Merge branch 'code_fixes' into 'master'

Code fixes

See merge request !16

.gitlab-ci.yml

@@ -36,8 +36,9 @@ vis.py:
   - python sim_controller.py "config/default.in" --no-figures
   - python vis.py "sim_output/default" --no-gui
 
-vis.py multi:
+vis.py all multi:
   script:
   - python sim_controller.py "config/default.in" --no-figures --compress
   - python sim_controller.py "config/default.in" --no-figures --compress
   - python vis.py "sim_output/default" --no-gui --all --multi
+  - python vis.py "sim_output/default" --no-gui --all --no-multi

ase_sim.py

@@ -16,7 +16,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 # ------------------------------
-# TODO: rename or merge with sim_controller or sim_creator?
+# TODO: merge with sim_controller or sim_creator?
 
 import os
 import math

config/Fe10Cr10Al_deep_200.in

@@ -22,6 +22,9 @@ pot_filename = potentials_deep.txt
 Cr = 0.10
 Al = 0.10
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/Fe10Cr20Al_normal_200_init-O.in → config/Fe10Cr10Al_normal_100.in

 [Job parameters]
-job_name = Fe10Cr20Al_normal_200_init-O
+job_name = Fe10Cr10Al_normal_100
 report_file = True
 
 [Simulation parameters]
 sim_type = ase_sim
-kT = 200
+kT = 100
 n_exchanges = 20000000
 n_frames = 200
-rand_ox = False
+rand_ox = True
 
 [Lattice parameters]
 bounds_scale = 25
@@ -20,10 +20,10 @@ pot_filename = potentials_normal.txt
 
 [Bulk dopants]
 Cr = 0.10
-Al = 0.20
+Al = 0.10
 
 [Empty space dopants]
-O = 0.10
+O = 0.001
 
 [Figure parameters]
 profile_mean_range = 200

config/Fe10Cr10Al_normal_200.in

@@ -22,6 +22,9 @@ pot_filename = potentials_normal.txt
 Cr = 0.10
 Al = 0.10
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/Fe10Cr10Al_normal_200_long.in

@@ -22,6 +22,9 @@ pot_filename = potentials_normal.txt
 Cr = 0.10
 Al = 0.10
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/Fe10Cr20Al_normal-zero-O_200.in → config/Fe10Cr10Al_normal_200_neg-O.in

 [Job parameters]
-job_name = Fe10Cr20Al_normal-zero-O_200
+job_name = Fe10Cr10Al_normal_200_neg-O
 report_file = True
 
 [Simulation parameters]
@@ -16,11 +16,14 @@ y_scale = 1
 z_scale = 1
 basis = Fe
 empty_space = 0.5
-pot_filename = potentials_normal-zero-O.txt
+pot_filename = potentials_normal_neg-O.txt
 
 [Bulk dopants]
 Cr = 0.10
-Al = 0.20
+Al = 0.10
+
+[Empty space dopants]
+O = 0.001
 
 [Figure parameters]
 profile_mean_range = 200

config/Fe10Cr10Al_normal_200_zero-O.in

+[Job parameters]
+job_name = Fe10Cr10Al_normal_200_zero-O
+report_file = True
+
+[Simulation parameters]
+sim_type = ase_sim
+kT = 200
+n_exchanges = 20000000
+n_frames = 200
+rand_ox = True
+
+[Lattice parameters]
+bounds_scale = 25
+x_scale = 1
+y_scale = 1
+z_scale = 1
+basis = Fe
+empty_space = 0.5
+pot_filename = potentials_normal_zero-O.txt
+
+[Bulk dopants]
+Cr = 0.10
+Al = 0.10
+
+[Empty space dopants]
+O = 0.001
+
+[Figure parameters]
+profile_mean_range = 200
+profile_anim_range = True
+energy_range = True
+diff_const = True
+Fe = s,#e06633
+Cr = o,#8a99c7
+Al = ^,#bfa6a6
+O = D,#ff0d0d
+X = x,#000000

config/Fe10Cr20Al_normal-neg-O_200.in → config/Fe10Cr10Al_normal_400.in

 [Job parameters]
-job_name = Fe10Cr20Al_normal-neg-O_200
+job_name = Fe10Cr10Al_normal_400
 report_file = True
 
