag_atom
temp_int(atom_size+1:) = 0
allocate(temp_real(3,m+atom_num+buffer_size)) call move_alloc(temp_int, tag_atom)
temp_real(:,1:atom_size) = r_atom
temp_real(:, atom_size+1:) = 0.0_dp allocate(temp_int(m+atom_size+buffer_size))
call move_alloc(temp_real, r_atom) temp_int(1:atom_size) = sbox_atom
temp_int(atom_size+1:) = 0
call move_alloc(temp_int, sbox_atom)
allocate(temp_real(3,m+atom_size+buffer_size))
temp_real(:,1:atom_size) = r_atom
temp_real(:, atom_size+1:) = 0.0_dp
call move_alloc(temp_real, r_atom)
end if
else
call alloc_ele_arrays(0,m)
end if end if
end subroutine end subroutine
subroutine add_element(type, size, lat, sbox, r) subroutine add_element(tag, type, size, lat, sbox, r)
!Subroutine which adds an element to the element arrays !Subroutine which adds an element to the element arrays
integer, intent(in) :: size, lat, sbox integer, intent(in) :: size, lat, sbox, tag
character(len=100), intent(in) :: type character(len=100), intent(in) :: type
real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node) real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node)
integer :: newtag
ele_num = ele_num + 1 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
else
newtag = tag
end if
!Check to see if we need to grow the arrays !Check to see if we need to grow the arrays
call grow_ele_arrays(1,0) call grow_ele_arrays(1,0)
tag_ele(ele_num) = newtag
type_ele(ele_num) = type type_ele(ele_num) = type
size_ele(ele_num) = size size_ele(ele_num) = size
lat_ele(ele_num) = lat lat_ele(ele_num) = lat
sbox_ele(ele_num) = sbox sbox_ele(ele_num) = sbox
r_node(:,:,:,ele_num) = r(:,:,:) r_node(:,:,:,ele_num) = r(:,:,:)
node_num = node_num + ng_node(lat)
end subroutine add_element end subroutine add_element
subroutine add_atom(type, sbox, r) subroutine add_atom(tag, type, sbox, r)
!Subroutine which adds an atom to the atom arrays !Subroutine which adds an atom to the atom arrays
integer, intent(in) :: type, sbox integer, intent(in) :: type, sbox, tag
real(kind=dp), intent(in), dimension(3) :: r real(kind=dp), intent(in), dimension(3) :: r
integer :: newtag
atom_num = atom_num+1 atom_num = atom_num+1
if(tag==0) then
newtag = atom_num !If we don't assign a tag then pass the tag as the atom_num
else
newtag = tag
end if
!Check to see if we need to grow the arrays !Check to see if we need to grow the arrays
call grow_ele_arrays(0,1) call grow_ele_arrays(0,1)
tag_atom(atom_num) = tag
type_atom(atom_num) = type type_atom(atom_num) = type
r_atom(:,atom_num) = r(:) r_atom(:,atom_num) = r(:)
sbox_atom(atom_num) = sbox sbox_atom(atom_num) = sbox
@ -295,12 +368,12 @@ module elements
integer :: i integer :: i
max_ng_node = 0
do i=1, n do i=1, n
select case(trim(adjustl(element_types(i)))) select case(trim(adjustl(element_types(i))))
case('fcc') case('fcc')
ng_node(i) = 8 ng_node(i) = 8
case('bcc')
ng_node(i) = 8
end select end select
if(ng_node(i) > max_ng_node) max_ng_node = ng_node(i) if(ng_node(i) > max_ng_node) max_ng_node = ng_node(i)
@ -309,10 +382,14 @@ module elements
subroutine set_max_esize subroutine set_max_esize
!This subroutine sets the maximum esize !This subroutine sets the maximum esize
max_esize=maxval(size_ele) if(allocated(size_ele)) then
max_esize=maxval(size_ele)
else
max_esize = 2
end if
end subroutine 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. !This subroutine returns the interpolated atoms from the elements.
!Arguments !Arguments
@ -322,15 +399,19 @@ module elements
real(kind=dp), dimension(3,max_basisnum, max_ng_node), intent(in) :: r_in !Nodal positions 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 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), 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 !Internal variables
integer :: it, is, ir, ibasis, inod, ia, bnum, lat_type_temp 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 real(kind=dp) :: t, s, r
!Initialize some variables !Initialize some variables
r_interp(:,:) = 0.0_dp r_interp(:,:) = 0.0_dp
type_interp(:) = 0 type_interp(:) = 0
if(present(data_interp)) data_interp = 0.0_dp
ia = 0 ia = 0
!Define bnum based on the input lattice type. If lat_type=0 then we are interpolating lattice points which means !Define bnum based on the input lattice type. If lat_type=0 then we are interpolating lattice points which means
@ -346,8 +427,7 @@ module elements
end select end select
select case(trim(adjustl(type))) select case(trim(adjustl(type)))
case('fcc') case('fcc','bcc')
allocate(a_shape(8))
!Now loop over all the possible sites !Now loop over all the possible sites
do it = 1, esize do it = 1, esize
t = (1.0_dp*(it-1)-(esize-1)/2)/(1.0_dp*(esize-1)/2) t = (1.0_dp*(it-1)-(esize-1)/2)/(1.0_dp*(esize-1)/2)
@ -363,6 +443,12 @@ module elements
type_interp(ia) = basis_type(ibasis,lat_type_temp) type_interp(ia) = basis_type(ibasis,lat_type_temp)
r_interp(:,ia) = r_interp(:,ia) + a_shape(inod) * r_in(:,ibasis,inod) 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
end do end do
@ -381,7 +467,7 @@ module elements
subroutine rhombshape(r,s,t, shape_fun) subroutine rhombshape(r,s,t, shape_fun)
!Shape function for rhombohedral elements !Shape function for rhombohedral elements
real(kind=8), intent(in) :: r, s, t 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(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 shape_fun(2) = (1.0+r)*(1.0-s)*(1.0-t)/8.0
@ -446,19 +532,21 @@ module elements
!We go from largest index to smallest index just to make sure that we don't miss !We go from largest index to smallest index just to make sure that we don't miss
!accidentally overwrite values which need to be deleted !accidentally overwrite values which need to be deleted
do i = num, 1, -1 do i = num, 1, -1
node_num = node_num - ng_node(lat_ele(sorted_index(i)))
if(sorted_index(i) == ele_num) then if(sorted_index(i) == ele_num) then
r_node(:,:,:,sorted_index(i)) = 0.0_dp r_node(:,:,:,sorted_index(i)) = 0.0_dp
type_ele(sorted_index(i)) ='' type_ele(sorted_index(i)) =''
size_ele(sorted_index(i)) = 0 size_ele(sorted_index(i)) = 0
lat_ele(sorted_index(i)) = 0 lat_ele(sorted_index(i)) = 0
sbox_ele(sorted_index(i)) = 0 sbox_ele(sorted_index(i)) = 0
tag_ele(sorted_index(i)) = 0
else else
node_num = node_num - ng_node(lat_ele(sorted_index(i)))
r_node(:,:,:,sorted_index(i)) = r_node(:,:,:,ele_num) r_node(:,:,:,sorted_index(i)) = r_node(:,:,:,ele_num)
type_ele(sorted_index(i)) = type_ele(ele_num) type_ele(sorted_index(i)) = type_ele(ele_num)
size_ele(sorted_index(i)) = size_ele(ele_num) size_ele(sorted_index(i)) = size_ele(ele_num)
lat_ele(sorted_index(i)) = lat_ele(ele_num) lat_ele(sorted_index(i)) = lat_ele(ele_num)
sbox_ele(sorted_index(i)) = sbox_ele(ele_num) sbox_ele(sorted_index(i)) = sbox_ele(ele_num)
tag_ele(sorted_index(i)) = tag_ele(ele_num)
end if end if
ele_num = ele_num - 1 ele_num = ele_num - 1
end do end do
@ -481,8 +569,7 @@ module elements
max_bd(:) = -huge(1.0_dp) max_bd(:) = -huge(1.0_dp)
min_bd(:) = huge(1.0_dp) min_bd(:) = huge(1.0_dp)
do i = 1, atom_num
do i = 1, atom_num
do j = 1, 3 do j = 1, 3
if (r_atom(j,i) > max_bd(j)) max_bd(j) = r_atom(j,i) + tol if (r_atom(j,i) > max_bd(j)) max_bd(j) = r_atom(j,i) + tol
if (r_atom(j,i) < min_bd(j)) min_bd(j) = r_atom(j,i) - tol if (r_atom(j,i) < min_bd(j)) min_bd(j) = r_atom(j,i) - tol
@ -616,17 +703,17 @@ module elements
esize = size_ele(ie) esize = size_ele(ie)
select case(iface) select case(iface)
case(1) case(1)
pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, -10.0_dp**-2.0_dp /) pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, -10.0_dp**(-2.0_dp) /)
case(2) case(2)
pos = (/ real(esize-1,dp)/2.0_dp, -10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp /) pos = (/ real(esize-1,dp)/2.0_dp, -10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp /)
case(3) case(3)
pos = (/ (esize-1)+10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /) pos = (/ (esize-1)+10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
case(4) case(4)
pos = (/ real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp /) pos = (/ real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp /)
case(5) case(5)
pos = (/ -10.0_dp**-2.0_dp, real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /) pos = (/ -10.0_dp**(-2.0_dp), real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp /)
case(6) case(6)
pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**-2.0_dp /) pos = (/ real(esize-1,dp)/2.0_dp, real(esize-1,dp)/2.0_dp, (esize-1)+10.0_dp**(-2.0_dp) /)
end select end select
!Now transform it to real space and adjust it to the position of the element in the first node. !Now transform it to real space and adjust it to the position of the element in the first node.
@ -648,4 +735,131 @@ module elements
end select end select
end subroutine end subroutine
subroutine lattice_map(in_bnum, in_btypes, in_ngnodes, in_lapa, lat_type)
!This subroutine maps an input lattice type to either a new lattice type or an existing one depending on basis_type and
!number of nodes at the atoms
integer, intent(in) :: in_ngnodes, in_bnum, in_btypes(10) !Input variables
real(kind=dp), intent(in) :: in_lapa
integer, intent(out) :: lat_type
integer j, ibasis
lat_type = 0
lat_loop:do j = 1, lattice_types
!Check all the lattice level variables
if ((basisnum(j) == in_bnum).and.(ng_node(j) == in_ngnodes).and.(is_equal(lapa(j),in_lapa))) then
!Now check lattice level variables
do ibasis = 1, basisnum(j)
if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle lat_loop
end do
lat_type = j
exit lat_loop
end if
end do lat_loop
!If it doesn't match an existing lattice type we add it
if( lat_type == 0) then
lattice_types = lattice_types + 1
basisnum(lattice_types) = in_bnum
basis_type(:,lattice_types) = in_btypes
ng_node(lattice_types) = in_ngnodes
lapa(lattice_types) = in_lapa
lat_type = lattice_types
end if
end subroutine lattice_map
subroutine get_interp_pos(i,j,k, ie, rout)
!This returns the position of an interpolated basis from an element ie.
!i, j, k should be in natural coordinates
integer, intent(in) :: i, j, k
real(kind=dp), dimension(3,max_basisnum), intent(out) :: rout
integer :: ie, ibasis, inod
real(kind=dp) :: a_shape(8), r, s, t
r = (1.0_dp*(i-1)-(size_ele(ie)-1)/2)/(1.0_dp*(size_ele(ie)-1)/2)
s = (1.0_dp*(j-1)-(size_ele(ie)-1)/2)/(1.0_dp*(size_ele(ie)-1)/2)
t = (1.0_dp*(k-1)-(size_ele(ie)-1)/2)/(1.0_dp*(size_ele(ie)-1)/2)
rout(:,:) = 0
do ibasis = 1, basisnum(lat_ele(ie))
do inod = 1, ng_node(lat_ele(ie))
call rhombshape(r,s,t,a_shape)
rout(:,ibasis) = rout(:,ibasis) + a_shape(inod) * r_node(:,ibasis,inod,ie)
end do
end do
end subroutine get_interp_pos
subroutine alloc_dat_arrays(n,m)
!This subroutine used to provide initial allocation for the atom and element data arrays
integer, intent(in) :: n,m !n-size of element arrays, m-size of atom arrays
integer :: allostat
!Allocate element arrays
if (n > 0) then
if (allocated(force_node)) then
deallocate(force_node, virial_node, energy_node)
end if
allocate(force_node(3,max_basisnum, max_ng_node, n), &
virial_node(6,max_basisnum, max_ng_node, n), &
energy_node(max_basisnum,max_ng_node,n), &
stat=allostat)
if(allostat > 0) then
print *, "Error allocating element data arrays in mode_metric because of:", allostat
stop
end if
end if
if (m > 0) then
if (allocated(force_atom)) then
deallocate(force_atom, virial_atom, energy_atom)
end if
allocate(force_atom(3, m), &
virial_atom(6, m), &
energy_atom(m), &
stat=allostat)
if(allostat > 0) then
print *, "Error allocating atom data arrays in mode_metric because of:", allostat
stop
end if
end if
end subroutine
subroutine add_atom_data(ia, eng, force, virial)
!Function which sets the atom data arrays
integer, intent(in) :: ia
real(kind=dp), intent(in) :: eng, force(3), virial(6)
energy_atom(ia) = eng
force_atom(:,ia) = force(:)
virial_atom(:,ia) = virial(:)
vflag = .true.
return
end subroutine add_atom_data
subroutine add_element_data(ie, eng, force, virial)
!Function which sets the element data arrays
integer, intent(in) :: ie
real(kind=dp), intent(in) :: eng(max_basisnum, max_ng_node), &
force(3,max_basisnum, max_ng_node), &
virial(6,max_basisnum,max_ng_node)
vflag = .true.
energy_node(:,:,ie) = eng
force_node(:,:,:,ie) = force
virial_node(:,:,:,ie) = virial
return
end subroutine add_element_data
subroutine reset_data
!This function resets all of the data arrays for the elements and atoms
atom_num = 0
ele_num = 0
node_num = 0
end subroutine reset_data
end module elements end module elements

