diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 35f4c7104d14fdb8a96ad0a2e0b05f6603c2ba7c..ebc6edfd08f8af1e5ebaa0d694015b67915852e8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -15,8 +15,8 @@ variables:
# them in a virtualenv and cache it as well.
cache:
paths:
- - .cache/pip
- - venv/
+ - .cache/pip
+ - venv/
before_script:
- python -V # Print out python version for debugging
@@ -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
diff --git a/ase_sim.py b/ase_sim.py
index 93b04f65aeae54a9f06ce026dd6b84bfe398d290..265315181c8f850c5429719f09fee77f38467d33 100644
--- a/ase_sim.py
+++ b/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
diff --git a/config/Fe10Cr10Al_deep_200.in b/config/Fe10Cr10Al_deep_200.in
index e691bcd0bc3a6ee0205b8e959e197638065e5711..bf4889c25d26fe9c599762b8daf7b8c2771f8d4d 100644
--- a/config/Fe10Cr10Al_deep_200.in
+++ b/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
diff --git a/config/Fe10Cr20Al_normal_200_init-O.in b/config/Fe10Cr10Al_normal_100.in
similarity index 85%
rename from config/Fe10Cr20Al_normal_200_init-O.in
rename to config/Fe10Cr10Al_normal_100.in
index 6efbafee46278b4fe0e75e39592f5fde62d1b5b0..b3448eef6b91357c030f5c92b2e8dbe8f62375be 100644
--- a/config/Fe10Cr20Al_normal_200_init-O.in
+++ b/config/Fe10Cr10Al_normal_100.in
@@ -1,13 +1,13 @@
[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
diff --git a/config/Fe10Cr10Al_normal_200.in b/config/Fe10Cr10Al_normal_200.in
index f9bc9cc4a81c96985df2ef875d7e3bd9c10bbea4..ea65c4186c5229a772dcb09a577195c5be286042 100644
--- a/config/Fe10Cr10Al_normal_200.in
+++ b/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
diff --git a/config/Fe10Cr10Al_normal_200_long.in b/config/Fe10Cr10Al_normal_200_long.in
index b57f78f6633496b65f87bae68b6d3e00b5486102..8153fa11ea0365b88151eaf0ec47756d3fa0297b 100644
--- a/config/Fe10Cr10Al_normal_200_long.in
+++ b/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
diff --git a/config/Fe10Cr20Al_normal-zero-O_200.in b/config/Fe10Cr10Al_normal_200_neg-O.in
similarity index 78%
rename from config/Fe10Cr20Al_normal-zero-O_200.in
rename to config/Fe10Cr10Al_normal_200_neg-O.in
index 8f2a114802c54b89f1c76f03ed020b8d317908af..42265d9d2d823b26c8bc24f81960c936a485f539 100644
--- a/config/Fe10Cr20Al_normal-zero-O_200.in
+++ b/config/Fe10Cr10Al_normal_200_neg-O.in
@@ -1,5 +1,5 @@
[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
diff --git a/config/Fe10Cr10Al_normal_200_zero-O.in b/config/Fe10Cr10Al_normal_200_zero-O.in
new file mode 100644
index 0000000000000000000000000000000000000000..d31ef0fc9d90f732cc4e647ba139e6dc19410c17
--- /dev/null
+++ b/config/Fe10Cr10Al_normal_200_zero-O.in
@@ -0,0 +1,37 @@
+[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
diff --git a/config/Fe10Cr20Al_normal-neg-O_200.in b/config/Fe10Cr10Al_normal_400.in
similarity index 78%
rename from config/Fe10Cr20Al_normal-neg-O_200.in
rename to config/Fe10Cr10Al_normal_400.in
index ee0ad0b7d94b1f7ac42a22bdb3d0bff630f8b4ea..a64c34eb5b23e0b47895a98a43a2ab66fbb4e2c5 100644
--- a/config/Fe10Cr20Al_normal-neg-O_200.in
+++ b/config/Fe10Cr10Al_normal_400.in
@@ -1,10 +1,10 @@
[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
diff --git a/config/Fe10Cr20Al_shallow_200.in b/config/Fe10Cr10Al_shallow_200.in
similarity index 86%
rename from config/Fe10Cr20Al_shallow_200.in
rename to config/Fe10Cr10Al_shallow_200.in
index b6f35504b1c7166110781fe89969a1d84917d30f..c204c1fed62fb44f6fca4ceeab10ac54e311d1c7 100644
--- a/config/Fe10Cr20Al_shallow_200.in
+++ b/config/Fe10Cr10Al_shallow_200.in
@@ -1,5 +1,5 @@
[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
diff --git a/config/Fe10Cr20Al_deep_200.in b/config/Fe10Cr20Al_deep_200.in
index a2c8dd6192485b57f456faff45bf7b14af6e387a..38398d97423defbbd4c3d9dc59791220acf6d99f 100644
--- a/config/Fe10Cr20Al_deep_200.in
+++ b/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
