diff --git a/README.rst b/README.rst
index ef4a09a4defd306897174acf34e7c691d1b11b2d..9be12f1ed019627bad89a38cf3880892ec1d557e 100644
--- a/README.rst
+++ b/README.rst
@@ -127,11 +127,11 @@ FILES
| │  ├── ruptured_Pd.xml # a fcc(100) like surface with some sites missing
| │  └── small.xml # demo file
| ├── tests/ # Unit tests and test data
-| └── tools # Entry points for command line interface
-| ├── kmcos
-| ├── kmcos.bat
-| ├── kmcos-build-standalone
-| └── kmcos-install-dependencies-ubuntu
+| ├── tools # Entry points for command line interface
+| │  ├── kmcos
+| │  ├── kmcos.bat
+| │  ├── kmcos-build-standalone
+| │  └── kmcos-install-dependencies-ubuntu
COPYRIGHT AND LICENSE
diff --git a/examples/0-README_for_Examples200423.txt b/examples/0-README_for_Examples200423.txt
index 01de53992c384d7863a84f5e35f1caf911eeea1a..0576b8d38b4efcc3fc0c54ba0a5c63173d1fe38c 100644
--- a/examples/0-README_for_Examples200423.txt
+++ b/examples/0-README_for_Examples200423.txt
@@ -8,7 +8,7 @@ Below is a list of the examples, then explanation of how to use them.
To use one of the examples, follow this type of procedure:
-python3 MyFirstSnapshots.py
+python3 MyFirstSnapshots__build.py
cd MyFirstSnapshots_local_smart
python3 runfile.py
diff --git a/examples/MyFirstDiffusion_local_smart/runfile_atoms_export.py b/examples/MyFirstDiffusion_local_smart/runfile_atoms_export.py
new file mode 100644
index 0000000000000000000000000000000000000000..4d628ffbd209e6a89e3785e249f8d25101dcd28a
--- /dev/null
+++ b/examples/MyFirstDiffusion_local_smart/runfile_atoms_export.py
@@ -0,0 +1,7 @@
+import pickle
+from kmcos.run import KMC_Model
+
+model = KMC_Model()
+NSTEPS = 1e6
+model.do_steps(NSTEPS)
+model.pickle_export_atoms("MyFirstDiffusion_atoms_" + str(NSTEPS) + ".pkl")
\ No newline at end of file
diff --git a/examples/MyFirstDiffusion_local_smart/runfile_atoms_import.py b/examples/MyFirstDiffusion_local_smart/runfile_atoms_import.py
new file mode 100644
index 0000000000000000000000000000000000000000..8a8c3a082b990f734304cb4ba24187b7908df6f7
--- /dev/null
+++ b/examples/MyFirstDiffusion_local_smart/runfile_atoms_import.py
@@ -0,0 +1,7 @@
+from ase.io import write
+import pickle
+
+filehandler = open('MyFirstDiffusion_atoms_1000000.0.pkl', 'rb')
+loaded_atoms_object = pickle.load(filehandler)
+filehandler.close()
+write('MyFirstDiffusion_atoms_1000000.0.png', loaded_atoms_object)
diff --git a/examples/MyFirstSnapshots_local_smart/runfile.py b/examples/MyFirstSnapshots_local_smart/runfile.py
index 7974c45e7c33d2b6da3dcf56912725ff8b39306f..4600417b93ca17949f5158a5a36dbd1ca689db0d 100644
--- a/examples/MyFirstSnapshots_local_smart/runfile.py
+++ b/examples/MyFirstSnapshots_local_smart/runfile.py
@@ -42,8 +42,15 @@ do_snapshots(sps, n_snapshots)
#The final command below writes the simulation details to the logfile
create_log()
+# plot_configuration(self, filename = '', resolution = 150, scale = 20, representation = '', plot_settings = {}):