128
src/functions.f90
Unescape View File

@ -271,4 +271,132 @@ END FUNCTION StrDnCase
norm_dis(1:3) = (rk - rl) norm_dis(1:3) = (rk - rl)
norm_dis(4) = norm2(rk-rl) norm_dis(4) = norm2(rk-rl)
end function end function
pure function matinv3(A) result(B)
!! Performs a direct calculation of the inverse of a 3×3 matrix.
real(kind=dp), intent(in) :: A(3,3) !! Matrix
real(kind=dp) :: B(3,3) !! Inverse matrix
real(kind=dp) :: detinv
if(abs(A(1,1)*A(2,2)*A(3,3) - A(1,1)*A(2,3)*A(3,2)&
- A(1,2)*A(2,1)*A(3,3) + A(1,2)*A(2,3)*A(3,1)&
+ A(1,3)*A(2,1)*A(3,2) - A(1,3)*A(2,2)*A(3,1)) < lim_zero) then
B(:,:) = 0
return
else
! Calculate the inverse determinant of the matrix
detinv = 1/(A(1,1)*A(2,2)*A(3,3) - A(1,1)*A(2,3)*A(3,2)&
- A(1,2)*A(2,1)*A(3,3) + A(1,2)*A(2,3)*A(3,1)&
+ A(1,3)*A(2,1)*A(3,2) - A(1,3)*A(2,2)*A(3,1))
! Calculate the inverse of the matrix
B(1,1) = +detinv * (A(2,2)*A(3,3) - A(2,3)*A(3,2))
B(2,1) = -detinv * (A(2,1)*A(3,3) - A(2,3)*A(3,1))
B(3,1) = +detinv * (A(2,1)*A(3,2) - A(2,2)*A(3,1))
B(1,2) = -detinv * (A(1,2)*A(3,3) - A(1,3)*A(3,2))
B(2,2) = +detinv * (A(1,1)*A(3,3) - A(1,3)*A(3,1))
B(3,2) = -detinv * (A(1,1)*A(3,2) - A(1,2)*A(3,1))
B(1,3) = +detinv * (A(1,2)*A(2,3) - A(1,3)*A(2,2))
B(2,3) = -detinv * (A(1,1)*A(2,3) - A(1,3)*A(2,1))
B(3,3) = +detinv * (A(1,1)*A(2,2) - A(1,2)*A(2,1))
end if
end function
pure function transpose3(A) result(B)
!!Transposes matrix A
real(kind=dp), intent(in) :: A(3,3)
real(kind=dp) :: B(3,3)
integer :: i, j
forall(i =1:3,j=1:3) B(i,j) = A(j,i)
end function transpose3
pure function sqrt3(A) result(B)
!This calculates the square of matrix A fulfilling the equation B*B = A according to
!the algorithm by Franca1989
real(kind=dp), intent(in) :: A(3,3)
real(kind=dp) :: B(3,3)
real(kind=dp) :: Ione, Itwo, Ithree, l, k, phi, Asq(3,3), lambda, Bone, Btwo, Bthree, p
!Step 1 is calculating the invariants of C
Ione = A(1,1) + A(2,2) + A(3,3)
Asq = matmul(A,A)
Itwo = 0.5_dp *(Ione*Ione - (Asq(1,1) + Asq(2,2) + Asq(3,3)))
Ithree = (A(1,1)*A(2,2)*A(3,3) - A(1,1)*A(2,3)*A(3,2)&
- A(1,2)*A(2,1)*A(3,3) + A(1,2)*A(2,3)*A(3,1)&
+ A(1,3)*A(2,1)*A(3,2) - A(1,3)*A(2,2)*A(3,1))
if (Ithree < 0) then
B(:,:)=0.0_dp
return
end if
!Check for an isotropic matrix
k = Ione*Ione - 3*Itwo
if (k < lim_zero) then
lambda = sqrt(Ione/3.0_dp)
B = lambda*identity_mat(3)
else
l = Ione*(Ione*Ione - 9.0_dp/2.0_dp * Itwo) + 27.0_dp/2.0_dp * Ithree
p = l/(k**(1.5_dp))
if (p > 1.0 ) then
B(:,:) = 0.0_dp
return
end if
if ((p< -1).or.(p>1)) then
B(:,:) = 0.0_dp
return
end if
phi = acos(p)
lambda = sqrt(1.0_dp/3.0_dp * (Ione + 2*sqrt(k)*cos(phi/3)))
!Now calculate invariantes of B
Bthree = sqrt(Ithree)
if((-lambda*lambda + Ione + 2*Ithree/lambda) < 0) then
B(:,:) = 0.0_dp
return
end if
Bone = lambda + sqrt(- lambda*lambda + Ione + 2*Ithree/lambda)
Btwo = (Bone*Bone - Ione)/2.0_dp
!Now calculate B
if(abs(Bone*Btwo -Bthree) < lim_zero) then
B(:,:) = 0.0_dp
return
end if
B = 1/(Bone*Btwo - Bthree) *(Bone*Bthree*identity_mat(3) + (Bone*Bone - Btwo)*A - matmul(A,A))
end if
end function sqrt3
pure function permutation(i,j,k) result(e)
!Calculates the permutation tensor
integer, intent(in) :: i,j,k
integer :: e
if ( ((i==1).and.(j==2).and.(k==3)).or. &
((i==2).and.(j==3).and.(k==1)).or. &
((i==3).and.(j==1).and.(k==2))) then
e=1
else if( ((i==2).and.(j==1).and.(k==3)).or. &
((i==1).and.(j==3).and.(k==2)).or. &
((i==3).and.(j==2).and.(k==1))) then
e=-1
else
e=0
end if
end function permutation
pure function evtogp(virial)
real(kind=dp), dimension(6), intent(in) :: virial
real(kind=dp), dimension(6) :: evtogp
evtogp = virial * 1e21_dp * 1.602176565e-19_dp
end function
end module functions end module functions