diff --git a/config/Fe10Cr20Al_normal-zero-O_200_long.in b/config/Fe10Cr20Al_normal-zero-O_200_long.in
deleted file mode 100644
index 13a31e7a547a76c91c66c7e6d99cea057cb87af6..0000000000000000000000000000000000000000
--- a/config/Fe10Cr20Al_normal-zero-O_200_long.in
+++ /dev/null
@@ -1,34 +0,0 @@
-[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
diff --git a/config/Fe10Cr20Al_normal_200.in b/config/Fe10Cr20Al_normal_200.in
index ca3615857c468256ed5374c79fb54afd54a16ef7..c94386f07e52876b4a6d3f5ee98dffa34a07e11b 100644
--- a/config/Fe10Cr20Al_normal_200.in
+++ b/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
diff --git a/config/Fe10Cr20Al_normal_200_large.in b/config/Fe10Cr20Al_normal_200_large.in
index df386bf9d12596455c0dbbcb5ac0bb2394866da1..f34894693cc101cac729f08f53f9e07e1335eb77 100644
--- a/config/Fe10Cr20Al_normal_200_large.in
+++ b/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
diff --git a/config/Fe10Cr20Al_normal_200_long.in b/config/Fe10Cr20Al_normal_200_long.in
index 0e0f87f25c7aa74b7aaadfa24cac5be128ddb6f7..c8ded1441ab43cdac978c11267f33008aad03df7 100644
--- a/config/Fe10Cr20Al_normal_200_long.in
+++ b/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
diff --git a/config/Fe10Cr20Al_normal_200_short.in b/config/Fe10Cr20Al_normal_200_short.in
index ced8fd86e844f10ac05f2c5c2214231b0f08aa33..4bd09191dd990691256f0472032a2b8863eb41dd 100644
--- a/config/Fe10Cr20Al_normal_200_short.in
+++ b/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
diff --git a/config/Fe10Cr20Al_normal_anneal.in b/config/Fe10Cr20Al_normal_anneal.in
index ed5d380e0f62f7f8cc21997e096379801d49b41b..ae5093eb2b87fb84ada57df9b5e718f962b39e59 100644
--- a/config/Fe10Cr20Al_normal_anneal.in
+++ b/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
diff --git a/config/Fe13Al_normal_200.in b/config/Fe13Al_normal_200.in
index bf53b1309471d383801e668869f8a679ba666c35..ed9718562a122920c217e141696b1ea1c722ae1a 100644
--- a/config/Fe13Al_normal_200.in
+++ b/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
diff --git a/config/anim_test.in b/config/anim_test.in
index 7376a1ad114b6ad2560e6b7647a9cc4b1f2026cf..dd3e23c5851505e733f5f0d3caeeb052f7a0fd56 100644
--- a/config/anim_test.in
+++ b/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
diff --git a/config/default.in b/config/default.in
index 5a26ec69946f999db6a368caf938cf1440172cb3..ceca80007ff1bc5deb2467afc9a8629a125d4cd5 100644
--- a/config/default.in
+++ b/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
diff --git a/config/dope_test.in b/config/dope_test.in
index 77dd52e05f4ecee6612a1662065f9380957b6fe5..7f7a7ecab8be60c240cce7a205675af9854be14d 100644
--- a/config/dope_test.in
+++ b/config/dope_test.in
@@ -22,3 +22,6 @@ pot_filename = potentials_original.txt
Al = 0.2
Cr = 0.2
X = 0.2
+
+[Empty space dopants]
+O = 0.001
diff --git a/config/figure_test.in b/config/figure_test.in
index 248cf5f0be97544830db81dffb48e64416fcb4ee..553810ab18763651fdf7899111792f83b5f0e7a0 100644
--- a/config/figure_test.in
+++ b/config/figure_test.in
@@ -22,6 +22,9 @@ pot_filename = potentials_original.txt
Cr = 0.10
Al = 0.05
+[Empty space dopants]
+O = 0.001
+
[Figure parameters]
profile_mean_range = >50
profile_anim_range = All
diff --git a/config/step_test.in b/config/step_test.in
index 55257253d0735ddcd184bd1b2fd680e963b6ccee..1af4d6485b5d77e4105528ccf2621c59f914d385 100644
--- a/config/step_test.in
+++ b/config/step_test.in
@@ -21,5 +21,8 @@ pot_filename = potentials_original.txt
Al = 0.05
Cr = 0.10
+[Empty space dopants]
+O = 0.001
+
[Empty space dopants]
O = 0.1
diff --git a/data/potentials_deep.txt b/data/potentials_deep.txt
index 3748d616c62da2896b794cc1de5e07a1f8e1e32a..59df58d63290c2bd790ce16947e2730da993e962 100644
--- a/data/potentials_deep.txt
+++ b/data/potentials_deep.txt
@@ -1,6 +1,6 @@
- Fe Cr Al O X
-Fe -100 -100 -100 -200 100
-Cr -100 -100 -500 100
-Al -100 -2500 100