+
#The first plot_configuration will use default arguments to construct the plot and export as "plottedConfiguration.png"
-sg.model.plot_configuration()
+#sg.model.plot_configuration()
+
+#The second plot_configuration will use the atomic argument to contruct the plot and export as "atomic_view.png"
+#for the filename, you can specify with or without the .png at the end. This function will automatically convert to .png file
+sg.model.plot_configuration(filename='MyFirstSnapshots_atomic_view', resolution=100, scale=20, representation='atomic')
+
plot_settings = {
"y_label": "y_direction",
@@ -58,4 +65,5 @@ plot_settings = {
"num_y_ticks": 3,
}
#the second plot_configuration here will construct the plot using the above dictionary and export the file as "Plot.png"
-sg.model.plot_configuration(plot_settings)
+# Note that the spatial representation plots by default, but you can always specify in representation
+sg.model.plot_configuration(representation='spatial', plot_settings=plot_settings)
\ No newline at end of file
diff --git a/kmcos/__init__.py b/kmcos/__init__.py
index 8906ac5d5a852b34018c3cfd9042bdd8eb226c96..d8f244700906566ec2d4a25297a399a967e890de 100644
--- a/kmcos/__init__.py
+++ b/kmcos/__init__.py
@@ -56,7 +56,8 @@ from __future__ import print_function
#import kmcos.io
-__version__ = "0.0.64"
+
+__version__ = "0.0.66"
VERSION = __version__
def evaluate_param_expression(param, parameters={}):
diff --git a/kmcos/run/__init__.py b/kmcos/run/__init__.py
index 509f7893d4364197c5b3216c25041998415bef1d..ae5cae90edcdcb2382d095069494142c4eb7db23 100644
--- a/kmcos/run/__init__.py
+++ b/kmcos/run/__init__.py
@@ -930,13 +930,16 @@ class KMC_Model(Process):
print('Wrote {filename}'.format(**locals()))
self.do_steps(skip)
- def show(self, *args, **kwargs):
+ def peek(self, *args, **kwargs):
"""Visualize the current configuration of the model using ASE ag."""
tag = kwargs.pop('tag', None)
ase = import_ase()
ase.visualize.view(self.get_atoms(tag=tag), *args, **kwargs)
+ def show(self):
+ return self.peek()
+
def view(self, scaleA = None):
"""Start current model in live view mode."""
from kmcos import view
@@ -1558,9 +1561,17 @@ class KMC_Model(Process):
if showFigure==False:
plt.close(fig0)
return fig0, ax0
+
+ def export_picture(self, filename, resolution, scale, **kwargs):
+ atoms = self.get_atoms(reset_time_overrun = False) #here, the self is the KMC_Model object
+ kmcos.run.png.MyPNG(atoms, show_unit_cell=False, scale=scale, model=self, **kwargs).write(filename=filename, resolution=resolution)
+ return
- def plot_configuration(self, plot_settings = {}):
+ def plot_configuration(self, filename = '', resolution = 150, scale = 20, representation = 'spatial', plot_settings = {}):
"""
+ representation is an optional argument for spatial and atomic view
+ You should specify as 'atomic' to see the atomic view. Leaving representation empty returns spatial view by default.