658
src/io.f90
Unescape View File

@ -4,13 +4,14 @@ module io
use parameters use parameters
use atoms use atoms
use box use box
use str
implicit none implicit none
integer :: outfilenum = 0, infilenum = 0 integer :: outfilenum = 0, infilenum = 0
character(len=100) :: outfiles(100), infiles(100) character(len=100) :: outfiles(100), infiles(100), in_lattice_type=''
logical :: force_overwrite logical :: force_overwrite
real(kind=dp) :: in_lapa=0.0
public public
contains contains
@ -59,7 +60,7 @@ module io
cycle cycle
end if end if
select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:)) 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 outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile outfiles(outfilenum) = temp_outfile
exit exit
@ -104,9 +105,11 @@ module io
call write_pycac(outfiles(i)) call write_pycac(outfiles(i))
case('cac') case('cac')
call write_lmpcac(outfiles(i)) call write_lmpcac(outfiles(i))
case('dump')
call write_ldump(outfiles(i))
case default case default
print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), & print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
" is not accepted for writing. Please select from: xyz and try again" " is not accepted for writing. Please select from: xyz, lmp, vtk, mb, restart, cac and try again"
stop stop
end select end select
@ -119,30 +122,41 @@ module io
!This is the simplest visualization subroutine, it writes out all nodal positions and atom positions to an xyz file !This is the simplest visualization subroutine, it writes out all nodal positions and atom positions to an xyz file
character(len=100), intent(in) :: file character(len=100), intent(in) :: file
integer :: i, inod, ibasis integer :: i, inod, ibasis, outn
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind') open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
!Write total number of atoms + elements !Write total number of atoms + elements
write(11, '(i16)') node_num+atom_num write(11, '(i16)') node_atoms+atom_num
!Write comment line !Write comment line
write(11, '(a)') "#Node + atom file created using cacmb" write(11, '(a)') "#Node + atom file created using cacmb"
outn=0
!Write nodal positions !Write nodal positions
do i = 1, ele_num do i = 1, ele_num
do inod = 1, ng_node(lat_ele(i)) do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i)) do ibasis = 1, basisnum(lat_ele(i))
write(11, '(i16, 3f23.15)') basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i) write(11, '(2i16, 3f23.15)') basis_type(ibasis,lat_ele(i)), 1, r_node(:,ibasis,inod,i)
outn = outn + 1
end do end do
end do end do
end do end do
if(outn /= node_atoms) then
print *, "outn", outn, " doesn't equal node_atoms ", node_atoms
end if
!Write atom positions !Write atom positions
do i = 1, atom_num do i = 1, atom_num
write(11, '(i16, 3f23.15)') type_atom(i), r_atom(:,i) write(11, '(2i16, 3f23.15)') type_atom(i), 0, r_atom(:,i)
outn = outn + 1
end do end do
if((outn-node_atoms) /= atom_num) then
print *, "outn", (outn-node_atoms), " doesn't equal atom_num ", atom_num
end if
!Finish writing !Finish writing
close(11) close(11)
end subroutine write_xyz end subroutine write_xyz
@ -161,8 +175,10 @@ module io
!Calculate total atom number !Calculate total atom number
write_num = atom_num write_num = atom_num
do i = 1,ele_num do i = 1,ele_num
if(type_ele(i) == 'fcc') write_num = write_num + basisnum(lat_ele(i))*size_ele(i)**3 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 end do
!Write total number of atoms + elements !Write total number of atoms + elements
write(11, '(i16, a)') write_num, ' atoms' write(11, '(i16, a)') write_num, ' atoms'
!Write number of atom types !Write number of atom types
@ -196,7 +212,7 @@ module io
do i = 1, ele_num do i = 1, ele_num
call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp) call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
select case(trim(adjustl(type_ele(i)))) select case(trim(adjustl(type_ele(i))))
case('fcc') case('fcc','bcc')
do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3 do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
interp_num = interp_num+1 interp_num = interp_num+1
call apply_periodic(r_interp(:,iatom)) call apply_periodic(r_interp(:,iatom))
@ -206,6 +222,88 @@ module io
end do end do
end subroutine write_lmp 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) subroutine write_lmpcac(file)
!This subroutine writes out a .lmp style dump file !This subroutine writes out a .lmp style dump file
character(len=100), intent(in) :: file character(len=100), intent(in) :: file
@ -339,6 +437,7 @@ module io
end do end do
close(11) close(11)
!Now we write the vtk file for the elements
open(unit=11, file='cg_'//trim(adjustl(file)), action='write', status='replace',position='rewind') open(unit=11, file='cg_'//trim(adjustl(file)), action='write', status='replace',position='rewind')
write(11,1) write(11,1)
write(11,2) write(11,2)
@ -357,6 +456,7 @@ module io
write(11,5) ele_num write(11,5) ele_num
do i = 1, ele_num do i = 1, ele_num
if(trim(adjustl(type_ele(i))) == 'fcc') write(11, '(i16)') 12 if(trim(adjustl(type_ele(i))) == 'fcc') write(11, '(i16)') 12
if(trim(adjustl(type_ele(i))) == 'bcc') write(11, '(i16)') 12
end do end do
write(11,12) ele_num write(11,12) ele_num
write(11,20) write(11,20)
@ -375,55 +475,32 @@ module io
!NOTE: This code doesn't work for arbitrary number of basis atoms per node. It assumes that the !NOTE: This code doesn't work for arbitrary number of basis atoms per node. It assumes that the
!each element has only 1 atom type at the node. !each element has only 1 atom type at the node.
character(len=100), intent(in) :: file character(len=100), intent(in) :: file
integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_num, & integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_type(50), unique_num, &
etype etype
real(kind=dp) :: box_vec(3) real(kind=dp) :: box_vec(3), masses(10)
1 format('time' / i16, f23.15) 1 format('time' / i16, f23.15)
2 format('number of elements' / i16) 2 format('number of elements' / i16)
3 format('number of nodes' / i16) 3 format('number of nodes' / i16)
4 format('element types' / i16)
5 format('number of atoms' / i16) 5 format('number of atoms' / i16)
6 format('number of grains' / i16)
7 format('boundary ' / 3a1) 7 format('boundary ' / 3a1)
8 format('box bound' / 6f23.15) 8 format('box bound' / 6f23.15)
9 format('box length' / 3f23.15) 9 format('box length' / 3f23.15)
10 format('box matrix') 10 format('box matrix')
11 format(3f23.15) 11 format(3f23.15)
12 format('coarse-grained domain') 12 format('coarse-grained domain')
13 format('ie ele_type grain_ele lat_type_ele'/ 'ip ibasis x y z') 13 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z')
14 format('atomistic domain' / 'ia grain_atom type_atom x y z') 14 format('atomistic domain' / 'ia type_atom x y z')
15 format('maximum lattice periodicity length' / 3f23.15) 19 format('max nodes per element and basis per nodes' / 2i16)
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)
20 format('max interpo per element' / i16) 20 format('max interpo per element' / i16)
21 format('atom types to elements') 21 format('atom types to elements')
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind') 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(11,1) timestep, total_time
write(11,2) ele_num 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)
end do eleloop
!Calculate the max number of atoms per element !Calculate the max number of atoms per element
select case(max_ng_node) select case(max_ng_node)
case(8) case(8)
@ -431,31 +508,19 @@ module io
case default case default
interp_max = 0 interp_max = 0
end select end select
write(11,20) interp_max write(11,20) interp_max
!Write
write(11,3) node_num write(11,3) node_num
write(11,19) max_ng_node write(11,19) max_ng_node, max_basisnum
write(11,4) unique_num
write(11,5) atom_num 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 do i = 1, atom_types
write(11,*) i, type_to_name(i) call atommass(type_to_name(i),masses(i))
end do 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(11,7) 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(11,8) 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) write(11,10)
!Current boxes are limited to being rectangular !Current boxes are limited to being rectangular
do i = 1,3 do i = 1,3
@ -463,35 +528,18 @@ module io
box_vec(i) = box_bd(2*i) - box_bd(2*i-1) box_vec(i) = box_bd(2*i) - box_bd(2*i-1)
write(11,11) box_vec write(11,11) box_vec
end do 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 !write the element information
if(ele_num > 0) then if(ele_num > 0) then
write(11,12) 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 ip = 0
write(11,13) write(11,13)
do i = 1, ele_num do i = 1, ele_num
!Figure out the ele type write(11, '(4i16)') i, basisnum(lat_ele(i)), 2, (size_ele(i)-1)
do j = 1, unique_num
if ( unique_size(j) == size_ele(i)) then
etype = j
exit
endif
end do
write(11, '(4i16)') i, etype, 1, basis_type(1,lat_ele(i))
do inod = 1, ng_node(lat_ele(i)) do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i)) do ibasis = 1, basisnum(lat_ele(i))
ip = ip + 1 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 end do
end do end do
@ -501,7 +549,7 @@ module io
if(atom_num /= 0) then if(atom_num /= 0) then
write(11,14) write(11,14)
do i = 1, atom_num 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 do
end if end if
@ -543,13 +591,13 @@ module io
!Write out atoms first !Write out atoms first
do i = 1, atom_num do i = 1, atom_num
write(11,*) i, type_atom(i), sbox_atom(i), r_atom(:,i) write(11,*) tag_atom(i), type_atom(i), sbox_atom(i), r_atom(:,i)
end do end do
!Write out the elements, this is written in two stages, one line for the element and then 1 line for !Write out the elements, this is written in two stages, one line for the element and then 1 line for
!every basis at every node !every basis at every node
do i = 1, ele_num do i = 1, ele_num
write(11, *) i, lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i) write(11, *) tag_ele(i), lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i)
do inod = 1, ng_node(lat_ele(i)) do inod = 1, ng_node(lat_ele(i))
do ibasis =1, basisnum(lat_ele(i)) do ibasis =1, basisnum(lat_ele(i))
write(11,*) inod, ibasis, r_node(:, ibasis, inod, i) write(11,*) inod, ibasis, r_node(:, ibasis, inod, i)
@ -579,34 +627,41 @@ module io
temp_infile = filename temp_infile = filename
end if end if
!Infinite loop which only exists if user provides valid filetype !Check to see if file exists, if it does then ask user if they would like to overwrite the file
do while(.true.) inquire(file=trim(temp_infile), exist=file_exists)
if (.not.file_exists) then
print *, "The file ", trim(adjustl(filename)), " does not exist. Please input an existing file to read."
stop 3
end if
!Check to see if file exists, if it does then ask user if they would like to overwrite the file select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
inquire(file=trim(temp_infile), exist=file_exists) case('restart', 'mb', 'cac')
if (.not.file_exists) then infilenum=infilenum+1
print *, "The file ", trim(adjustl(filename)), " does not exist. Please input a filename that exists" infiles(infilenum) = temp_infile
read(*,*) temp_infile case('out')
cycle if(atom_types == 0) then
print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
stop 3
end if end if
select case(trim(adjustl(mode)))
select case(temp_infile(scan(temp_infile,'.',.true.)+1:)) case('--calc', '--convert','--metric')
case('restart', 'mb') infilenum = infilenum+1
infilenum=infilenum+1 infiles(infilenum) = temp_infile
infiles(infilenum) = temp_infile case default
exit print *, "Files of type .out cannot be used with mode ", trim(adjustl(mode))
case default stop 3
print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
"please input a filename with extension from following list: mb, restart."
read(*,*) temp_infile
end select end select
end do
case default
print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
"please input a filename with extension from following list: mb, restart, cac, or out."
stop 3
end select
end subroutine get_in_file end subroutine get_in_file
subroutine read_in(i, displace, temp_box_bd) subroutine read_in(i, displace, temp_box_bd)
!This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine !This subroutine reads in file i
integer, intent(in) :: i integer, intent(in) :: i
real(kind=dp), dimension(3), intent(in) :: displace real(kind=dp), dimension(3), intent(in) :: displace
@ -618,9 +673,13 @@ module io
call read_mb(infiles(i), displace, temp_box_bd) call read_mb(infiles(i), displace, temp_box_bd)
case('restart') case('restart')
call read_pycac(infiles(i), displace, temp_box_bd) call read_pycac(infiles(i), displace, temp_box_bd)
case('cac')
call read_lmpcac(infiles(i), displace, temp_box_bd)
case('out')
call read_pycac_out(infiles(i), displace, temp_box_bd)
case default case default
print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), & print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
" is not accepted for writing. Please select from: mb and try again" " is not accepted for reading. Please select from: mb,restart,cac,out and try again"
stop stop
end select end select
@ -655,7 +714,7 @@ module io
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i) temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i) temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
end do end do
call grow_box(temp_box_bd) call grow_box(temp_box_bd)
!Read in the number of sub_boxes and allocate the variables !Read in the number of sub_boxes and allocate the variables
read(11, *) n read(11, *) n
@ -738,19 +797,19 @@ module io
do i = 1, in_atoms do i = 1, in_atoms
read(11,*) j, type, sbox, r(:) read(11,*) j, type, sbox, r(:)
r = r+newdisplace r = r+newdisplace
call add_atom(new_type_to_type(type), sbox+sub_box_num, r) call add_atom(j, new_type_to_type(type), sbox+sub_box_num, r)
end do end do
!Read the elements !Read the elements
do i = 1, in_eles do i = 1, in_eles
read(11, *) l, type, size, sbox, etype read(11, *) j, type, size, sbox, etype
do inod = 1, ng_node(type) do inod = 1, ng_node(type)
do ibasis =1, basisnum(type) do ibasis =1, basisnum(type)
read(11,*) j, k, r_innode(:, ibasis, inod) read(11,*) k, l, r_innode(:, ibasis, inod)
r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace
end do end do
end do end do
call add_element(etype, size, new_lattice_map(type), sbox+sub_box_num, r_innode) call add_element(j, etype, size, new_lattice_map(type), sbox+sub_box_num, r_innode)
end do end do
!Close the file being read !Close the file being read
@ -773,48 +832,42 @@ module io
real(kind=dp), dimension(3), intent(in) :: displace real(kind=dp), dimension(3), intent(in) :: displace
real(kind = dp), dimension(6), intent(out) :: temp_box_bd real(kind = dp), dimension(6), intent(out) :: temp_box_bd
integer :: i, inod, ibasis, j, k, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, & integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
atom_type_map(10), etype_map(10), etype, lat_type, new_lattice_map(10), & atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
atom_type atom_type, stat
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(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=100) :: textholder, in_lattype_map(10)
character(len=2) :: atomic_element character(len=2) :: atomic_element
!First open the file !First open the file
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind') open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
!Disregard unneeded information !Read the timestep information
do i = 1, 3 read(11,*) textholder
read(11,*) textholder read(11,*) timestep, total_time
end do
!Read element number !Read element number
read(11,*) textholder
read(11,*) in_eles read(11,*) in_eles
!Discard info and read ng_max_node !Discard info and read ng_max_node and max_basisnum
do i = 1, 5 do i = 1, 5
read(11,*) textholder read(11,*) textholder
end do end do
read(11,*) max_ng_node read(11,*) max_ng_node, max_basisnum
!Read element types (only needed inside this subroutine)
read(11,*) textholder
read(11,*) ele_types
!Read in atom num !Read in atom num
read(11,*) textholder read(11,*) textholder
read(11,*) in_atoms read(11,*) in_atoms
!read in lattice_types and atom types !read in atom masses
do i = 1,3 read(11, *) textholder
read(11,*) textholder read(11, '(a)') textholder
end do j = tok_count(textholder)
read(11,*) in_lat_num, in_atom_types read(textholder, *) (atomic_masses(i), i=1, j)
!Read define atom_types by name !Read define atom_types by mass
read(11,*) textholder
do i = 1, in_atom_types 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)) call add_atom_type(atomic_element, atom_type_map(i))
end do end do
@ -822,22 +875,6 @@ module io
read(11,*) textholder read(11,*) textholder
read(11,*) box_bc 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 box boundaries and displace them if necessary
read(11,*) temp_box_bd(:) read(11,*) temp_box_bd(:)
do i = 1, 3 do i = 1, 3
@ -865,64 +902,21 @@ module io
sub_box_bd(:, sub_box_num+1) = temp_box_bd sub_box_bd(:, sub_box_num+1) = temp_box_bd
!Read in more useless info !Read in more useless info
do i = 1, 10 do i = 1, 9
read(11,*) textholder read(11,*) textholder
end do 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 !Now start reading the elements
if(in_eles > 0) then if(in_eles > 0) then
read(11,*) textholder
read(11,*) textholder read(11,*) textholder
do i = 1, in_eles do i = 1, in_eles
read(11,*) j, etype, k, lat_type read(11,*) j, etype, k, lat_type
do inod = 1, 8 do inod = 1, 8
read(11, *) j, k, r_in(:,1,inod) read(11, *) k, l, r_in(:,1,inod)
r_in(:,1,inod) = r_in(:,1,inod) + newdisplace r_in(:,1,inod) = r_in(:,1,inod) + newdisplace
end do end do
call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in) call add_element(j, in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
end do end do
end if end if
@ -935,9 +929,13 @@ module io
end if end if
do i = 1, in_atoms do i = 1, in_atoms
read(11,*) j, k, atom_type, r_in_atom(:) read(11,*, iostat=stat) j, k, atom_type, r_in_atom(:)
if(stat > 0) then
print *, j
stop
end if
r_in_atom = r_in_atom + newdisplace r_in_atom = r_in_atom + newdisplace
call add_atom(atom_type_map(atom_type), sub_box_num + 1, r_in_atom) call add_atom(j,atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
end do end do
!Close file !Close file
close(11) close(11)
@ -949,4 +947,274 @@ module io
call set_max_esize call set_max_esize
end if end if
end subroutine read_pycac end subroutine read_pycac
subroutine read_pycac_out(file, displace, temp_box_bd)
!This subroutine reads in the pyCAC dump file
!Arguments
character(len=100), intent(in) :: file
real(kind=dp), dimension(3), intent(in) :: displace
real(kind=dp), dimension(6), intent(out) :: temp_box_bd
!Internal Variables
integer :: i, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
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(10,8), fe(3,10,8), ve(6,10,8), re(3,10,8)
character(len=100) :: textholder, fcc
character(len=1000) :: line
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 = 10
if (max_ng_node==0) max_ng_node=8
fcc="fcc"
!Skip header comment lines
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)
call alloc_dat_arrays(in_eles, in_atoms)
!Read boundary information
read(11,*) textholder, box_bc(1:1), box_bc(2:2), box_bc(3:3), temp_box_bd(:)
do i = 1, 3
if (abs(displace(i)) > lim_zero) then
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
else
newdisplace(i)=displace(i)
end if
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
end do
call grow_box(temp_box_bd)
!Allocate sub_box boundaries
if (sub_box_num == 0) then
call alloc_sub_box(1)
else
call grow_sub_box(1)
end if
!Because orientations and other needed sub_box information isn't really
!present within the .cac file we just default a lot of it.
sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
sub_box_bd(:, sub_box_num+1) = temp_box_bd
sub_box_num = sub_box_num + 1
if(in_atoms > 0 ) then
!Read atom header
read(11,*) textholder
do ia = 1, in_atoms
read(11,'(a)') line(:)
read(line,*) tag, type, ra(:), ea, fa(:), va(:)
call add_atom(tag, type, sub_box_num, ra)
call add_atom_data(atom_num, ea, fa, va)
end do
end if
if(in_eles > 0) then
!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, 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
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
real(kind=dp), dimension(3), intent(in) :: displace
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
character(len=100) :: textholder, element_type
character(len=2) :: atom_species
integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10), esize, &
lat_type
real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), newdisplace(3)
!First check to make sure that we have set the needed variables
if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then
print *, "Please use set_cac to set needed parameters to read in .cac file"
stop 3
end if
!Open the file
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 = 10
if (max_ng_node==0) max_ng_node=8
!Read header information
read(11, *) textholder
!Read number of elements
read(11, *) ele_in, textholder
read(11, *) type_in, textholder
!Read box_boundaries
read(11,*) temp_box_bd(1:2), textholder
read(11,*) temp_box_bd(3:4), textholder
read(11,*) temp_box_bd(5:6), textholder
!Shift the box boundaries if needed
do i = 1, 3
if (abs(displace(i)) > lim_zero) then
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
else
newdisplace(i)=displace(i)
end if
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
end do
!Grow box boundaries
call grow_box(temp_box_bd)
!Allocate sub_box
if (sub_box_num == 0) then
call alloc_sub_box(1)
else
call grow_sub_box(1)
end if
!Because orientations and other needed sub_box information isn't really
!present within the .cac file we just default a lot of it.
sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
sub_box_bd(:, sub_box_num+1) = temp_box_bd
sub_box_num = sub_box_num + 1
!Read useless information
read(11,*) textholder
!Read atomic masses
do i = 1, type_in
read(11,*) j, mass, textholder
call ATOMMASSSPECIES(mass, atom_species)
call add_atom_type(atom_species, type_map(i))
end do
!Read useless info
read(11,*) textholder
!Start the reading loop
do i = 1, ele_in
read(11,*) j, element_type, in_basis, esize
!Check to see if we need to grow the max_basis_num
select case(trim(adjustl(element_type)))
case('Eight_Node')
!Read in all the data
do j = 1, 8*in_basis
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
end do
!Now calculate the lattice vectors and shift the nodal points from the corners to the center of the unit cell
!Please check the nodal numbering figure in the readme in order to understand which nodes are used for the
!calculation
lat_vec(:,1) = (r_in(:,1,2) - r_in(:,1,1))/(2*esize)
lat_vec(:,2) = (r_in(:,1,4) - r_in(:,1,1))/(2*esize)
lat_vec(:,3) = (r_in(:,1,5) - r_in(:,1,1))/(2*esize)
!Now shift all the nodal positions
select case(trim(adjustl(in_lattice_type)))
case('fcc','FCC')
do ibasis = 1, in_basis
r_in(:,ibasis,1) = r_in(:,ibasis,1) + lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,2) = r_in(:,ibasis,2) - lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,3) = r_in(:,ibasis,3) - lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,4) = r_in(:,ibasis,4) + lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
r_in(:,ibasis,5) = r_in(:,ibasis,5) + lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,6) = r_in(:,ibasis,6) - lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,7) = r_in(:,ibasis,7) - lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
r_in(:,ibasis,8) = r_in(:,ibasis,8) + lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
end do
case default
print *, in_lattice_type, " is not an accepted lattice type. Please select from: fcc"
end select
!Now map it to either an existing or new lattice type
call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
!Now add the element
call add_element(0,in_lattice_type, esize, lat_type, sub_box_num, r_in(:,1:max_basisnum,1:max_ng_node))
case('Atom')
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,1,1)
call add_atom(0,in_basis_types(ibasis), sub_box_num, r_in(:,1,1))
end select
end do
end subroutine read_lmpcac
subroutine set_cac(apos)
!This code parses input values
integer, intent(in) :: apos
integer :: arglen, arg_pos
character(len=100) :: textholder
arg_pos = apos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) then
print *, "Missing lattice parameter for set_input_lat"
end if
read(textholder,*) in_lapa
print *, in_lapa
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) then
print *, "Missing lattice type for set_input_lat"
end if
read(textholder,*) in_lattice_type
print *, in_lattice_type
end subroutine set_cac
subroutine set_types(apos)
!This code
integer, intent(in) :: apos
integer :: i, j,arglen, arg_pos, ntypes
character(len=100) :: textholder
arg_pos = apos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing numtypes in io"
read(textholder,*) ntypes
do i=1,ntypes
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
call add_atom_type(textholder, j)
end do
return
end subroutine set_types
end module io end module io