-O -200 100
-X 0
+ Fe Cr Al O X
+Fe -100 -100 -100 -200 100
+Cr -100 -100 -1000 100
+Al -100 -2500 100
+O -200 100
+X 0
diff --git a/data/potentials_normal-neg-O.txt b/data/potentials_normal-neg-O.txt
deleted file mode 100644
index 57ec875fc9beb89164a73928c70b5e53e85d0090..0000000000000000000000000000000000000000
--- a/data/potentials_normal-neg-O.txt
+++ /dev/null
@@ -1,6 +0,0 @@
- Fe Cr Al O X
-Fe -100 -100 -100 -200 100
-Cr -100 -100 -600 100
-Al -100 -900 100
-O -400 100
-X 0
diff --git a/data/potentials_normal-zero-O.txt b/data/potentials_normal-zero-O.txt
deleted file mode 100644
index 5656ed5e1deaabdb9ccc504c91a4f9ceff21b0f4..0000000000000000000000000000000000000000
--- a/data/potentials_normal-zero-O.txt
+++ /dev/null
@@ -1,6 +0,0 @@
- Fe Cr Al O X
-Fe -100 -100 -100 -200 100
-Cr -100 -100 -600 100
-Al -100 -900 100
-O 0 100
-X 0
diff --git a/data/potentials_normal.txt b/data/potentials_normal.txt
index 0dbe341d2f845644077d5a1cf01dd550ff6ece62..263a6c124affc519f6786bd023e21638c6c16d00 100644
--- a/data/potentials_normal.txt
+++ b/data/potentials_normal.txt
@@ -1,6 +1,6 @@
- Fe Cr Al O X
-Fe -100 -100 -100 -200 100
-Cr -100 -100 -600 100
-Al -100 -900 100
-O -200 100
-X 0
+ Fe Cr Al O X
+Fe -100 -100 -100 -200 100
+Cr -100 -100 -600 100
+Al -100 -900 100
+O -200 100
+X 0
diff --git a/data/potentials_normal_neg-O.txt b/data/potentials_normal_neg-O.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8509aad709bb9528b0354ba805bd78ee0fd38fec
--- /dev/null
+++ b/data/potentials_normal_neg-O.txt
@@ -0,0 +1,6 @@
+ Fe Cr Al O X
+Fe -100 -100 -100 -200 100
+Cr -100 -100 -600 100
+Al -100 -900 100
+O -400 100
+X 0
diff --git a/data/potentials_normal_zero-O.txt b/data/potentials_normal_zero-O.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f806b619804b6d9e9d2d717e36c89da0b5127133
--- /dev/null
+++ b/data/potentials_normal_zero-O.txt
@@ -0,0 +1,6 @@
+ Fe Cr Al O X
+Fe -100 -100 -100 -200 100
+Cr -100 -100 -600 100
+Al -100 -900 100
+O 0 100
+X 0
diff --git a/data/potentials_original.txt b/data/potentials_original.txt
index 274b0fc2b5d769fbe52ea44c257d67bc5d141b9c..5c5945d482fe167dda9188343c8bd28bd7e27c5e 100644
--- a/data/potentials_original.txt
+++ b/data/potentials_original.txt
@@ -1,6 +1,6 @@
- Fe Cr Al O X
-Fe -20 -20 -20 0 10
-Cr -20 -20 -10 10
-Al -20 -20 10
-O 0 10
-X 0
+ Fe Cr Al O X
+Fe -20 -20 -20 0 10
+Cr -20 -20 -10 10
+Al -20 -20 10
+O 0 10
+X 0
diff --git a/data/potentials_shallow.txt b/data/potentials_shallow.txt
index 52afd6744b90fe36b2f835971a03288af60e935f..2b34502747405a304427d37dcbe9308a8f5bf312 100644
--- a/data/potentials_shallow.txt
+++ b/data/potentials_shallow.txt
@@ -1,6 +1,6 @@
- Fe Cr Al O X
-Fe -100 -100 -100 0 100
-Cr -100 -100 -200 100
-Al -100 -400 100
-O -100 100
-X 0
+ Fe Cr Al O X
+Fe -100 -100 -100 -200 100
+Cr -100 -100 -400 100
+Al -100 -600 100
+O -200 100
+X 0
diff --git a/sim_controller.py b/sim_controller.py
index e064881bb6b4150d06b67a4a988ced5cf6d2b38c..f61774ae36bd662ce5cae05d82db583b1735a5fb 100644
--- a/sim_controller.py
+++ b/sim_controller.py
@@ -22,7 +22,6 @@ import os
import shutil
import sys
import time
-import zipfile
from collections import OrderedDict
import ase
@@ -125,9 +124,9 @@ class SimController(object):
for element, item in self.figure_params.items()
if element in ase.data.chemical_symbols])
print("Drawing figures")
- z_positions, dict_concs_mean, energy_list, frame_list = vis.read_plot_data(figure_out_path,
- symbol_marker_color_dict,
- figure_range_dict)
+ z_positions, dict_concs_mean, energy_list, frame_list = sim_utilities.read_conc_data(figure_out_path,
+ symbol_marker_color_dict,
+ figure_range_dict)
vis.draw_figures(z_positions,
dict_concs_mean,
@@ -263,8 +262,8 @@ class SimController(object):
diff_const_file.write(diff_const_file_line + "\n")
diff_const_file.close()
- def save_data(self, file_path):
- data_matrix = []
+ def save_conc(self, file_path):
