From 32ab5a60583be60dba15af52922180e779199318 Mon Sep 17 00:00:00 2001
From: Alex Selimov <alsel@tuta.io>
Date: Tue, 19 May 2020 16:16:26 -0400
Subject: [PATCH] Added basic basis functionality to code

---
 README.md           | 17 +++++++----------
 src/io.f90          |  2 +-
 src/mode_create.f90 | 30 ++++++++++++++++--------------
 3 files changed, 24 insertions(+), 25 deletions(-)

diff --git a/README.md b/README.md
index 2bb3db2..5bdd240 100644
--- a/README.md
+++ b/README.md
@@ -75,16 +75,6 @@ There is no default dimensions as duplicate is the default option. This command
 
 Example: `dimensions 100 100 100` 
 
-**ZigZag**
-
-```
-zigzag boolx booly boolz
-```
-
-Default zigzag is `f f f`. This command specifies whether a boundary should be left jagged (i.e. in essence not filled in). If `boolx` is `t` than the x dimension is left jagged and if it is `f` then the x dimension is filled.
-
-*Example:* `zigzag t f t` gives a box with jagged edges in the x and z and filled edges in the y.
-
 **Origin**
 
 ```
@@ -95,6 +85,13 @@ Default origin is `0 0 0`. This command just sets the origin for where the simul
 
 *Example:* `origin 10 0 1`
 
+**Basis**
+
+```
+basis basisnum bname bx by bz
+```
+
+This function allows you to define a custom basis. `bname bx by bz` must be repeated `basisnum` times.
 ### Mode Convert
 
 ```
diff --git a/src/io.f90 b/src/io.f90
index f929e29..d178baf 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -161,7 +161,7 @@ module io
         !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) == 'fcc') write_num = write_num + basisnum(lat_ele(i))*size_ele(i)**3
         end do
         !Write total number of atoms + elements
         write(11, '(i16, a)') write_num, ' atoms'
diff --git a/src/mode_create.f90 b/src/mode_create.f90
index 4e92492..ed60daf 100644
--- a/src/mode_create.f90
+++ b/src/mode_create.f90
@@ -166,6 +166,7 @@ module mode_create
         integer ::  ori_pos, i, j, arglen, stat
         character(len=100) :: textholder
         character(len=20) :: orient_string
+        character(len=2) :: btype
         logical :: isortho, isrighthanded
 
 
@@ -206,20 +207,6 @@ module mode_create
                     call parse_ori_vec(orient_string, orient(i,:))
                     arg_pos = arg_pos+1
 
-                    ! ori_pos=2
-                    ! do j = 1,3
-                    !     if (orient_string(ori_pos:ori_pos) == '-') then 
-                    !         ori_pos = ori_pos + 1
-                    !         read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
-                    !         if (stat>0) STOP "Error reading orient value"
-                    !         orient(i,j) = -orient(i,j)
-                    !         ori_pos = ori_pos + 1
-                    !     else
-                    !         read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
-                    !         if(stat>0) STOP "Error reading orient value"
-                    !         ori_pos=ori_pos + 1
-                    !     end if
-                    ! end do
                 end do
 
             !If the duplicate command is passed then we extract the information on the new bounds.
@@ -245,6 +232,21 @@ module mode_create
                     read(textholder, *) origin(i)
                     arg_pos = arg_pos + 1
                 end do
+            case('basis')
+                call get_command_argument(arg_pos, textholder)
+                read(textholder, *) basisnum(1)
+                arg_pos = arg_pos + 1
+                max_basisnum=basisnum(1)
+                do i = 1, max_basisnum
+                    call get_command_argument(arg_pos, btype)
+                    arg_pos = arg_pos+1
+                    call add_atom_type(btype, basis_type(i,1))
+                    do j = 1, 3
+                        call get_command_argument(arg_pos, textholder)
+                        read(textholder, *) basis_pos(j,i)
+                        arg_pos=arg_pos+1
+                    end do
+                end do
 
             case default
                 !If it isn't an option then you have to exit