21
src/main.f90
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@ -15,6 +15,7 @@ program main
use parameters use parameters
use elements use elements
use io use io
use caller
integer :: i, end_mode_arg, arg_num, arg_pos integer :: i, end_mode_arg, arg_num, arg_pos
@ -60,6 +61,11 @@ program main
!This lets us know if we need to wrap atomic positions back into the cell !This lets us know if we need to wrap atomic positions back into the cell
case('-wrap') case('-wrap')
wrap_flag=.true. wrap_flag=.true.
case('-set_cac')
call set_cac(i)
case('-set_types')
call set_types(i)
end select end select
end do end do
!Determine if a mode is being used and what it is. The first argument has to be the mode !Determine if a mode is being used and what it is. The first argument has to be the mode
@ -68,7 +74,8 @@ program main
argument = trim(adjustl(argument)) argument = trim(adjustl(argument))
if (argument(1:2) == '--') then if (argument(1:2) == '--') then
call call_mode(end_mode_arg, argument) mode = argument
call call_mode(end_mode_arg)
end if end if
!Check to make sure a mode was called !Check to make sure a mode was called
@ -105,11 +112,13 @@ program main
if(bound_called) call def_new_box if(bound_called) call def_new_box
!Check to make sure a file was passed to be written out and then write out !Check to make sure a file was passed to be written out and then write out
! Before building do a check on the file ! Before building do a check on the file
if (outfilenum == 0) then if ((trim(adjustl(mode)) /= "--metric").and.(trim(adjustl(mode)) /= "--calc"))then
argument = 'none' if ((outfilenum == 0)) then
call get_out_file(argument) argument = 'none'
call get_out_file(argument)
end if
call write_out
end if end if
call write_out
end program main end program main

95
src/mode_calc.f90
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@ -0,0 +1,95 @@
module mode_calc
!This mode is used to calculate various quantities based on input information
use parameters
use io
use subroutines
use elements
use box
character(len=100) :: calc_opt
real(kind=dp), allocatable :: calculated(:)
public
contains
subroutine calc(arg_pos)
!Main calling subroutine for mode_create
integer, intent(out) :: arg_pos
print *, '------------------------Mode Calc----------------------------'
!First parse command
call parse(arg_pos)
print *, "Calculating ", trim(adjustl(calc_opt)), " for ", ele_num, " elements and ", atom_num, " atoms."
!Now call the correct calc function based on calc_opt
select case(trim(adjustl(calc_opt)))
case('tot_virial')
allocate(calculated(6))
call calc_tot_virial
case default
print *, trim(adjustl(calc_opt)), " is not accepted as a calc option in mode_calc"
stop 3
end select
end subroutine calc
subroutine parse(arg_pos)
!This parses the mode calc options
integer, intent(out) :: arg_pos
character(len = 100) :: infile
integer:: arglen
real(kind=dp) :: temp_box_bd(6)
call get_command_argument(2, infile, arglen)
if (arglen == 0 ) stop "Missing calc option in mode calc"
call get_in_file(infile)
call read_in(1, (/0.0_dp, 0.0_dp, 0.0_dp /), temp_box_bd)
call grow_box(temp_box_bd)
call get_command_argument(3, calc_opt, arglen)
if (arglen == 0 ) stop "Missing calc option in mode calc"
arg_pos = 4
end subroutine parse
subroutine calc_tot_virial
!Calculate the the total box pressure in GPa
integer :: i, j, ibasis, inod
real(kind=dp) :: avg_virial(6)
!First check to make sure that the virial was set for the atoms/elements
if(.not.vflag) then
print *, "Virial data has not been sent/may not be available with your current input file "
stop 3
end if
!Sum the atom virials
calculated = 0
do i = 1, atom_num
do j = 1, 6
calculated(j) = calculated(j) + virial_atom(j, i)
end do
end do
!Sum the nodal virials
do i = 1, ele_num
avg_virial(:) = 0
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
do j = 1,6
avg_virial(j) = avg_virial(j) + virial_node(j,ibasis,inod,i)/(basisnum(lat_ele(i))*ng_node(lat_ele(i)))
end do
end do
end do
!Now add the total virial from the element
calculated = calculated + avg_virial*(esize**3.0_dp)
end do
!Now calculate the total box virial and convert to GPa
calculated = evtogp(calculated)/box_volume()
print *, "Total virial is calculated as : (v11, v22, v33, v32, v31, v21)"
print *, calculated
end subroutine
end module mode_calc

3
src/mode_convert.f90
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@ -14,6 +14,7 @@ module mode_convert
character(len=100) :: infile character(len=100) :: infile
real(kind = dp) :: temp_box_bd(6) real(kind = dp) :: temp_box_bd(6)
!First read in the file !First read in the file
temp_box_bd(:) = 0.0_dp
call get_command_argument(2, infile) call get_command_argument(2, infile)
call get_in_file(infile) call get_in_file(infile)
call read_in(1, (/0.0_dp,0.0_dp,0.0_dp/), temp_box_bd) call read_in(1, (/0.0_dp,0.0_dp,0.0_dp/), temp_box_bd)
@ -21,4 +22,4 @@ module mode_convert
arg_pos = 3 arg_pos = 3
end subroutine convert end subroutine convert
end module mode_convert end module mode_convert

164
src/mode_create.f90
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@ -10,14 +10,15 @@ module mode_create
implicit none implicit none
character(len=100) :: name, element_type character(len=100) :: name, element_type
real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), & real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3) orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3)
integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), & integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
basis_pos(3,10) basis_pos(3,10), esize_nums, esize_index(10)
logical :: dup_flag, dim_flag logical :: dup_flag, dim_flag, efill
real(kind=dp), allocatable :: r_lat(:,:,:), r_atom_lat(:,:) real(kind=dp), allocatable :: r_lat(:,:,:), r_atom_lat(:,:)
integer, allocatable :: elat(:)
public public
contains contains
@ -26,7 +27,7 @@ module mode_create
integer, intent(out) :: arg_pos integer, intent(out) :: arg_pos
integer :: i, ibasis, inod integer :: i, ibasis, inod, ei, curr_esize
real(kind=dp), allocatable :: r_node_temp(:,:,:) real(kind=dp), allocatable :: r_node_temp(:,:,:)
print *, '-----------------------Mode Create---------------------------' print *, '-----------------------Mode Create---------------------------'
@ -45,6 +46,7 @@ module mode_create
basisnum = 0 basisnum = 0
lat_ele_num = 0 lat_ele_num = 0
lat_atom_num = 0 lat_atom_num = 0
efill = .false.
!First we parse the command !First we parse the command
call parse_command(arg_pos) call parse_command(arg_pos)
@ -63,10 +65,17 @@ module mode_create
do i = 1, 8 do i = 1, 8
box_vert(:,i) = duplicate(:)*esize*lattice_space(:)*cubic_cell(:,i) + (origin(:)/lattice_parameter) box_vert(:,i) = duplicate(:)*esize*lattice_space(:)*cubic_cell(:,i) + (origin(:)/lattice_parameter)
end do end do
!Now get the rotated box vertex positions in lattice space. Should be integer units !Now get the rotated box vertex positions in lattice space. Should be integer units and get the new maxlen
box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1 select case(trim(adjustl(element_type)))
case('fcc')
box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1
maxbd = maxval(matmul(orient,matmul(fcc_mat,box_lat_vert)),2)
case('bcc')
box_lat_vert = int(matmul(bcc_inv, matmul(orient_inv, box_vert)))+1
maxbd = maxval(matmul(orient,matmul(bcc_mat,box_lat_vert)),2)
end select
!Find the new maxlen !Find the new maxlen
maxbd = maxval(matmul(orient,matmul(fcc_mat,box_lat_vert)),2)
do i = 1, 3 do i = 1, 3
box_bd(2*i) = maxval(box_vert(i,:)) - 0.25_dp*lattice_space(i) box_bd(2*i) = maxval(box_vert(i,:)) - 0.25_dp*lattice_space(i)
box_bd(2*i-1) = origin(i)-0.25_dp*lattice_space(i) box_bd(2*i-1) = origin(i)-0.25_dp*lattice_space(i)
@ -83,7 +92,12 @@ module mode_create
box_vert(:,i) = (cubic_cell(:,i)*box_len(:) + origin(:))/lattice_parameter box_vert(:,i) = (cubic_cell(:,i)*box_len(:) + origin(:))/lattice_parameter
end do end do
!Now get the rotated box vertex positions in lattice space. Should be integer units !Now get the rotated box vertex positions in lattice space. Should be integer units
box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1 select case(trim(adjustl(element_type)))
case('fcc')
box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1
case('bcc')
box_lat_vert = int(matmul(bcc_inv, matmul(orient_inv, box_vert)))+1
end select
!Now get the box_bd in lattice units !Now get the box_bd in lattice units
do i = 1, 3 do i = 1, 3
@ -105,10 +119,10 @@ module mode_create
end do end do
end do end do
do i = 1,3 do i = 1,3
box_bd(2*i) = maxval(r_node_temp(i,:,:))+10.0_dp**-6.0_dp box_bd(2*i) = maxval(r_node_temp(i,:,:))+10.0_dp**(-6.0_dp)
box_bd(2*i-1) = minval(r_node_temp(i,:,:)) - 10.0_dp**-6.0_dp box_bd(2*i-1) = minval(r_node_temp(i,:,:)) - 10.0_dp**(-6.0_dp)
end do end do
call add_element(element_type, esize, 1, 1, r_node_temp) call add_element(0,element_type, esize, 1, 1, r_node_temp)
end if end if
!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 we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays
@ -117,10 +131,11 @@ module mode_create
!Call the build function with the correct transformation matrix !Call the build function with the correct transformation matrix
select case(trim(adjustl(element_type))) select case(trim(adjustl(element_type)))
case('fcc') case('fcc')
call build_with_rhomb(box_lat_vert, fcc_mat) call build_with_rhomb(box_lat_vert, fcc_mat)
case('bcc')
call build_with_rhomb(box_lat_vert, bcc_mat)
case default case default
print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ", & print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ",&
"element type" "element type"
stop 3 stop 3
end select end select
@ -135,7 +150,7 @@ module mode_create
if(lat_atom_num > 0) then if(lat_atom_num > 0) then
do i = 1, lat_atom_num do i = 1, lat_atom_num
do ibasis = 1, basisnum(1) do ibasis = 1, basisnum(1)
call add_atom(basis_type(ibasis, 1), 1, (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis)) call add_atom(0,basis_type(ibasis, 1), 1, (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis))
end do end do
end do end do
deallocate(r_atom_lat) deallocate(r_atom_lat)
@ -148,7 +163,8 @@ module mode_create
r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis) r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis)
end do end do
end do end do
call add_element(element_type, esize, 1, 1, r_node_temp)
call add_element(0,element_type, elat(i), 1, 1, r_node_temp)
end do end do
end if end if
end if end if
@ -248,6 +264,8 @@ module mode_create
end do end do
end do end do
case('efill')
efill=.true.
case default case default
!If it isn't an option then you have to exit !If it isn't an option then you have to exit
arg_pos = arg_pos -1 arg_pos = arg_pos -1
@ -272,13 +290,20 @@ module mode_create
lattice_space(i) = 0.5_dp * lattice_space(i) lattice_space(i) = 0.5_dp * lattice_space(i)
!Check if one direction is 112 !Check if one direction is 112
else if ((is_equal(abs(orient(i,1)), abs(orient(i,2))).and.(is_equal(abs(orient(i,3)),2.0_dp*abs(orient(i,1))))).or.& else if((is_equal(abs(orient(i,1)), abs(orient(i,2))).and.(is_equal(abs(orient(i,3)),2.0_dp*abs(orient(i,1))))).or.&
(is_equal(abs(orient(i,2)), abs(orient(i,3))).and.(is_equal(abs(orient(i,1)),2.0_dp*abs(orient(i,2))))).or.& (is_equal(abs(orient(i,2)), abs(orient(i,3))).and.(is_equal(abs(orient(i,1)),2.0_dp*abs(orient(i,2))))).or.&
(is_equal(abs(orient(i,3)), abs(orient(i,1))).and.(is_equal(abs(orient(i,2)),2.0_dp*abs(orient(i,3))))))& (is_equal(abs(orient(i,3)), abs(orient(i,1))).and.(is_equal(abs(orient(i,2)),2.0_dp*abs(orient(i,3))))))&
then then
lattice_space(i) = 0.5_dp * lattice_space(i) lattice_space(i) = 0.5_dp * lattice_space(i)
end if
end do
case('bcc')
do i = 1, 3
!Check if the direction is 111
if((is_equal(abs(orient(i,1)),abs(orient(i,2)))).and.(is_equal(abs(orient(i,2)),abs(orient(i,3))))) then
lattice_space(i) = 0.5_dp * lattice_space(i)
end if end if
end do end do
end select end select
@ -313,14 +338,19 @@ module mode_create
integer, dimension(3,8), intent(in) :: box_in_lat !The box vertices transformed to lattice space integer, dimension(3,8), intent(in) :: box_in_lat !The box vertices transformed to lattice space
real(kind=dp), dimension(3,3), intent(in) :: transform_matrix !The transformation matrix from lattice_space to real space real(kind=dp), dimension(3,3), intent(in) :: transform_matrix !The transformation matrix from lattice_space to real space
!Internal variables !Internal variables
integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), & integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), efill_size, &
vlat(3), temp_lat(3,8), m, n, o vlat(3), temp_lat(3,8), m, n, o, j, k, nump_ele, efill_temp_lat(3,8), filzero(3), bd_ele_lat(6),&
real(kind=dp) :: v(3), temp_nodes(3,1,8) efill_ele(3,8), ebd(6)
real(kind=dp) :: v(3), temp_nodes(3,1,8), r(3), centroid_bd(6)
logical, allocatable :: lat_points(:,:,:) logical, allocatable :: lat_points(:,:,:)
logical :: node_in_bd(8) logical :: node_in_bd(8), add, lat_points_ele(esize,esize,esize), intersect_bd(3)
!Do some value initialization !Do some value initialization
max_esize = esize max_esize = esize
do i = 1,3
centroid_bd(2*i) = -huge(1.0_dp)
centroid_bd(2*i-1) = huge(1.0_dp)
end do
!First find the bounding lattice points (min and max points for the box in each dimension) !First find the bounding lattice points (min and max points for the box in each dimension)
numlatpoints = 1 numlatpoints = 1
@ -415,8 +445,9 @@ module mode_create
!Now build the finite element region !Now build the finite element region
lat_ele_num = 0 lat_ele_num = 0
lat_atom_num = 0 lat_atom_num = 0
allocate(r_lat(3,8,numlatpoints/esize)) allocate(r_lat(3,8,numlatpoints/esize), elat(numlatpoints/esize))
ele(:,:) = (esize-1) * cubic_cell(:,:)
!Redefined the second 3 indices as the number of elements that fit in the bounds !Redefined the second 3 indices as the number of elements that fit in the bounds
do i = 1, 3 do i = 1, 3
bd_in_array(3+i) = bd_in_array(i)/esize bd_in_array(3+i) = bd_in_array(i)/esize
@ -444,17 +475,19 @@ module mode_create
!Check to see if the lattice point values are greater then the array limits !Check to see if the lattice point values are greater then the array limits
if(any(vlat > shape(lat_points)).or.any(vlat < 1)) then if(any(vlat > shape(lat_points)).or.any(vlat < 1)) then
continue continue
!If within array boundaries check to see if it is a lattice point !If within array boundaries check to see if it is a lattice point
else if(lat_points(vlat(1),vlat(2),vlat(3))) then else if(lat_points(vlat(1),vlat(2),vlat(3))) then
node_in_bd(inod) = .true. node_in_bd(inod) = .true.
end if end if
end do end do
!If we are on the first round of element building then we can just add the element if all(node_in_bd) is
!true
if(all(node_in_bd)) then if(all(node_in_bd)) then
lat_ele_num = lat_ele_num+1 lat_ele_num = lat_ele_num+1
r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:) r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
elat(lat_ele_num) = esize
!Now set all the lattice points contained within an element to false !Now set all the lattice points contained within an element to false
do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:)) do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:)) do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))
@ -464,11 +497,83 @@ module mode_create
end do end do
end do end do
!If any nodes are in the boundary and we want to efill then run the efill code
else if(any(node_in_bd).and.efill) then
!Pull out the section of the lat points array
lat_points_ele(:,:,:)=.false.
do i = 1,3
if (minval(temp_lat(i,:)) <lim_zero) then
bd_ele_lat(2*i-1) = 1
else
bd_ele_lat(2*i-1) = minval(temp_lat(i,:))
end if
if(maxval(temp_lat(i,:))>size(lat_points,i)) then
bd_ele_lat(2*i) = size(temp_lat(i,:))
else
bd_ele_lat(2*i) = maxval(temp_lat(i,:))
end if
end do
lat_points_ele(1:(bd_ele_lat(2)-bd_ele_lat(1)),1:(bd_ele_lat(4)-bd_ele_lat(3)),&
1:(bd_ele_lat(6)-bd_ele_lat(5)))= lat_points(bd_ele_lat(1):bd_ele_lat(2), &
bd_ele_lat(3):bd_ele_lat(4), &
bd_ele_lat(5):bd_ele_lat(6))
!Now start looping through elements and try to fit as many as you can
efill_size = esize-2
i=1
j=1
k=1
nump_ele = count(lat_points_ele)
do i = 1, 3
filzero(i) = bd_ele_lat(2*i-1) -1
end do
do while(efill_size>min_efillsize)
!First check whether there are enough lattice points to house the current element size
efill_ele=cubic_cell*(efill_size-1)
if (nump_ele < efill_size**3) then
efill_size = efill_size - 2
else
ze: do k = 1, (esize-efill_size)
ye: do j = 1, (esize-efill_size)
xe: do i = 1, (esize-efill_size)
do inod = 1,8
vlat = efill_ele(:,inod) + (/ i, j, k /)
if (.not.lat_points_ele(vlat(1),vlat(2),vlat(3))) cycle xe
do o = 1,3
v(o) = real(vlat(o) + filzero(o) + bd_in_lat(2*o-1) -5)
end do
temp_nodes(:,1, inod) = matmul(orient, matmul(transform_matrix, v))
efill_temp_lat(:,inod) = vlat
end do
do o = 1,3
ebd(2*o-1) = minval(efill_temp_lat(o,:))
ebd(2*o) = maxval(efill_temp_lat(o,:))
end do
lat_ele_num = lat_ele_num+1
r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
elat(lat_ele_num) = efill_size
nump_ele = nump_ele - efill_size**3
!Now set all the lattice points contained within an element to false
do o = ebd(5), ebd(6)
do n = ebd(3), ebd(4)
do m = ebd(1), ebd(2)
lat_points(m+filzero(1),n+filzero(2),o+filzero(3)) = .false.
lat_points_ele(m,n,o) = .false.
end do
end do
end do
end do xe
end do ye
end do ze
efill_size = efill_size-2
end if
end do
end if end if
end do end do
end do end do
end do end do
!Now figure out how many lattice points could not be contained in elements !Now figure out how many lattice points could not be contained in elements
allocate(r_atom_lat(3,count(lat_points))) allocate(r_atom_lat(3,count(lat_points)))
lat_atom_num = 0 lat_atom_num = 0
@ -518,6 +623,5 @@ module mode_create
STOP 3 STOP 3
end subroutine error_message end subroutine error_message
end module mode_create end module mode_create