+ conc_matrix = []
conc_file_header = "z "
for symbol in self.symbol_marker_color_dict:
conc_file_header += symbol + " "
@@ -295,19 +294,19 @@ class SimController(object):
conc = dict_concs_per_symbol_per_z[symbol][i]
conc_file_line += str(conc) + " "
conc_file_data_list.append(conc)
- data_matrix.append(conc_file_data_list)
+ conc_matrix.append(conc_file_data_list)
- # data_matrix = np.array(data_matrix)
- np.savetxt(file_path, data_matrix, header=conc_file_header, fmt='%.6f')
+ # conc_matrix = np.array(conc_matrix)
+ np.savetxt(file_path, conc_matrix, header=conc_file_header, fmt='%.6f')
def write_frame(self, i_str, job_out_path):
- sim_data_folder_path = os.path.join(job_out_path, 'sim_data')
- if not os.path.exists(sim_data_folder_path):
- os.mkdir(sim_data_folder_path)
+ sim_frames_folder_path = os.path.join(job_out_path, 'sim_frames')
+ if not os.path.exists(sim_frames_folder_path):
+ os.mkdir(sim_frames_folder_path)
sim_conc_folder_path = os.path.join(job_out_path, 'sim_conc')
if not os.path.exists(sim_conc_folder_path):
os.mkdir(sim_conc_folder_path)
- sim_data_file_path = os.path.join(sim_data_folder_path, sim_data_filename.format(i=i_str))
+ sim_frames_file_path = os.path.join(sim_frames_folder_path, sim_frames_filename.format(i=i_str))
sim_conc_file_path = os.path.join(sim_conc_folder_path, sim_conc_filename.format(i=i_str))
self.sim.atoms.info['kT'] = self.last_kT
@@ -322,8 +321,8 @@ class SimController(object):
energy_file.write("frame energy\n")
with open(energy_file_path, 'a') as energy_file:
energy_file.write(" ".join([i_str, str(self.sim.atoms.calc.results['energy']), "\n"]))
- self.sim.write(sim_data_file_path)
- self.save_data(sim_conc_file_path)
+ self.sim.write(sim_frames_file_path)
+ self.save_conc(sim_conc_file_path)
def make_config_file(conf_filename='default.in'):
@@ -336,7 +335,7 @@ def make_config_file(conf_filename='default.in'):
conf_writer['Simulation parameters'] = OrderedDict((('sim_type', 'ase_sim'),
('kT', '200'),
('n_exchanges', '10000'),
- ('n_frames', '200'),
+ ('n_frames', '20'),
('rand_ox', 'True')))
conf_writer['Lattice parameters'] = OrderedDict((('bounds_scale', '10'),
('x_scale', '1'),
@@ -346,9 +345,9 @@ def make_config_file(conf_filename='default.in'):
('empty_space', '0.5'),
('pot_filename', 'potentials_normal.txt')))
conf_writer['Bulk dopants'] = OrderedDict((('Al', '0.10'), ('Cr', '0.10')))
- conf_writer['Empty space dopants'] = {'O': '0.00'}
+ conf_writer['Empty space dopants'] = {'O': '0.001'}
conf_writer['Figure parameters'] = OrderedDict((('profile_mean_range', '150-200'),
- ('profile_anim_range', 'False'),
+ ('profile_anim_range', 'True'),
('energy_range', 'True'),
('diff_const', 'True'),
('Fe', 's,#e06633'),
@@ -424,12 +423,11 @@ for sim_ctrl in sim_controllers:
job_out_path = sim_utilities.rename_existing_path(os.path.join(jobs_out_path, folder_time))
os.makedirs(job_out_path)
- # TODO: do not assume folder for data
shutil.copy(os.path.join('data', sim_ctrl.lattice_params['pot_filename']),
os.path.join(job_out_path, sim_ctrl.lattice_params['pot_filename']))
shutil.copy(sim_ctrl.conf_filename, os.path.join(job_out_path, os.path.split(sim_ctrl.conf_filename)[1]))
- sim_data_filename = 'frame-{i}.xyz'
+ sim_frames_filename = 'frame-{i}.xyz'
sim_conc_filename = 'frame-{i}.txt'
n_frames_width = len(str(sim_ctrl.sim_params['n_frames']))
@@ -476,10 +474,10 @@ for sim_ctrl in sim_controllers:
# update console two times per second
if time.time() - print_time >= 0.5:
- print("\rWrote frame {i}/{n}".format(i=i_str, n=str(sim_ctrl.sim_params['n_frames'])), end="")
+ print("\rWrote frame {i}/{n}".format(i=i_str, n=sim_ctrl.sim_params['n_frames']), end="")
print_time = time.time()
- print("\rWrote frame {}/{}".format(str(sim_ctrl.sim_params['n_frames']), str(sim_ctrl.sim_params['n_frames'])),
+ print("\rWrote frame {}/{}".format(sim_ctrl.sim_params['n_frames'], sim_ctrl.sim_params['n_frames']),