 [Simulation parameters]
 sim_type = ase_sim
-kT = 200
+kT = 400
 n_exchanges = 20000000
 n_frames = 200
 rand_ox = True
@@ -16,11 +16,14 @@ y_scale = 1
 z_scale = 1
 basis = Fe
 empty_space = 0.5
-pot_filename = potentials_normal-neg-O.txt
+pot_filename = potentials_normal.txt
 
 [Bulk dopants]
 Cr = 0.10
-Al = 0.20
+Al = 0.10
+
+[Empty space dopants]
+O = 0.001
 
 [Figure parameters]
 profile_mean_range = 200

config/Fe10Cr20Al_shallow_200.in → config/Fe10Cr10Al_shallow_200.in

 [Job parameters]
-job_name = Fe10Cr20Al_shallow_200
+job_name = Fe10Cr10Al_shallow_200
 report_file = True
 
 [Simulation parameters]
@@ -20,7 +20,10 @@ pot_filename = potentials_shallow.txt
 
 [Bulk dopants]
 Cr = 0.10
-Al = 0.20
+Al = 0.10
+
+[Empty space dopants]
+O = 0.001
 
 [Figure parameters]
 profile_mean_range = 200

config/Fe10Cr20Al_deep_200.in

@@ -22,6 +22,9 @@ pot_filename = potentials_deep.txt
 Cr = 0.10
 Al = 0.20
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/Fe10Cr20Al_normal-zero-O_200_long.in

-[Job parameters]
-job_name = Fe10Cr20Al_normal-zero-O_200_long
-report_file = True
-
-[Simulation parameters]
-sim_type = ase_sim
-kT = 200
-n_exchanges = 100000000
-n_frames = 200
-rand_ox = True
-
-[Lattice parameters]
-bounds_scale = 25
-x_scale = 1
-y_scale = 1
-z_scale = 1
-basis = Fe
-empty_space = 0.5
-pot_filename = potentials_normal-zero-O.txt
-
-[Bulk dopants]
-Cr = 0.10
-Al = 0.20
-
-[Figure parameters]
-profile_mean_range = 200
-profile_anim_range = True
-energy_range = True
-diff_const = True
-Fe = s,#e06633
-Cr = o,#8a99c7
-Al = ^,#bfa6a6
-O = D,#ff0d0d
-X = x,#000000

config/Fe10Cr20Al_normal_200.in

@@ -22,6 +22,9 @@ pot_filename = potentials_normal.txt
 Cr = 0.10
 Al = 0.20
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/Fe10Cr20Al_normal_200_large.in

@@ -22,6 +22,9 @@ pot_filename = potentials_normal.txt
 Cr = 0.10
 Al = 0.20
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/Fe10Cr20Al_normal_200_long.in

@@ -22,6 +22,9 @@ pot_filename = potentials_normal.txt
 Cr = 0.10
 Al = 0.20
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/Fe10Cr20Al_normal_200_short.in

@@ -22,6 +22,9 @@ pot_filename = potentials_normal.txt
 Cr = 0.10
 Al = 0.20
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 20
 profile_anim_range = True

config/Fe10Cr20Al_normal_anneal.in

@@ -25,6 +25,9 @@ pot_filename = potentials_normal.txt
 Cr = 0.10
 Al = 0.20
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/Fe13Al_normal_200.in

@@ -21,6 +21,9 @@ pot_filename = potentials_normal.txt
 [Bulk dopants]
 Al = 0.13
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = 200
 profile_anim_range = True

config/anim_test.in

@@ -22,6 +22,9 @@ pot_filename = potentials_original.txt
 Al = 0.10
 Cr = 0.10
 
+[Empty space dopants]
+O = 0.001
+
 [Figure parameters]
 profile_mean_range = >100
 profile_anim_range = >10

config/default.in

@@ -6,7 +6,7 @@ report_file = True
 sim_type = ase_sim
 kT = 200
 n_exchanges = 10000
-n_frames = 200
+n_frames = 20
 rand_ox = True
 
 [Lattice parameters]
@@ -23,11 +23,11 @@ Al = 0.10
 Cr = 0.10
 
 [Empty space dopants]
-O = 0.00
+O = 0.001
 
 [Figure parameters]
 profile_mean_range = 150-200
-profile_anim_range = False
+profile_anim_range = True
 energy_range = True
 diff_const = True
 Fe = s,#e06633