5
src/mode_merge.f90
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@ -25,6 +25,7 @@ module mode_merge
shift_flag = .false. shift_flag = .false.
shift_vec(:) = 0.0_dp shift_vec(:) = 0.0_dp
temp_box_bd(:) = 0.0_dp
!First we parse the merge command !First we parse the merge command
call parse_command(arg_pos) call parse_command(arg_pos)
@ -41,7 +42,6 @@ module mode_merge
if ((i==1).or.(trim(adjustl(dim)) == 'none')) then if ((i==1).or.(trim(adjustl(dim)) == 'none')) then
call read_in(i, displace, temp_box_bd) call read_in(i, displace, temp_box_bd)
call grow_box(temp_box_bd)
else else
select case(trim(adjustl(dim))) select case(trim(adjustl(dim)))
case('x') case('x')
@ -53,7 +53,6 @@ module mode_merge
end select end select
call read_in(i, displace, temp_box_bd) call read_in(i, displace, temp_box_bd)
call grow_box(temp_box_bd)
end if end if
if(shift_flag) call shift(new_starts, i) if(shift_flag) call shift(new_starts, i)
@ -168,4 +167,4 @@ module mode_merge
end if end if
end subroutine shift end subroutine shift
end module mode_merge end module mode_merge

249
src/mode_metric.f90
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@ -0,0 +1,249 @@
module mode_metric
!This mode is used to calculate continuum metrics for the j
use parameters
use io
use elements
use neighbors
implicit none
integer :: nfiles
character(len=100) :: metric_type
real(kind=dp) :: rc_off
!Save reference positions
integer :: np, npreal, nmet
real(kind=dp), allocatable :: r_zero(:,:), r_curr(:,:), met(:,:)
public
contains
subroutine metric(arg_pos)
!This is the main calling subroutine for the metric code
integer, intent(out) :: arg_pos
character(len=100) :: infile, outfile
integer :: i, ibasis, inod, np_temp, ppos
real(kind=dp), dimension(6) :: temp_box_bd
!These are the variables containing the cell list information
integer, dimension(3) :: cell_num
integer, allocatable :: num_in_cell(:,:,:), which_cell(:,:)
integer, allocatable :: cell_list(:,:,:,:)
!Parse the command arguments
call parse_command(arg_pos)
!Now read the first file
call read_in(1, (/ 0.0_dp, 0.0_dp, 0.0_dp /), temp_box_bd)
np = atom_num + max_basisnum*max_ng_node*ele_num
allocate(r_zero(3,atom_num+max_basisnum*max_ng_node*ele_num), &
r_curr(3,atom_num+max_basisnum*max_ng_node*ele_num))
r_zero(:,:) = -huge(1.0_dp)
!Set up the met variable for the user desired metric
select case(trim(adjustl(metric_type)))
case('def_grad')
allocate(met(9, np))
case('microrotation')
allocate(met(4,np))
end select
!Now set the reference positions
call convert_positions(r_zero, npreal)
!Now calculate the neighbor list for the reference configuration
call calc_neighbor(5.0_dp, r_zero, np)
!Reset element and box
call reset_data
call reset_box
!Now loop over new files
do i = 2, nfiles
call read_in(i, (/ 0.0_dp, 0.0_dp, 0.0_dp /), temp_box_bd)
call convert_positions(r_curr, np_temp)
if (npreal /= np_temp) then
print *, "Error in mode_metric where number of points in ", i, "th file is ", np_temp, " and number of points in" &
// "reference file is", npreal
end if
call calc_metric
!Now create the output file num and write out to xyz format
ppos = scan(trim(infiles(i)),".", BACK= .true.)
if ( ppos > 0 ) then
outfile = infiles(i)(1:ppos)//'xyz'
else
outfile = infiles(i)//'.xyz'
end if
call write_metric_xyz(outfile)
call reset_data
call reset_box
end do
end subroutine metric
subroutine parse_command(arg_pos)
!This subroutine parses the arguments for mode metric
integer, intent(out) :: arg_pos
integer :: i, arglen
character(len=100) :: textholder
logical :: file_exists
!First read the metric to be used
call get_command_argument(2,metric_type,arglen)
if (arglen == 0) stop "Incomplete mode metric command, check documentation"
select case(trim(adjustl(metric_type)))
case("microrotation", "def_grad")
continue
case default
print *, "Mode metric does not accept metric ", metric_type, ". Please select from: microrotation, def_grad"
stop 3
end select
!Now read the cutoff radius
call get_command_argument(3,textholder,arglen)
if (arglen == 0) stop "Incomplete mode metric command, check documentation"
read(textholder, *) rc_off
!Now read the number of files to read and allocate the variables
call get_command_argument(4, textholder, arglen)
if (arglen == 0) stop "Incomplete mode metric command, check documentation"
read(textholder, *) nfiles
!Now read the files to be read
do i = 1, nfiles
call get_command_argument(4+i, textholder, arglen)
call get_in_file(textholder)
end do
arg_pos = 5+nfiles
return
end subroutine parse_command
subroutine calc_metric
!This subroutine calculates the continuum metric that we require
integer :: i, j, k, nei, ip, jp
real(kind=dp) :: def_grad(3,3), omega(3,3), eta(3,3), rij(3), eta_inv(3,3), ftf(3,3), &
U(3,3), R(3,3), Rskew(3,3), oldrij(3)
!Loop over all points
do ip = 1, np
eta(:,:) = 0.0_dp
omega(:,:) = 0.0_dp
def_grad(:,:) = 0.0_dp
do jp = 1, nei_num(ip)
!Calculate the neighbor vec in current configuration
nei = nei_list(jp, ip)
rij = r_curr(:,nei) - r_curr(:,ip)
oldrij = r_zero(:,nei) - r_zero(:,ip)
!Calculate eta and omega
do i = 1,3
do j = 1,3
omega(i,j) = omega(i,j) + rij(i) * oldrij(j)
eta(i,j) = eta(i,j) + oldrij(i) * oldrij(j)
end do
end do
end do
eta_inv=matinv3(eta)
def_grad=matmul(omega,eta_inv)
select case(trim(adjustl(metric_type)))
case('def_grad')
k = 1
do i = 1,3
do j = 1, 3
met(k, ip) = def_grad(i,j)
k = k + 1
end do
end do
case('microrotation')
met(:,ip) = 0.0_dp
if(.not.all(def_grad == 0)) then
!Now calculate microrotation
ftf = matmul(transpose3(def_grad), def_grad)
U = sqrt3(ftf)
if(.not.all(abs(U) < lim_zero)) then
R = matmul(def_grad, matinv3(U))
Rskew = 0.5_dp * ( R - transpose3(R))
do k =1,3
do j = 1,3
do i = 1,3
met(k,ip) = met(k,ip) -0.5*permutation(i,j,k)*Rskew(i,j)
end do
end do
end do
met(4,ip) = norm2(met(1:3,ip))
end if
end if
end select
end do
return
end subroutine
subroutine convert_positions(rout, npoints)
!This subroutine just converts current atom and element arrays to a single point based form
real(kind=dp), dimension(3,atom_num+max_ng_node*max_basisnum*ele_num), intent(inout) :: rout
integer, intent(out) :: npoints
integer :: i, inod, ibasis
npoints=0
if(atom_num > 0) then
do i = 1, atom_num
rout(:,tag_atom(i)) = r_atom(:,i)
npoints = npoints + 1
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))
rout(:, atom_num+(tag_ele(i)-1)*max_ng_node*max_basisnum + (inod-1)*max_basisnum + ibasis) &
= r_node(:,ibasis,inod,i)
npoints = npoints + 1
end do
end do
end do
end if
end subroutine convert_positions
subroutine write_metric_xyz(outfile)
character(len=100), intent(in) :: outfile
integer :: i, inod, ibasis
real(kind = dp) :: r(3), eng
open (unit=11, file=trim(adjustl(outfile)), action='write', position='rewind', status = 'replace')
!Write the header
write(11,*) npreal
select case(metric_type)
case('def_grad')
write(11,*) "type element x y z F11 F12 F13 F21 F22 F23 F31 F32 F33"
case('microrotation')
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,*) type_atom(i), 0, r_atom(:,i), met(:,tag_atom(i))
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))
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
end do
end if
end subroutine write_metric_xyz
end module mode_metric