flush=True)
end_time = time.time()
sim_ctrl.sim_time = sim_utilities.format_time(end_time - start_time)
@@ -496,8 +494,6 @@ for sim_ctrl in sim_controllers:
# ------------------------------
if not arguments.no_figures and sim_ctrl.figure_params:
- # TODO: do not duplicate code
-
figure_range_dict = sim_utilities.parse_figure_range_str(sim_ctrl.figure_params)
if len([fig_range for fig_range in figure_range_dict.values() if fig_range is not False]) > 0 or \
@@ -507,16 +503,7 @@ for sim_ctrl in sim_controllers:
if arguments.compress:
print("Compressing frames...", end="")
sys.stdout.flush()
- frames_zipfile = zipfile.ZipFile(os.path.join(job_out_path, 'sim_data.zip'), 'w',
- compression=zipfile.ZIP_DEFLATED)
- sim_data_folder_path = os.path.join(job_out_path, 'sim_data')
- for filename in os.listdir(sim_data_folder_path):
- frames_zipfile.write(os.path.join(sim_data_folder_path, filename), os.path.join('sim_data', filename))
- os.remove(os.path.join(sim_data_folder_path, filename))
- frames_zipfile.testzip()
- frames_zipfile.close()
- os.rmdir(sim_data_folder_path)
-
+ sim_utilities.compress_frames(job_out_path)
print("OK")
print("")
diff --git a/sim_utilities.py b/sim_utilities.py
index c3f97d6a4c6f63420c0b047770fff4134e019f70..52cf9c005949ef18482d9ad124dedb19bd6a48f3 100644
--- a/sim_utilities.py
+++ b/sim_utilities.py
@@ -19,16 +19,51 @@
import configparser
import math
import os
+import zipfile
from collections import OrderedDict
import ase
import numpy as np
+def average_filter_function(data):
+ """
+ Applies a 3-wide average filter to data to make it smoother.
+
+ :param data: the list of data to filter
+ :return: filtered data
+ """
+ temp_data = []
+ for i in range(len(data)):
+ sum = data[i]
+ if i == 0:
+ sum += data[i] + data[i + 1]
+ elif i == len(data) - 1:
+ sum += data[i - 1] + data[i]
+ else:
+ sum += data[i - 1] + data[i + 1]
+ temp_data.append(sum / 3)
+ return temp_data
+
+
class ParsingError(Exception):
pass
+def compress_frames(job_out_path):
+ data_name = 'sim_frames'
+ frames_zipfile = zipfile.ZipFile(os.path.join(job_out_path, data_name + '.zip'), 'w',
+ compression=zipfile.ZIP_DEFLATED)
+ sim_frames_folder_path = os.path.join(job_out_path, data_name)
+ for filename in os.listdir(sim_frames_folder_path):
+ frames_zipfile.write(os.path.join(sim_frames_folder_path, filename), os.path.join(data_name, filename))
+ frames_zipfile.testzip()
+ os.remove(os.path.join(sim_frames_folder_path, filename))
+ frames_zipfile.close()
+ os.rmdir(sim_frames_folder_path)
+
+
+# TODO: combine all three range parsing methods
def convert_bool_to_range(range_list):
if range_list is True:
return [(0, math.inf)]
@@ -111,23 +146,21 @@ def parse_conf(conf_filename):
# n_exchanges and kT
single_value_keys = {'n_exchanges', 'kT'}
multiple_value_keys = {'n_steps_high', 'n_steps_fall', 'n_steps_low', 'kT_high', 'kT_low'}
-
- if not single_value_keys.issubset(sim_params.keys()) and \
- not multiple_value_keys.issubset(sim_params.keys()):
+ if not single_value_keys.issubset(sim_params.keys()) and not multiple_value_keys.issubset(sim_params.keys()):
sim_params['n_exchanges'] = default_reader['Simulation parameters']['n_exchanges']
sim_params['kT'] = default_reader['Simulation parameters']['kT']
# constant values
if single_value_keys.issubset(sim_params.keys()):
sim_params['n_exchanges'] = int(sim_params['n_exchanges'])
- n_steps_per_frame = int(sim_params['n_exchanges'] / sim_params['n_frames'])
sim_params['kT'] = int(sim_params['kT'])
# annealing
elif multiple_value_keys.issubset(sim_params.keys()):
sim_params['n_exchanges'] = [int(sim_params['n_steps_high']),
int(sim_params['n_steps_fall']),
int(sim_params['n_steps_low'])]
- n_steps_per_frame = int(sum(sim_params['n_exchanges']) / sim_params['n_frames'])
sim_params['kT'] = [int(sim_params['kT_high']), int(sim_params['kT_low'])]
+ else:
+ raise ParsingError("Unrecognized kT definition.")