+
plot_settings is a dictionary that allows for the plot to change given the arguements
EX:
"y_label": "test",
@@ -1572,12 +1583,24 @@ class KMC_Model(Process):
"dpi": 220,
"speciesName": False
plot_configuration will make a graph named 'plottedConfiguration.png,' unless specified by 'figure_name' in plot_settings
- """
- config = self._get_configuration().tolist()
- species = self.species_tags
- species_coordinates = self.get_species_coordinates(config, species)
- self.create_plot(species_coordinates, species, plot_settings)
-
+ """
+ if representation == 'atomic':
+ if 'show_unit_cell' in plot_settings:
+ show_unit_cell = plot_settings['show_unit_cell']
+ else:
+ show_unit_cell = True
+ if 'kwargs' in plot_settings:
+ kwargs = plot_settings['kwargs']
+ else:
+ kwargs = {} #default for kwargs is a blank dictionary
+ self.export_picture(filename = filename, resolution = resolution, scale = scale)
+
+ if (representation == 'spatial') or (representation == 'circles'):
+ config = self._get_configuration().tolist()
+ species = self.species_tags
+ species_coordinates = self.get_species_coordinates(config, species)
+ self.create_plot(species_coordinates, species, plot_settings)
+
def _put(self, site, new_species, reduce=False):
"""
Works exactly like put, but without updating the database of
@@ -1983,6 +2006,21 @@ class KMC_Model(Process):
self._set_configuration(config)
self._adjust_database()
+ def pickle_export_atoms(self, filename = ""):
+ # takes atoms object in filename and turns it into a .pkl file
+ import pickle
+ if filename == "":
+ filename = "atoms_export.pkl"
+ else:
+ if filename[-4:] == '.pkl':
+ filename.replace('.pkl', '.pkl')
+ else:
+ filename = filename + '.pkl'
+ filehandler = open(filename, 'wb')
+ pickle.dump(self.get_atoms(), filehandler)
+ filehandler.close()
+
+
class Model_Parameters(object):
"""Holds all user defined parameters of a model in
concise form. All user defined parameters can be
diff --git a/kmcos/run/png.py b/kmcos/run/png.py
index 39e6d93d045582d68dd313d90326a9ebfefaa30c..f2030c34eb354bd1653b4d7b5d0ba9c88bed870f 100644
--- a/kmcos/run/png.py
+++ b/kmcos/run/png.py
@@ -16,6 +16,7 @@ class MyPNG(PNG):
model=None,
scale=20) :
+ self.atoms = atoms
self.numbers = atoms.get_atomic_numbers()
self.colors = colors
self.model = model
@@ -114,7 +115,6 @@ class MyPNG(PNG):
self.filename = filename
self.write_header(resolution=resolution)
self.write_info()
- self.write_body()
self.write_trailer(resolution=resolution)
def write_info(self):
@@ -140,8 +140,9 @@ class MyPNG(PNG):
text.draw(self.renderer)
def write_header(self, resolution=72):
- from matplotlib.backends.backend_agg import RendererAgg, Figure
+ from matplotlib.backends.backend_agg import RendererAgg
from matplotlib.backend_bases import GraphicsContextBase
+ from matplotlib.figure import Figure
try:
from matplotlib.transforms import Value
@@ -157,23 +158,20 @@ class MyPNG(PNG):
self.gc.set_linewidth(.2)
def write_trailer(self, resolution=72):
+ import matplotlib
renderer = self.renderer
if hasattr(renderer._renderer, 'write_png'):
# Old version of matplotlib:
renderer._renderer.write_png(self.filename)
else:
- from matplotlib import _png
- # buffer_rgba does not accept arguments from version 1.2.0
- # https://github.com/matplotlib/matplotlib/commit/f4fee350f9fbc639853bee76472d8089a10b40bd
- import matplotlib
- if matplotlib.__version__ < '1.2.0':
- x = renderer._renderer.buffer_rgba(0, 0)
- _png.write_png(renderer._renderer.buffer_rgba(0, 0),
- renderer.width, renderer.height,
- self.filename, resolution)
+ from ase.io import write
+ #self.atoms.rotate(a=0.5, (0,1,0), rotate_self=True)
+ if self.filename == "":
+ write('atomic_view.png', self.atoms)
else:
- x = renderer._renderer.buffer_rgba()
- _png.write_png(renderer._renderer.buffer_rgba(),
- #renderer.width, renderer.height,
- self.filename, resolution)
+ if self.filename[-4:] == '.png':
+ self.filename.replace('.png', '.png')
+ else:
+ self.filename = self.filename + '.png'
+ write(self.filename, self.atoms)