142
src/neighbors.f90
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@ -0,0 +1,142 @@
module neighbors
use parameters
use elements
use subroutines
use functions
integer, allocatable :: nei_list(:,:), nei_num(:)
real(kind=dp), allocatable :: init_vec(:,:,:), output(:), microrotation(:,:)
public
contains
subroutine build_cell_list(numinlist, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
!This subroutine builds a cell list based on rc_off
!----------------------------------------Input/output variables-------------------------------------------
integer, intent(in) :: numinlist !The number of points within r_list
real(kind=dp), dimension(3,numinlist), intent(in) :: r_list !List of points to be used for the construction of
!the cell list.
real(kind=dp), intent(in) :: rc_off ! Cutoff radius which dictates the size of the cells
integer, dimension(3), intent(inout) :: cell_num !Number of cells in each dimension.
integer, allocatable, intent(inout) :: num_in_cell(:,:,:) !Number of points within each cell
integer, allocatable, intent(inout) :: cell_list(:,:,:,:) !Index of points from r_list within each cell.
integer, dimension(3,numinlist), intent(out) :: which_cell !The cell index for each point in r_list
!----------------------------------------Begin Subroutine -------------------------------------------
integer :: i, j, cell_lim, c(3)
real(kind=dp) :: box_len(3)
integer, allocatable :: resize_cell_list(:,:,:,:)
!First calculate the number of cells that we need in each dimension
do i = 1,3
box_len(i) = box_bd(2*i) - box_bd(2*i-1)
cell_num(i) = int(box_len(i)/(rc_off/2))+1
end do
!Initialize/allocate variables
cell_lim = 10
allocate(num_in_cell(cell_num(1),cell_num(2),cell_num(3)), cell_list(cell_lim, cell_num(1), cell_num(2), cell_num(3)))
!Now place points within cell
do i = 1, numinlist
!Check to see if the current point is a filler point and if so just skip it
if(r_list(1,i) < -huge(1.0_dp)+1) cycle
!c is the position of the cell that the point belongs to
do j = 1, 3
c(j) = int((r_list(j,i)-box_bd(2*j-1))/(rc_off/2)) + 1
end do
!Place the index in the correct position, growing if necessary
num_in_cell(c(1),c(2),c(3)) = num_in_cell(c(1),c(2),c(3)) + 1
if (num_in_cell(c(1),c(2),c(3)) > cell_lim) then
allocate(resize_cell_list(cell_lim+10,cell_num(1),cell_num(2),cell_num(3)))
resize_cell_list(1:cell_lim, :, :, :) = cell_list
resize_cell_list(cell_lim+1:, :, :, :) = 0
call move_alloc(resize_cell_list, cell_list)
end if
cell_list(num_in_cell(c(1),c(2),c(3)),c(1),c(2),c(3)) = i
which_cell(:,i) = c
end do
return
end subroutine build_cell_list
subroutine calc_neighbor(rc_off, r_list, n)
!This function populates the neighbor list in this module
real(kind=dp), intent(in) :: rc_off
integer, intent(in) :: n
real(kind=dp), dimension(3,n) :: r_list
integer :: i, c(3), ci, cj, ck, num_nei, nei
!Variables for cell list code
integer, dimension(3) ::cell_num
integer, allocatable :: num_in_cell(:,:,:), cell_list(:,:,:,:)
integer :: which_cell(3,n)
!First reallocate the neighbor list codes
if (allocated(nei_list)) then
deallocate(nei_list,nei_num)
end if
allocate(nei_list(100,n),nei_num(n))
!Now first pass the position list and and point num to the cell algorithm
call build_cell_list(n, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
!Now loop over every point and find it's neighbors
pointloop: do i = 1, n
!First check to see if the point is a filler point, if so then skip it
if(r_list(1,i) < -Huge(-1.0_dp)+1) cycle
!c is the position of the cell that the point
c = which_cell(:,i)
!Loop over all neighboring cells
do ci = -1, 1, 1
do cj = -1, 1, 1
do ck = -1, 1, 1
!First check to make sure that the neighboring cell exists
if(any((c + (/ ck, cj, ci /)) == 0)) cycle
if( (c(1) + ck > cell_num(1)).or.(c(2) + cj > cell_num(2)).or. &
(c(3) + ci > cell_num(3))) cycle
do num_nei = 1, num_in_cell(c(1) + ck, c(2) + cj, c(3) + ci)
nei = cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci)
!Check to make sure the atom isn't the same index as the atom we are checking
!and that the neighbor hasn't already been deleted
if((nei /= i)) then
!Now check to see if it is in the cutoff radius, if it is add it to the neighbor list for that
!atom and calculate the initial neighbor vector
if (norm2(r_list(:,nei)-r_list(:,i)) < rc_off) then
nei_num(i) = nei_num(i) + 1
nei_list(nei_num(i), i) = nei
end if
end if
end do
end do
end do
end do
end do pointloop
return
end subroutine calc_neighbor
end module neighbors

98
src/opt_deform.f90
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@ -0,0 +1,98 @@
module opt_deform
!This module constains the deform option which applies a uniaxial strain to the system
use parameters
use subroutines
use elements
use box
implicit none
real(kind=dp), save :: applied_strain
integer, save :: sdim
public
contains
subroutine deform(arg_pos)
!This subroutine applies the simulation box deformation to the system
integer, intent(inout) :: arg_pos
character(len=1) :: dims(3)
integer :: i, j, k
real(kind=dp) :: frac_atom(atom_num), frac_node(max_basisnum, max_ng_node, ele_num)
!initialize some variables
dims(1) = 'x'
dims(2) = 'y'
dims(3) = 'z'
!First parse the input command
call parse_deform(arg_pos)
print *, '-----------------------Option Deform------------------------'
!Now convert all positions in the specified dimension to fractional coordinates
do i = 1, atom_num
frac_atom(i) = (r_atom(sdim, i) - box_bd(2*sdim-1))/(box_bd(2*sdim)-box_bd(2*sdim-1))
end do
do i = 1, ele_num
do j = 1, ng_node(lat_ele(i))
do k = 1, basisnum(lat_ele(i))
frac_node(k,j,i) = (r_node(sdim,k,j,i) - box_bd(2*sdim-1))/(box_bd(2*sdim)-box_bd(2*sdim-1))
end do
end do
end do
print *, "Original box bounds in ", dims(sdim), " are ", box_bd(2*sdim-1:2*sdim)
box_bd(2*sdim) = box_bd(2*sdim) + applied_strain
print *, "New box bounds are ", box_bd(2*sdim-1:2*sdim)
!Now reassign the positions
do i = 1, atom_num
r_atom(sdim,i) = frac_atom(i)*(box_bd(2*sdim)-box_bd(2*sdim-1)) + box_bd(2*sdim-1)
end do
do i = 1, ele_num
do j = 1, ng_node(lat_ele(i))
do k = 1, basisnum(lat_ele(i))
r_node(sdim,k,j,i) = frac_node(k,j,i)*(box_bd(2*sdim)-box_bd(2*sdim-1)) + box_bd(2*sdim-1)
end do
end do
end do
end subroutine deform
subroutine parse_deform(arg_pos)
integer, intent(inout) :: arg_pos
integer :: arg_len
character(len=100) :: textholder
!Pull out the dimension to be strained
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arg_len)
if (arg_len == 0) stop "Missing dim in deform command"
select case(trim(adjustl(textholder)))
case('x','X')
sdim = 1
case('y','Y')
sdim = 2
case('z','Z')
sdim = 3
case default
print *, "Dimension ", trim(adjustl(textholder)), " is not accepted. Please select either x, y, or z"
end select
!Now pull out the strain vector, currently only accepts a real number by which to reduce the simulation cell size by in
!that dimension
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arg_len)
if (arg_len == 0) stop "Missing strain in deform command"
read(textholder, *) applied_strain
arg_pos = arg_pos + 1
end subroutine parse_deform
end module opt_deform

1
src/opt_delete.f90
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@ -3,6 +3,7 @@ module opt_delete
use parameters use parameters
use subroutines use subroutines
use elements use elements
use neighbors
implicit none implicit none

150
src/opt_disl.f90
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@ -9,6 +9,7 @@ module opt_disl
implicit none implicit none
integer :: vloop_size ! Number of atoms to remove in planar vacancy cluster 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), dimension(3) :: line, slip_plane, centroid!dislocation line, slip plane vectors, centroid,
real(kind=dp) :: burgers(3) !burgers vector of loop 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 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-----------------------' print *, '--------------------Option Dislocation-----------------------'
select case(trim(adjustl(option))) select case(trim(adjustl(option)))
case('-disl')
call parse_disl(arg_pos)
call disl
case('-dislgen') case('-dislgen')
call parse_dislgen(arg_pos) call parse_dislgen(arg_pos)
call dislgen call dislgen
@ -43,6 +47,146 @@ module opt_disl
end select end select
end subroutine dislocation 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) subroutine parse_dislgen(arg_pos)
!Parse dislgen command !Parse dislgen command
@ -123,6 +267,7 @@ module opt_disl
call matrix_inverse(ss_ori, 3, ss_inv) call matrix_inverse(ss_ori, 3, ss_inv)
!Apply the rotation !Apply the rotation
print *, ss_inv
disp_transform = matmul(sub_box_ori(:,:,i), ss_inv) disp_transform = matmul(sub_box_ori(:,:,i), ss_inv)
call matrix_inverse(disp_transform,3,inv_transform) call matrix_inverse(disp_transform,3,inv_transform)
@ -183,8 +328,6 @@ module opt_disl
end do end do
end if end if
!Now make sure all atoms are wrapped back into the simulation cell
call wrap_atoms
end subroutine dislgen end subroutine dislgen
@ -398,8 +541,6 @@ module opt_disl
end do end do
return return
!Now make sure all atoms are wrapped back into the simulation cell
call wrap_atoms
end subroutine end subroutine
!******************************************************** !********************************************************
@ -561,7 +702,6 @@ module opt_disl
!Now reset the list for the scanning algorithm !Now reset the list for the scanning algorithm
delete_num = 0 delete_num = 0
!Now scan over all atoms again and find the closest vloop_size number of atoms to the initial atom
!that reside on the same plane. If loop_radius is > 0 then we build a circular vacancy cluster !that reside on the same plane. If loop_radius is > 0 then we build a circular vacancy cluster
if(loop_radius > 0) then if(loop_radius > 0) then
do i = 1, atom_num do i = 1, atom_num