# rand_ox
if 'rand_ox' not in sim_params.keys():
@@ -193,7 +226,6 @@ def parse_conf(conf_filename):
figure_params = None
return job_params, sim_params, lattice_params, bulk_dopants, empty_space_dopants, figure_params
-# TODO: combine all three range parsing methods
def parse_figure_range_str(figure_params):
@@ -201,7 +233,6 @@ def parse_figure_range_str(figure_params):
figure_str_list = ['profile_mean_range', 'profile_anim_range', 'energy_range']
# TODO: merge with vis
- # TODO: support for '1-200, true'
for figure_str in figure_str_list:
if figure_str in figure_params.keys():
figure_range = figure_params[figure_str]
@@ -226,10 +257,11 @@ def parse_param_str_to_bool(parameter):
elif parameter.lower() in ['false', 'f', 'no', 'n', 'off', 'none']:
return False
else:
- # TODO: specify file somehow; raise without message and catch in outer context?
+ # TODO: specify file name somehow; raise without message and catch in outer context?
raise ParsingError('unknown boolean type: "{}"'.format(parameter))
+# TODO: combine all three range parsing methods
def parse_range_str(parameter, lim_min=0, lim_max=math.inf):
"""
Converts a range specified in a string into a list of upper and lower bounds.
@@ -255,6 +287,7 @@ def parse_range_str(parameter, lim_min=0, lim_max=math.inf):
return ids
+# TODO: combine all three range parsing methods
def range_list_to_indexes(ranges, indexes):
ids = set()
for index in indexes:
@@ -271,6 +304,84 @@ def range_list_to_indexes(ranges, indexes):
return sorted(list(ids))
+def read_conc_data(in_path, symbol_marker_color_dict, figure_range_dict):
+ # ------------------------------
+ # CALCULATING MEAN
+ # ------------------------------
+ # TODO: make easier to understand
+ # TODO: stop shadowing names from outer scope
+ frame_list = []
+ dict_concs_per_element = {}
+ energy_list = []
+ z_positions = []
+
+ # read concentrations
+ conc_path = os.path.join(in_path, "sim_conc")
+ file_list = [entry for entry in os.listdir(conc_path) if entry.endswith(".txt")]
+
+ with open(os.path.join(in_path, "energy.txt"), 'r') as energy_file:
+ energy_file_header = energy_file.readline()
+ while True:
+ energy_file_line = energy_file.readline()
+ if energy_file_line == "":
+ break
+
+ energy_list.append(float(energy_file_line.split()[1]))
+
+ for filename in file_list:
+ conc_file_path = os.path.join(conc_path, filename)
+ with open(conc_file_path, 'r') as conc_file:
+ symbols = conc_file.readline().split()[2:]
+ dict_concs_per_z = {}
+ for symbol1, symbol2 in zip(symbols, symbol_marker_color_dict):
+ dict_concs_per_z[symbol1] = []
+
+ if not symbol1 == symbol2:
+ raise Exception
+
+ while True:
+ conc_file_line = conc_file.readline()
+ if conc_file_line == "":
+ break
+
+ values = conc_file_line.split()
+ z_pos = float(values.pop(0))
+ if z_pos not in z_positions:
+ z_positions.append(z_pos)
+
+ for symbol, value in zip(symbol_marker_color_dict, values):
+ dict_concs_per_z[symbol].append(float(value))
+
+ frame_list.append(dict_concs_per_z)
+
+ # convert list of frame data to lists of data per element
+ for i, dict_concs_per_z in enumerate(frame_list):
+ for symbol, concs_list in dict_concs_per_z.items():
+ if symbol not in dict_concs_per_element.keys():
+ dict_concs_per_element[symbol] = []
+ for z_pos in z_positions:
+ dict_concs_per_element[symbol].append([])
+ for i, z_pos in enumerate(z_positions):
+ dict_concs_per_element[symbol][i].append(concs_list[i])
+
+ # collect the average concentrations into a list per symbol and z-level
+ dict_concs_mean = {}
+ profile_mean_range = figure_range_dict['profile_mean_range']
+ for symbol, concs_list in dict_concs_per_element.items():
+ if symbol not in dict_concs_mean.keys():
+ dict_concs_mean[symbol] = [0] * len(z_positions)
+ for z, concs in enumerate(concs_list):
+ indexes = range_list_to_indexes(profile_mean_range, range(len(concs)))
+ array_mask = [True] * len(concs)
+ for i, _ in enumerate(concs):
+ if i in indexes:
+ array_mask[i] = False
+ masked_concs = np.ma.array(concs, mask=array_mask)
+ dict_concs_mean[symbol][z] = np.mean(masked_concs)
+
+ return z_positions, dict_concs_mean, energy_list, frame_list
+
+
def read_job_name_and_end_energy(report_file):
energy_report_str = "Final potential energy: "
job_name = report_file.readline()
@@ -352,7 +463,7 @@ def single_xyz_anim_to_multiple(filename):
atomlines = []
for i in range(int(num_atoms)):
atomlines.append(sim_output_file.readline())
- sim_frame_file = open(os.path.join("sim_data", "frame-{frame}.xyz".format(frame=frame)), "w")
+ sim_frame_file = open(os.path.join("sim_frames", "frame-{frame}.xyz".format(frame=frame)), "w")
sim_frame_file.write(num_atoms + comment)
for atomline in atomlines:
sim_frame_file.write(atomline)
@@ -361,4 +472,4 @@ def single_xyz_anim_to_multiple(filename):
else:
break
- sim_output_file.close()
\ No newline at end of file
+ sim_output_file.close()
diff --git a/vis.py b/vis.py
index e0cb73bdefa433fc5f22a45f18f3e1fb100a5a34..c4e6bb660774efbc92e5dfdddc4f79d9892c82a7 100644
--- a/vis.py
+++ b/vis.py
@@ -17,7 +17,6 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# ------------------------------
import os
-import math
import argparse
# import matplotlib.animation as ani
@@ -30,104 +29,6 @@ import ase
import sim_utilities
-def average_filter_function(data):
- """
- Applies a 3-wide average filter to data to make it smoother.
-
- :param data: the list of data to filter
- :return: filtered data
- """
- temp_data = []
- for i in range(len(data)):
- sum = data[i]
- if i == 0:
- sum += data[i] + data[i + 1]
- elif i == len(data) - 1:
- sum += data[i - 1] + data[i]
- else:
- sum += data[i - 1] + data[i + 1]
- temp_data.append(sum / 3)
- return temp_data
-
-
-def read_plot_data(in_path, symbol_marker_color_dict, figure_range_dict):
- # ------------------------------
- # CALCULATING MEAN
- # ------------------------------
- # TODO: make easier to understand
- # TODO: stop shadowing names from outer scope
- frame_list = []
- dict_concs_per_element = {}
- energy_list = []
- z_positions = []
-
- # read concentrations
- conc_path = os.path.join(in_path, "sim_conc")
- file_list = [entry for entry in os.listdir(conc_path) if entry.endswith(".txt")]
-
- with open(os.path.join(in_path, "energy.txt"), 'r') as energy_file:
- energy_file_header = energy_file.readline()
- while True:
- energy_file_line = energy_file.readline()
- if energy_file_line == "":
- break
-
- energy_list.append(float(energy_file_line.split()[1]))
-
- for filename in file_list:
- conc_file_path = os.path.join(conc_path, filename)
- with open(conc_file_path, 'r') as conc_file:
- symbols = conc_file.readline().split()[2:]
- dict_concs_per_z = {}
- for symbol1, symbol2 in zip(symbols, symbol_marker_color_dict):
- dict_concs_per_z[symbol1] = []
-
- if not symbol1 == symbol2:
- raise Exception
-
- while True:
- conc_file_line = conc_file.readline()
- if conc_file_line == "":
- break
-
- values = conc_file_line.split()
- z_pos = float(values.pop(0))
- if z_pos not in z_positions:
- z_positions.append(z_pos)
-
- for symbol, value in zip(symbol_marker_color_dict, values):
- dict_concs_per_z[symbol].append(float(value))
-
- frame_list.append(dict_concs_per_z)
-
- # convert list of frame data to lists of data per element
- for i, dict_concs_per_z in enumerate(frame_list):
- for symbol, concs_list in dict_concs_per_z.items():
- if symbol not in dict_concs_per_element.keys():
- dict_concs_per_element[symbol] = []
- for z_pos in z_positions:
- dict_concs_per_element[symbol].append([])
- for i, z_pos in enumerate(z_positions):
- dict_concs_per_element[symbol][i].append(concs_list[i])
-
- # collect the average concentrations into a list per symbol and z-level
- dict_concs_mean = {}
- profile_mean_range = figure_range_dict['profile_mean_range']
- for symbol, concs_list in dict_concs_per_element.items():
- if symbol not in dict_concs_mean.keys():
- dict_concs_mean[symbol] = [0] * len(z_positions)
- for z, concs in enumerate(concs_list):
- indexes = sim_utilities.range_list_to_indexes(profile_mean_range, range(len(concs)))
- array_mask = [True] * len(concs)
- for i, _ in enumerate(concs):
- if i in indexes:
- array_mask[i] = False
- masked_concs = np.ma.array(concs, mask=array_mask)
- dict_concs_mean[symbol][z] = np.mean(masked_concs)
-
- return z_positions, dict_concs_mean, energy_list, frame_list
-
-
def draw_figures(z_positions, dict_concs_mean, energy_list, frame_list, fig_range_dict, symbol_marker_color_dict, no_gui, average_filter, out_path):
import matplotlib
if no_gui:
@@ -149,7 +50,7 @@ def draw_figures(z_positions, dict_concs_mean, energy_list, frame_list, fig_rang
# ------------------------------
# DRAWING FIGURES
# ------------------------------
- # TODO: change if to functions
+ # TODO: change if to functions?