418
src/opt_group.f90
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@ -8,10 +8,10 @@ module opt_group
use box use box
implicit none implicit none
integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2 integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num, group_type, notsize
character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), tip_radius, bwidth real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), radius, bwidth, shell_thickness
logical :: displace, delete, max_remesh, refine logical :: displace, delete, max_remesh, refine, group_nodes, flip, efill, refinefill
integer, allocatable :: element_index(:), atom_index(:) integer, allocatable :: element_index(:), atom_index(:)
@ -22,31 +22,58 @@ module opt_group
!Main calling function for the group option !Main calling function for the group option
integer, intent(inout) :: arg_pos integer, intent(inout) :: arg_pos
print *, '-----------------------Option Group-------------------------' print *, '------------------------------------------------------------'
print *, 'Option Group'
print *, '------------------------------------------------------------'
group_ele_num = 0 group_ele_num = 0
group_atom_num = 0 group_atom_num = 0
remesh_size=0 remesh_size=0
random_num=0
group_type=0
notsize=0
displace=.false. displace=.false.
delete=.false. delete=.false.
max_remesh=.false. max_remesh=.false.
refine = .false. refine = .false.
flip = .false.
if(allocated(element_index)) deallocate(element_index) if(allocated(element_index)) deallocate(element_index)
if(allocated(atom_index)) deallocate(atom_index) if(allocated(atom_index)) deallocate(atom_index)
call parse_group(arg_pos) call parse_group(arg_pos)
call get_group
!Now call the transformation functions for the group !Now call the transformation functions for the group
if(displace) call displace_group if(refine) then
call get_group
call refine_group
end if
if(refinefill) then
call get_group
call refinefill_group
end if
if(displace)then
call get_group
call displace_group
end if
if(remesh_size > 0) call remesh_group if(delete)then
call get_group
call delete_group
end if
if(delete) call delete_group if(remesh_size > 0)then
call get_group
call remesh_group
end if
if(refine) call refine_group if(group_type > 0) then
call get_group
call change_group_type
end if
end subroutine group end subroutine group
@ -67,7 +94,7 @@ module opt_group
continue continue
case default case default
print *, "Select_type ", trim(adjustl(type)), " is not an accept group selection criteria. ", & print *, "Select_type ", trim(adjustl(type)), " is not an accept group selection criteria. ", &
"Please select from atoms, nodes, or both." "Please select from atoms, elements, or both."
end select end select
arg_pos = arg_pos + 1 arg_pos = arg_pos + 1
@ -158,7 +185,7 @@ module opt_group
arg_pos = arg_pos + 1 arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen) call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing tip radius in group notch command" if (arglen==0) STOP "Missing tip radius in group notch command"
read(textholder,*) tip_radius read(textholder,*) radius
!Calculate the vertex positions !Calculate the vertex positions
vertices(:,1) = centroid vertices(:,1) = centroid
@ -188,7 +215,7 @@ module opt_group
!Now update the centroid so that the desire tip diameter matches the wedge with !Now update the centroid so that the desire tip diameter matches the wedge with
if (bwidth > 0) then if (bwidth > 0) then
centroid(dim1) = centroid(dim1) + 2*tip_radius*(H)/bwidth centroid(dim1) = centroid(dim1) + 2*radius*(H)/bwidth
end if end if
!Read the ID type shape for group !Read the ID type shape for group
case('id') case('id')
@ -280,7 +307,7 @@ module opt_group
case('elements','element') case('elements','element')
if (group_ele_num > 0) then if (group_ele_num > 0) then
print *, "Elements specifier used more than once in group id command with type both, either use type ", & print *, "Elements specifier used more than once in group id command with type both, either use type ",&
"elements or include atoms identifier" "elements or include atoms identifier"
stop 3 stop 3
@ -300,6 +327,47 @@ module opt_group
if(i ==1) arg_pos = arg_pos + 1 if(i ==1) arg_pos = arg_pos + 1
end do end do
end select end select
case('sphere')
!First extract the sphere centroid
do i = 1, 3
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing sphere centroid in group command"
call parse_pos(i, textholder, centroid(i))
end do
!Now get the tip radius
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing sphere radius in group command"
read(textholder, *) radius
case('shell')
!First extract the shell centroid
do i = 1, 3
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing shell centroid in group command"
call parse_pos(i, textholder, centroid(i))
end do
!Now get the radius
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing shell radius in group command"
read(textholder, *) radius
!Now get the shell thickness
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing shell thickness in group command"
read(textholder, *) shell_thickness
case('all')
!Do nothing if the shape is all
continue
case default case default
print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", & print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", &
"for accepted group shapes." "for accepted group shapes."
@ -325,6 +393,8 @@ module opt_group
end do end do
case('refine') case('refine')
refine=.true. refine=.true.
case('refinefill')
refinefill=.true.
case('remesh') case('remesh')
arg_pos = arg_pos + 1 arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen) call get_command_argument(arg_pos, textholder, arglen)
@ -334,6 +404,28 @@ module opt_group
max_remesh =.true. max_remesh =.true.
case('delete') case('delete')
delete=.true. delete=.true.
case('nodes')
group_nodes=.true.
case('random')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing number of random atoms in group command"
read(textholder, *) random_num
case('flip')
flip=.true.
case('efill')
efill=.true.
case('type')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing atom type for group"
call add_atom_type(textholder, group_type)
case('notsize')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen ==0) stop "Missing notsize size"
read(textholder, *) notsize
print *, "Ignoring elements with size ", notsize
case default case default
!If it isn't an available option to opt_disl then we just exit !If it isn't an available option to opt_disl then we just exit
exit exit
@ -344,34 +436,38 @@ module opt_group
subroutine get_group subroutine get_group
!This subroutine finds all elements and/or atoms within the group boundaries !This subroutine finds all elements and/or atoms within the group boundaries
!specified by the user. !specified by the user.
integer :: i, j, inod, ibasis integer :: i, j, inod, ibasis, temp, node_in_out(max_ng_node)
integer, allocatable :: resize_array(:) integer, allocatable :: resize_array(:)
real(kind=dp) :: r_center(3) real(kind=dp) :: r_center(3), rand
select case(trim(adjustl(shape))) select case(trim(adjustl(shape)))
case('block') case('block')
print *, "Group has block shape with boundaries: ", block_bd print *, "Group has block shape with boundaries: ", block_bd
case ('wedge') case ('wedge')
print *, "Group has wedge shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices print *, "Group has wedge shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices
case ('notch')
print *, "Group has notch shape with dim1", dim1, "and dim2", dim2, " tip radius ", radius, "and vertices ", &
vertices
case('id') case('id')
print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms." print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
return return
case('sphere')
print *, "Group has sphere shape with centroid ", centroid(:), " and radius ", radius
case('all')
print *, "Group has all of type ", type
end select end select
!Allocate variables to arbitrary size !Reset group if needed
if(allocated(element_index)) deallocate(element_index,atom_index)
group_ele_num = 0
group_atom_num = 0
allocate(element_index(1024), atom_index(1024)) allocate(element_index(1024), atom_index(1024))
!Check the type to see whether we need to find the elements within the group !Check the type to see whether we need to find the elements within the group
select case(trim(adjustl(type))) select case(trim(adjustl(type)))
case('elements', 'both') case('elements', 'both')
do i = 1, ele_num do i = 1, ele_num
r_center(:) = 0.0_dp if(in_group_ele(size_ele(i), lat_ele(i), r_node(:,:,:,i))) then
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
r_center = r_center + r_node(:,ibasis,inod,i)/(basisnum(lat_ele(i))*ng_node(lat_ele(i)))
end do
end do
if (in_group(r_center)) then
group_ele_num = group_ele_num + 1 group_ele_num = group_ele_num + 1
if(group_ele_num > size(element_index)) then if(group_ele_num > size(element_index)) then
allocate(resize_array(size(element_index) + 1024)) allocate(resize_array(size(element_index) + 1024))
@ -381,15 +477,29 @@ module opt_group
end if end if
element_index(group_ele_num) = i element_index(group_ele_num) = i
end if end if
end do end do
end select
!Check the type to see if we need to find the atoms within the group if(random_num > 0) then
!If we have the random option enabled then we select random_num number of elements from the group and overwrite
!the group with those elements
do i = 1, random_num
call random_number(rand)
j = i + floor((group_ele_num+1-i)*rand)
temp = element_index(j)
element_index(j) = element_index(i)
element_index(i) = temp
end do
group_ele_num = random_num
end if
end select
!Check the type to see if we need to find the atoms within the group
select case(trim(adjustl(type))) select case(trim(adjustl(type)))
case('atoms','both') case('atoms','both')
do i = 1, atom_num do i = 1, atom_num
if(in_group(r_atom(:,i))) then if(in_group(r_atom(:,i)).neqv.flip) then
group_atom_num = group_atom_num + 1 group_atom_num = group_atom_num + 1
if (group_atom_num > size(atom_index)) then if (group_atom_num > size(atom_index)) then
allocate(resize_array(size(atom_index) + 1024)) allocate(resize_array(size(atom_index) + 1024))
@ -401,6 +511,19 @@ module opt_group
atom_index(group_atom_num) = i atom_index(group_atom_num) = i
end if end if
end do end do
if(random_num > 0) then
!If we have the random option enabled then we select random_num number of atom from the group and overwrite
!the group with those atom
do i = 1, random_num
call random_number(rand)
j = i + floor((group_atom_num+1-i)*rand)
temp = atom_index(j)
atom_index(j) = atom_index(i)
atom_index(i) = temp
end do
group_atom_num = random_num
end if
end select end select
j = 0 j = 0
@ -450,7 +573,7 @@ module opt_group
end subroutine displace_group end subroutine displace_group
subroutine refine_group subroutine refine_group
!This command is used to remesh the group to a desired element size !This command is used to refine the group to full atomistics
integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_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) real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
@ -469,7 +592,7 @@ module opt_group
!here as well to make sure they are in the box !here as well to make sure they are in the box
do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3 do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
call apply_periodic(r_interp(:,j)) call apply_periodic(r_interp(:,j))
call add_atom(type_interp(j), sbox_ele(ie), r_interp(:,j)) call add_atom(0,type_interp(j), sbox_ele(ie), r_interp(:,j))
end do end do
end do end do
!Once all atoms are added we delete all of the elements !Once all atoms are added we delete all of the elements
@ -477,7 +600,110 @@ module opt_group
print *, group_ele_num, " elements of group are refined to ", atom_num -orig_atom_num, " atoms." print *, group_ele_num, " elements of group are refined to ", atom_num -orig_atom_num, " atoms."
end if end if
end subroutine end subroutine refine_group
subroutine refinefill_group
!This command is used to refine the group to full atomistics
integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num, m, n, o, esize, &
ele(3,8), new_ele_num, ibasis, inod, vlat(3), nump_ele, added_points
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), rfill(3,max_basisnum,max_ng_node), ravg(3), ratom(3,max_basisnum)
logical :: lat_points(max_esize, max_esize, max_esize)
!Refining to atoms
if(group_ele_num > 0) then
orig_atom_num = atom_num
new_ele_num = 0
!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)
do i = 1, group_ele_num
ie = element_index(i)
!Find all possible elements that we can make while making sure they aren't in the group
lat_points(1:size_ele(ie),1:size_ele(ie),1:size_ele(ie)) = .true.
!Now calculate the number of elemets which are available for remeshing
nump_ele = size_ele(ie)**3
do o =1, size_ele(ie)
do n = 1, size_ele(ie)
do m =1, size_ele(ie)
call get_interp_pos(m,n,o,i,rfill(:,:,1))
ravg(:) = 0
do ibasis = 1, basisnum(lat_ele(ie))
ravg = ravg + rfill(:,ibasis, 1)/basisnum(lat_ele(ie))
end do
if( in_group(ravg)) then
nump_ele = nump_ele - 1
end if
end do
end do
end do
!Now start the remeshing loop for the element
esize = size_ele(ie) - 2
added_points=0
do while(esize > min_efillsize)
if(nump_ele < min_efillsize**3) then
exit
else if (nump_ele < esize**3) then
esize = esize - 2
else
ele = cubic_cell*(esize-1)
do o = 1, size_ele(ie) - esize
do n = 1, size_ele(ie) - esize
latloop:do m = 1, size_ele(ie) - esize
do inod = 1, ng_node(lat_ele(ie))
vlat = ele(:,inod) + (/ m, n, o /)
if (.not.lat_points(vlat(1), vlat(2),vlat(3))) cycle latloop
call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod))
end do
!Check to make sure all lattice points exist for the current element
if(any(.not.lat_points(m:m+esize-1, n:n+esize-1, o:o+esize-1))) cycle latloop
if (.not.in_group_ele(esize, lat_ele(ie), rfill)) then
nump_ele=nump_ele - esize**3
lat_points(m:m+esize-1, n:n+esize-1, o:o+esize-1) = .false.
call add_element(0,type_ele(ie), esize, lat_ele(ie), sbox_ele(ie), rfill)
new_ele_num = new_ele_num + 1
added_points = added_points + esize**3
end if
end do latloop
end do
end do
esize=esize-2
end if
end do
!Now add the leftover lattice points as atoms
do o = 1, size_ele(ie)
do n = 1, size_ele(ie)
do m = 1, size_ele(ie)
if(lat_points(m,n,o)) then
call get_interp_pos(m,n,o, ie, ratom(:,:))
do ibasis = 1, basisnum(lat_ele(ie))
call apply_periodic(ratom(:,ibasis))
call add_atom(0, basis_type(ibasis,lat_ele(ie)), sbox_ele(ie), ratom(:,ibasis))
added_points=added_points + 1
end do
end if
end do
end do
end do
if (added_points /= (size_ele(ie)**3)) then
print *, "Element ", ie, " is refined incorrectly in refinefill"
end if
end do
!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 and ", new_ele_num, &
" elements."
end if
end subroutine refinefill_group
subroutine remesh_group subroutine remesh_group
!This command is used to remesh the group to a desired element size !This command is used to remesh the group to a desired element size
@ -705,7 +931,8 @@ module opt_group
!Add the element, for the sbox we just set it to the same sbox that we get the orientation !Add the element, for the sbox we just set it to the same sbox that we get the orientation
!from. In this case it is from the sbox of the first atom in the group. !from. In this case it is from the sbox of the first atom in the group.
new_ele = new_ele+1 new_ele = new_ele+1
call add_element(remesh_ele_type, working_esize, ilat, sbox_atom(atom_index(1)),r_new_node) call add_element(0,remesh_ele_type, working_esize, ilat, &
sbox_atom(atom_index(1)),r_new_node)
end if end if
end if end if
@ -726,7 +953,7 @@ module opt_group
lat_points(ix,iy,iz) = .false. lat_points(ix,iy,iz) = .false.
r = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat) r = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat)
new_atom=new_atom+1 new_atom=new_atom+1
call add_atom(basis_type(1,ilat), is, r) call add_atom(0,basis_type(1,ilat), is, r)
end if end if
end do end do
end do end do
@ -755,11 +982,40 @@ module opt_group
call delete_elements(group_ele_num, element_index) call delete_elements(group_ele_num, element_index)
end subroutine delete_group end subroutine delete_group
subroutine change_group_type
!This subroutine changes all atoms and nodes at atoms within a group to a specific type
integer :: i, j, ltype,ibasis, inod, basis_type(10)
print *, "Changing ", group_atom_num, " atoms and ", group_ele_num, " elements to atom type ", group_type
!Change all atom group types
do i = 1, group_atom_num
j = atom_index(i)
type_atom(j) = group_type
end do
!Map to a new lattice type for all element
do i =1, group_ele_num
j = element_index(i)
ltype = lat_ele(j)
do ibasis = 1, basisnum(ltype)
basis_type(ibasis) = group_type
end do
call lattice_map(basisnum(ltype), basis_type, ng_node(ltype), lapa(ltype), lat_ele(j))
end do
end subroutine change_group_type
subroutine split_group_elements
!
end subroutine split_group_elements
function in_group(r) function in_group(r)
!This subroutine determines if a point is within the group boundaries !This subroutine determines if a point is within the group boundaries
real(kind=dp), intent(in) :: r(3) real(kind=dp), intent(in) :: r(3)
real(kind=dp) :: r_notch real(kind=dp) :: rnorm
integer :: dim3, i integer :: dim3, i
logical :: in_group logical :: in_group
@ -779,9 +1035,95 @@ module opt_group
if (r(dim1) < centroid(dim1)) in_group = .false. if (r(dim1) < centroid(dim1)) in_group = .false.
end if end if
r_notch = sqrt((r(dim1) - centroid(dim1))**2 + (r(dim3)-centroid(dim3))**2) rnorm = sqrt((r(dim1) - centroid(dim1))**2 + (r(dim3)-centroid(dim3))**2)
in_group = in_group.or.(r_notch < tip_radius) in_group = in_group.or.(rnorm < radius)
end select case('sphere')
rnorm = norm2(r(:) - centroid(:))
if (rnorm <= radius) then
in_group = .true.
else
in_group = .false.
end if
case('shell')
rnorm = norm2(r(:) - centroid(:))
if ((rnorm >= radius).and.(rnorm<=(radius + shell_thickness))) then
in_group = .true.
else
in_group = .false.
end if
case('all')
in_group = .true.
end select
end function in_group end function in_group
function in_group_ele(esize, elat, rn)
!This figures out if the elements are in the group boundaries
real(kind=dp), intent(in) :: rn(3,max_basisnum, max_ng_node)
integer, intent(in) :: esize, elat
logical :: in_group_ele
integer :: i, inod, ibasis, node_in_out(max_ng_node)
real(kind=dp) :: r_center(3)
in_group_ele=.false.
if(trim(adjustl(shape)) == 'shell') then
node_in_out(:) = -1
!First calculate whether each element node is within the shell region, inside the shell sphere, or outside the
!shell region
nodeloop:do inod = 1, ng_node(elat)
r_center(:)=0.0_dp
do ibasis = 1, basisnum(elat)
r_center(:)= r_center(:) + rn(:,ibasis,inod)/basisnum(elat)
end do
if((in_group(rn(:, ibasis, inod)).neqv.flip).and.(size_ele(i)/=notsize)) then
node_in_out(inod) = 2
exit nodeloop
end if
shape ='sphere'
if((in_group(rn(:, ibasis, inod)).neqv.flip).and.(esize/=notsize)) then
node_in_out(inod) = 1
else
node_in_out(inod) = 0
end if
shape='shell'
end do nodeloop
!If any nodes are within the shell region, or if the shell region interescts an element then add it to the group
if(any(node_in_out == 2).or.(any(node_in_out==1).and.(any(node_in_out==0)))) then
in_group_ele=.true.
return
end if
else if(.not.(group_nodes)) then
r_center(:) = 0.0_dp
do inod = 1, ng_node(elat)
do ibasis = 1, basisnum(elat)
r_center = r_center + rn(:,ibasis,inod)/(basisnum(elat)*ng_node(elat))
end do
end do
if ((in_group(r_center).neqv.flip).and.(esize/= notsize)) then
in_group_ele=.true.
return
end if
else if(group_nodes) then
r_center(:) = 0.0_dp
do inod = 1, ng_node(elat)
do ibasis = 1, basisnum(elat)
if ((in_group(rn(:,ibasis,inod)).neqv.flip).and.(esize/=notsize)) then
in_group_ele=.true.
return
end if
end do
end do
end if
end function in_group_ele
end module opt_group end module opt_group