# ------------------------------
# MEAN FIGURE
# ------------------------------
@@ -179,7 +80,7 @@ def draw_figures(z_positions, dict_concs_mean, energy_list, frame_list, fig_rang
# draw on filtered figure
if average_filter:
plt.figure(figure_mean_filtered.number)
- plt.plot(z_positions, average_filter_function(data), marker=marker, color=color, label=label,
+ plt.plot(z_positions, sim_utilities.average_filter_function(data), marker=marker, color=color, label=label,
zorder=2)
# set mean figure appearance and save it
plt.figure(figure_mean.number)
@@ -227,7 +128,7 @@ def draw_figures(z_positions, dict_concs_mean, energy_list, frame_list, fig_rang
atom_dict_concs = frame_list[0]
data = atom_dict_concs[symbol]
if average_filter:
- data = average_filter_function(data)
+ data = sim_utilities.average_filter_function(data)
line = plt.plot(z_positions, data, marker=marker, color=color, label=label,
zorder=2)
lines.append((symbol, line[0]))
@@ -251,7 +152,7 @@ def draw_figures(z_positions, dict_concs_mean, energy_list, frame_list, fig_rang
for symbol, line in lines:
data = atom_dict_concs[symbol]
if average_filter:
- data = average_filter_function(data)
+ data = sim_utilities.average_filter_function(data)
line.set_data(z_positions, data)
figure_anim.set_size_inches(7, 7)
n_frames_width = len(str(len(frame_list)))
@@ -332,6 +233,7 @@ if __name__ == '__main__':
arg_parser.add_argument('job_path', help='path to a finished job')
arg_parser.add_argument('--all', action='store_true', help='plot all found jobs')
arg_parser.add_argument('--multi', action='store_true', help='combine concentrations from multiple simulations')
+ arg_parser.add_argument('--no-multi', action='store_true', help='plot each simulation separately')
arg_parser.add_argument('--no-gui', action='store_true', help='draw the figures only to files')
arg_parser.add_argument('--average-filter', action='store_true',
help='apply a filter to smooth the concentration profile')
@@ -395,6 +297,10 @@ if __name__ == '__main__':
if arguments.multi:
multi_enable = True
+ print("Plotting combined concentrations from all simulations.")
+ elif arguments.no_multi:
+ multi_enable = False
+ print("Plotting all simulations separately.")
else:
multi_enable = False
if len(job_selection) > 1:
@@ -415,13 +321,6 @@ if __name__ == '__main__':
multi_combined_energy_list.append([])
if multi_enable:
- # TODO: is this needed? only jobs with the same name are accepted
- for job_frame_numbers1 in job_frame_numbers_list:
- for job_frame_numbers2 in job_frame_numbers_list:
- if job_frame_numbers1 != job_frame_numbers2:
- print("Jobs do not have the same length.")
- exit(2)
-
multi_folder = "multi plot from {} to {}".format(os.path.basename(job_paths[job_selection[0]]),
os.path.basename(job_paths[job_selection[-1]]))
multi_path = sim_utilities.rename_existing_path(os.path.join(job_path, multi_folder))
@@ -430,6 +329,13 @@ if __name__ == '__main__':
multi_report_file = open(os.path.join(multi_path, "multi_report.txt"), "w")
multi_report_file.write("List of included simulations:\n")
+ # TODO: is this needed? only jobs with the same name are accepted
+ for job_frame_numbers1 in job_frame_numbers_list:
+ for job_frame_numbers2 in job_frame_numbers_list:
+ if job_frame_numbers1 != job_frame_numbers2:
+ print("Jobs do not have the same length.")
+ exit(2)
+
for job_index in job_selection:
if job_index not in job_indices:
raise IndexError("List index out of range.")
@@ -456,10 +362,12 @@ if __name__ == '__main__':
symbol_marker_color_dict = OrderedDict([(element, (item.split(',')[0], item.split(',')[1]))
for element, item in figure_params.items()
if element in ase.data.chemical_symbols])
- z_positions, dict_concs_mean, energy_list, frame_list = read_plot_data(sim_path,
- symbol_marker_color_dict,
- figure_range_dict)
+ z_positions, dict_concs_mean, \
+ energy_list, frame_list = sim_utilities.read_conc_data(sim_path,
+ symbol_marker_color_dict,
+ figure_range_dict)
if not multi_enable:
+ print("Drawing figures for {}...".format(os.path.basename(sim_path)), end="")
draw_figures(z_positions,
dict_concs_mean,
energy_list,
@@ -469,8 +377,9 @@ if __name__ == '__main__':
arguments.no_gui,
arguments.average_filter,
sim_path)
-
- if multi_enable:
+ print("OK")
+ else:
+ print("Collecting data from {}...".format(os.path.basename(sim_path)), end="")
# go through the list of frames and collect the concentrations for this simulation
# and add them to a combined list per z per symbol per frame
for i_frame, frame in enumerate(frame_list):
@@ -499,10 +408,12 @@ if __name__ == '__main__':
multi_combined_dict_concs_mean[symbol][i_z_pos].append(conc)
multi_report_file.write("{}\n".format(os.path.basename(sim_path)))
+ print("OK")
figure_range_dict["diff_const"] = False
if multi_enable:
+ print("Drawing combined plot...", end="")
for i_frame, frame in enumerate(frame_list):
for symbol, conc_per_z in frame.items():
for i_z_pos, conc in enumerate(conc_per_z):
@@ -523,3 +434,4 @@ if __name__ == '__main__':
multi_path)
multi_report_file.close()
+ print("OK")