37
src/opt_orient.f90
Unescape View File

@ -11,18 +11,19 @@ module opt_orient
real(kind=dp), save :: new_orient(3,3) real(kind=dp), save :: new_orient(3,3)
real(kind=dp), dimension(6) :: orig_box_bd real(kind=dp), dimension(6) :: orig_box_bd
real(kind=dp), allocatable :: orig_sub_box_ori(:,:,:) real(kind=dp), allocatable :: orig_sub_box_ori(:,:,:)
character(len=3) :: orig_box_bc
public public
contains contains
subroutine orient(arg_pos) subroutine orient_opt(arg_pos)
integer, intent(inout) :: arg_pos integer, intent(inout) :: arg_pos
integer :: i, ibasis, inod integer :: i, j, k, ibasis, inod
logical :: isortho, isrighthanded logical :: isortho, isrighthanded, matching
real(kind=dp) :: inv_sub_box_ori(3,3,sub_box_num) real(kind=dp) :: inv_sub_box_ori(3,3,sub_box_num)
character(len=3) :: old_box_bc
!First parse the orient command !First parse the orient command
call parse_orient(arg_pos) call parse_orient(arg_pos)
@ -63,12 +64,25 @@ module opt_orient
!Save original box boundaries !Save original box boundaries
orig_box_bd = box_bd orig_box_bd = box_bd
!Now find new box boundaries, have to temporarily define the box as shrink wrapped for def new box to work !Now find new box boundaries, if any orientations are the same we leave them as they are. If they are different then we have
old_box_bc = box_Bc !to shrink wrap them
box_bc = 'sss'
call def_new_box orig_box_bc = box_bc
box_bc = old_box_bc do i = 1,3
end subroutine orient matching=.true.
sbox_loop:do j = 1, sub_box_num
do k = 1, 3
if(.not.is_equal(orig_sub_box_ori(i,k,j), new_orient(i,k))) then
matching = .false.
exit sbox_loop
end if
end do
end do sbox_loop
if(.not.matching) box_bc(i:i)='s'
end do
call def_new_box
end subroutine orient_opt
subroutine parse_orient(arg_pos) subroutine parse_orient(arg_pos)
!This parses the orient option !This parses the orient option
@ -129,8 +143,9 @@ module opt_orient
end do end do
end do end do
!Restore original box boundaries !Restore original box boundaries and box BC
box_bd = orig_box_bd box_bd = orig_box_bd
box_bc = orig_box_bc
end subroutine unorient end subroutine unorient
subroutine sbox_ori(arg_pos) subroutine sbox_ori(arg_pos)

131
src/opt_redef_box.f90
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@ -0,0 +1,131 @@
module opt_redef_box
use box
use elements
use subroutines
implicit none
character(len=3) :: redef_dim, new_bc
real(kind=dp) :: new_bd(6)
public
contains
subroutine redef_box(arg_pos)
!This is the main calling function for opt_redef_box
integer, intent(inout) :: arg_pos
integer :: i, inod, ibasis, iatom, delete_list(atom_num), delete_num, type_interp(max_basisnum*max_esize**3)
real(kind=dp):: r_interp(3, max_basisnum*max_esize**3)
logical :: node_out(8)
!First parse the argument
call parse_redef_box(arg_pos)
print *, '------------------------------------------------------------'
print *, 'Option redef_box'
print *, '------------------------------------------------------------'
!Now first filter atoms that don't fit in the new box bounds and delete them
delete_num = 0
do i = 1, atom_num
if(.not.in_block_bd(r_atom(:,i),new_bd)) then
delete_num = delete_num + 1
delete_list(delete_num) = i
end if
end do
call delete_atoms(delete_num, delete_list(1:delete_num))
!Now loop over all elements
delete_num = 0
delete_list(:) = 0
do i = 1, ele_num
!Determine if all nodes are within the new boundaries
node_out(:) = .false.
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
if(.not.in_block_bd(r_node(:,ibasis,inod,i), new_bd)) then
node_out(inod) = .true.
end if
end do
end do
!If all nodes are out just add the element to the delete list
if(all(node_out)) then
delete_num = delete_num +1
delete_list(delete_num) = i
!If any nodes are out we add the element to the delete list, but then loop over the interpoalted atoms to figure out
!which ones fit inside the boundary to keep the box rectangular
else if (any(node_out)) then
delete_num = delete_num +1
delete_list(delete_num) = i
call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
!loop over all interpolated atoms and add them to the system
do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
if(in_block_bd(r_interp(:,iatom), new_bd)) then
call add_atom(0,type_interp(iatom), sbox_ele(i), r_interp(:,iatom))
end if
end do
end if
end do
call delete_elements(delete_num, delete_list(1:delete_num))
print *, "Old box_bd: ", box_bd, " is redefined to new box boundaries: ", new_bd
box_bd=new_bd
box_bc = new_bc
end subroutine redef_box
subroutine parse_redef_box(arg_pos)
!Parse the command
integer, intent(inout) :: arg_pos
integer :: i, j, arglen
character(len=100) textholder
!First read in the dimensions that we are redefining
redef_dim = ''
arg_pos=arg_pos+1
call get_command_argument(arg_pos, redef_dim, arglen)
select case(trim(adjustl(redef_dim)))
case('x','y','z','xy','yx','xz','zx','yz','zy','xyz','yxz','xzy','zyx','zxy','yzx')
continue
case default
print *, "Incorrect redef_dim ", redef_dim, "please select any permuation of x, y, z, xy, yz, xz, xyz"
stop 3
end select
!Now read in the new dimensions
new_bd = box_bd
new_bc = box_bc
do i = 1, 3
select case(trim(adjustl(redef_dim(i:i))))
case('x')
j = 1
case('y')
j = 2
case('z')
j = 3
case default
exit
end select
arg_pos=arg_pos +1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen == 0) stop "Missing a box dimension in opt_redef_box"
call parse_pos(j, textholder,new_bd(2*j-1))
arg_pos=arg_pos +1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen == 0) stop "Missing a box dimension in opt_redef_box"
call parse_pos(j, textholder,new_bd(2*j))
new_bc(j:j) = 's'
end do
arg_pos = arg_pos + 1
end subroutine parse_redef_box
end module opt_redef_box

176
src/opt_slip_plane.f90
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@ -0,0 +1,176 @@
module opt_slip_plane
use parameters
use elements
use functions
use subroutines
implicit none
integer :: sdim
real(kind=dp) :: spos
logical :: efill
public
contains
subroutine run_slip_plane(arg_pos)
!Main calling function for the slip_plane option
integer, intent(inout) :: arg_pos
integer :: ie, ia, slip_enum, old_atom_num, esize, new_ele_num, n, m, o, ele(3,8), nump_ele, inod, vlat(3), ibasis
integer, allocatable :: slip_eles(:), temp_int(:)
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), rfill(3,max_basisnum, max_ng_node), ratom(3,max_basisnum), &
maxp, minp
integer :: type_interp(max_basisnum*max_esize**3)
logical :: lat_points(max_esize,max_esize, max_esize)
print *, '---------------------Option Slip_Plane----------------------'
!Initialize variables
efill = .false.
slip_enum = 0
old_atom_num = atom_num
!!Parse the argument
call parse(arg_pos)
!If we are running the efill code then we have to initiate some variables
if(efill) then
new_ele_num = 0
end if
allocate(slip_eles(1024))
!Now loop over all elements, find which ones intersect
do ie = 1, ele_num
if( (spos < maxval(r_node(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)),ie))).and. &
(spos > minval(r_node(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)),ie)))) then
slip_enum = slip_enum + 1
if (slip_enum > size(slip_eles)) then
allocate(temp_int(size(slip_eles)+1024))
temp_int(1:size(slip_eles)) = slip_eles
temp_int(size(slip_eles)+1:) = 0
call move_alloc(temp_int, slip_eles)
end if
slip_eles(slip_enum) = ie
!If we aren't efilling then just refine the element
if(.not.efill) then
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
do ia = 1, basisnum(lat_ele(ie)) * size_ele(ie)**3
call apply_periodic(r_interp(:,ia))
call add_atom(0, type_interp(ia), sbox_ele(ie), r_interp(:,ia))
end do
!If we are efilling then the code is slightly more complex
else
!First populate the lat points array
lat_points(1:size_ele(ie),1:size_ele(ie), 1:size_ele(ie)) = .true.
!Now start trying to remesh the region, leaving the slip plane as a discontinuity
esize = size_ele(ie) - 2
nump_ele = size_ele(ie)**3
do while(esize > min_efillsize)
if(nump_ele < esize**3) then
esize = esize - 2
else
ele = cubic_cell*(esize -1)
do o = 1, size_ele(ie) - esize
do n = 1, size_ele(ie) - esize
latloop:do m = 1, size_ele(ie) - esize
do inod = 1, ng_node(lat_ele(ie))
vlat = ele(:,inod) + (/ m, n, o /)
if (.not.lat_points(vlat(1), vlat(2),vlat(3))) cycle latloop
call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod))
end do
!Check to make sure all lattice points exist for the current element
if(any(.not.lat_points(m:m+esize-1, n:n+esize-1, o:o+esize-1))) cycle latloop
!Check to see if the plane intersects this element if not then add it
maxp = maxval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie))))
minp = minval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie))))
if(.not.(spos < maxp).and.(spos > minp))then
nump_ele = nump_ele - esize**3
lat_points(m:m+esize-1, n:n+esize-1, o:o+esize-1) = .false.
call add_element(0, type_ele(ie), esize, lat_ele(ie), sbox_ele(ie), rfill)
new_ele_num = new_ele_num + 1
end if
end do latloop
end do
end do
end if
esize= esize-2
end do
! Now add the leftover lattice points as atoms
do o = 1, size_ele(ie)
do n = 1, size_ele(ie)
do m = 1, size_ele(ie)
if(lat_points(m,n,o)) then
call get_interp_pos(m,n,o, ie, ratom(:,:))
do ibasis = 1, basisnum(lat_ele(ie))
call apply_periodic(r_atom(:,ibasis))
call add_atom(0, basis_type(ibasis,lat_ele(ie)), sbox_ele(ie), ratom(:,ibasis))
end do
end if
end do
end do
end do
end if
end if
end do
!Once we finish adding elements delete the old ones
call delete_elements(slip_enum, slip_eles(1:slip_enum))
!Output data
if(.not.efill) then
print *, "We refine ", slip_enum, " elements into ", atom_num - old_atom_num , " atoms"
else
print *, "We refine ", slip_enum, " elements into ", atom_num - old_atom_num , " atoms and ", new_ele_num, " elements"
end if
end subroutine run_slip_plane
subroutine parse(arg_pos)
!This subroutine parses the input arguments to the mode
integer, intent(inout) :: arg_pos
integer :: arglen
character(len = 100) :: textholder
!First read the dimension
arg_pos = arg_pos +1
call get_command_argument(arg_pos,textholder, arglen)
if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
!Check to make sure that the dimension is correct
select case(trim(adjustl(textholder)))
case('x','X')
sdim = 1
case('y','Y')
sdim = 2
case('z','Z')
sdim = 3
case default
print *, "Error: dimension ", trim(adjustl(textholder)), " is not accepted. Please select from x, y, or z"
end select
!Now parse the position of the slip plane
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
call parse_pos(sdim, textholder, spos)
!Now check to see if efill was passed
arg_pos = arg_pos + 1
if(.not.(arg_pos > command_argument_count())) then
call get_command_argument(arg_pos, textholder, arglen)
if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
if(trim(adjustl(textholder)) == "efill") then
arg_pos = arg_pos +1
efill = .true.
end if
end if
end subroutine parse
end module opt_slip_plane

7
src/parameters.f90
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@ -3,7 +3,8 @@ module parameters
implicit none implicit none
!Default precision !Default precision
integer, parameter :: dp= selected_real_kind(15,307) integer, parameter :: dp= selected_real_kind(15,307), &
min_efillsize = 11
!Parameters for floating point tolerance !Parameters for floating point tolerance
real(kind=dp), parameter :: lim_zero = epsilon(1.0_dp), & real(kind=dp), parameter :: lim_zero = epsilon(1.0_dp), &
lim_large = huge(1.0_dp), & lim_large = huge(1.0_dp), &
@ -12,5 +13,7 @@ module parameters
!Numeric constants !Numeric constants
real(kind=dp), parameter :: pi = 3.14159265358979323846_dp real(kind=dp), parameter :: pi = 3.14159265358979323846_dp
!Mode type that is being called
character(len=100) :: mode
end module parameters end module parameters

33
src/str.f90
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@ -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

61
src/subroutines.f90
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@ -198,66 +198,6 @@ module subroutines
end do end do
end subroutine end subroutine
subroutine build_cell_list(numinlist, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
!This subroutine builds a cell list based on rc_off
!----------------------------------------Input/output variables-------------------------------------------
integer, intent(in) :: numinlist !The number of points within r_list
real(kind=dp), dimension(3,numinlist), intent(in) :: r_list !List of points to be used for the construction of
!the cell list.
real(kind=dp), intent(in) :: rc_off ! Cutoff radius which dictates the size of the cells
integer, dimension(3), intent(inout) :: cell_num !Number of cells in each dimension.
integer, allocatable, intent(inout) :: num_in_cell(:,:,:) !Number of points within each cell
integer, allocatable, intent(inout) :: cell_list(:,:,:,:) !Index of points from r_list within each cell.
integer, dimension(3,numinlist), intent(out) :: which_cell !The cell index for each point in r_list
!----------------------------------------Begin Subroutine -------------------------------------------
integer :: i, j, cell_lim, c(3)
real(kind=dp) :: box_len(3)
integer, allocatable :: resize_cell_list(:,:,:,:)
!First calculate the number of cells that we need in each dimension
do i = 1,3
box_len(i) = box_bd(2*i) - box_bd(2*i-1)
cell_num(i) = int(box_len(i)/(rc_off/2))+1
end do
!Initialize/allocate variables
cell_lim = 10
allocate(num_in_cell(cell_num(1),cell_num(2),cell_num(3)), cell_list(cell_lim, cell_num(1), cell_num(2), cell_num(3)))
!Now place points within cell
do i = 1, numinlist
!c is the position of the cell that the point belongs to
do j = 1, 3
c(j) = int((r_list(j,i)-box_bd(2*j-1))/(rc_off/2)) + 1
end do
!Place the index in the correct position, growing if necessary
num_in_cell(c(1),c(2),c(3)) = num_in_cell(c(1),c(2),c(3)) + 1
if (num_in_cell(c(1),c(2),c(3)) > cell_lim) then
allocate(resize_cell_list(cell_lim+10,cell_num(1),cell_num(2),cell_num(3)))
resize_cell_list(1:cell_lim, :, :, :) = cell_list
resize_cell_list(cell_lim+1:, :, :, :) = 0
call move_alloc(resize_cell_list, cell_list)
end if
cell_list(num_in_cell(c(1),c(2),c(3)),c(1),c(2),c(3)) = i
which_cell(:,i) = c
end do
return
end subroutine build_cell_list
subroutine check_right_ortho(ori, isortho, isrighthanded) subroutine check_right_ortho(ori, isortho, isrighthanded)
!This subroutine checks whether provided orientations in the form: !This subroutine checks whether provided orientations in the form:
! | x1 x2 x3 | ! | x1 x2 x3 |
@ -301,4 +241,5 @@ module subroutines
return return
end subroutine check_right_ortho end subroutine check_right_ortho
end module subroutines end module subroutines

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