From 3dff7d4af94201d7fc837e2eb2fb90287294c9ab Mon Sep 17 00:00:00 2001
From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com>
Date: Tue, 16 Aug 2022 15:24:21 -0400
Subject: [PATCH 1/8] improving movies images filenames
---
kmcos/run/__init__.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/kmcos/run/__init__.py b/kmcos/run/__init__.py
index 72454801..8a460b07 100644
--- a/kmcos/run/__init__.py
+++ b/kmcos/run/__init__.py
@@ -837,9 +837,10 @@ class KMC_Model(Process):
os.mkdir('exported_movie_images')
image_folder = './exported_movie_images'
# os.chdir(image_folder)
+ digitsLength = len(str(frames)) #we will need to add some zeros to get the images in order.
for i in range(frames):
self.do_steps(steps)
- self.export_picture(filename = image_folder + "/" + filename + str(i), resolution = resolution, scale = scale)
+ self.export_picture(filename = image_folder + "/" + filename + str(i).zfill(digitsLength), resolution = resolution, scale = scale)
#os.chdir("..")
image_files = [os.path.join(image_folder,img) for img in os.listdir(image_folder) if img.endswith(".png")]
clip = moviepy.video.io.ImageSequenceClip.ImageSequenceClip(image_files, fps=fps)
--
GitLab
From 33fc0fc770a380a827787da0508360250cac172a Mon Sep 17 00:00:00 2001
From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com>
Date: Tue, 16 Aug 2022 15:24:50 -0400
Subject: [PATCH 2/8] Update installation.rst
---
doc/source/installation/installation.rst | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/source/installation/installation.rst b/doc/source/installation/installation.rst
index 5e6e5239..93ce1a7a 100644
--- a/doc/source/installation/installation.rst
+++ b/doc/source/installation/installation.rst
@@ -51,7 +51,7 @@ The easiest way to install kmcos is to use one of the automatic installers::
bash install-kmcos-linux-venv.bash #use 'bash install-kmcos-linux-user.bash' if you are not using a venv. #For the develop branch, use install-kmcos-linux-venv-develop.bash or install-kmcos-linux-user-develop.bash
-For personal computer usage (not on a supercomputer), it is a good idea to also run the following command, which will add the kmcos viewer::
+For personal computer usage (not on a supercomputer), it is a good idea to also run the following command, which will add the kmcos viewer and movie maker::
bash install-kmcos-complete-linux-venv-Ubuntu20.bash #this is for Ubuntu20. There is also an Ubuntu18 version.
--
GitLab
From fe70ed2eb8157895039c5e01dce9a0c08079374a Mon Sep 17 00:00:00 2001
From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com>
Date: Tue, 16 Aug 2022 15:25:15 -0400
Subject: [PATCH 3/8] Update __init__.py
---
kmcos/__init__.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/kmcos/__init__.py b/kmcos/__init__.py
index e378a8ea..b4c04ebb 100644
--- a/kmcos/__init__.py
+++ b/kmcos/__init__.py
@@ -50,7 +50,7 @@ from __future__ import print_function
-__version__ = "0.0.75"
+__version__ = "0.0.76"
VERSION = __version__
def evaluate_param_expression(param, parameters={}):
--
GitLab
From 0b6cd1908f816a22ccfb7aee8cc9c2a87cb94c33 Mon Sep 17 00:00:00 2001
From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com>
Date: Tue, 16 Aug 2022 16:36:54 -0400
Subject: [PATCH 4/8] Update MyFirstThrottling.py
---
examples/MyFirstThrottling/MyFirstThrottling.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/examples/MyFirstThrottling/MyFirstThrottling.py b/examples/MyFirstThrottling/MyFirstThrottling.py
index 1a954fc0..e66c9dc3 100644
--- a/examples/MyFirstThrottling/MyFirstThrottling.py
+++ b/examples/MyFirstThrottling/MyFirstThrottling.py
@@ -322,3 +322,4 @@ kmc_model.add_process(**temporary_kwargs_dictionary)
kmc_model.filename = model_name + ".xml"
kmc_model.save_model()
+kmcos.compile(kmc_model)
\ No newline at end of file
--
GitLab
From ff414632f6d959d9652741bb1598d6947a129882 Mon Sep 17 00:00:00 2001
From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com>
Date: Tue, 16 Aug 2022 17:08:25 -0400
Subject: [PATCH 5/8] improvement in export_import_library.py
---
.../export_import_library.py | 17 +++++++++++++++--
.../export_import_library.py | 17 +++++++++++++++--
.../export_import_library.py | 2 +-
.../export_import_library.py | 17 +++++++++++++++--
.../export_import_library.py | 2 +-
.../export_import_library.py | 17 +++++++++++++++--
6 files changed, 62 insertions(+), 10 deletions(-)
diff --git a/examples/MyFirstTPD_DesorptionOnly_local_smart/export_import_library.py b/examples/MyFirstTPD_DesorptionOnly_local_smart/export_import_library.py
index 8beb3d77..fe29e884 100644
--- a/examples/MyFirstTPD_DesorptionOnly_local_smart/export_import_library.py
+++ b/examples/MyFirstTPD_DesorptionOnly_local_smart/export_import_library.py
@@ -23,7 +23,7 @@ class module_export_import:
with open(self.save_filename, 'wt') as f:
for module_var in module_vars:
module_var_val = getattr(self.module, module_var)
- if type(module_var_val) is str:
+ if (type(module_var_val) == type('str')) or (type(module_var_val) == type(b'str')):
# We need to make sure string values get printed as string
# values or they won't be read properly on reload
f.write(module_var + " = '" + str(module_var_val) + "'\n")
@@ -61,7 +61,20 @@ class module_export_import:
module_var_val = module_var_val.strip()
# Convert to an actual Python object
- module_var_val = ast.literal_eval(module_var_val)
+ # Workaround for sets as literal_eval can't handle them in
+ # Python 2.7
+ if 'set' in module_var_val:
+ # Extract the bracketed portion which can be converted into
+ # a list
+ module_var_val = module_var_val[4:-1]
+
+ # Convert to a list
+ module_var_val = ast.literal_eval(module_var_val)
+
+ # Convert list to a set
+ module_var_val = set(module_var_val)
+ else:
+ module_var_val = ast.literal_eval(module_var_val)
# Store it in the module
setattr(self.module, module_var, module_var_val)
diff --git a/examples/MyFirstTPD_Precovered_local_smart/export_import_library.py b/examples/MyFirstTPD_Precovered_local_smart/export_import_library.py
index b9869b27..fe29e884 100644
--- a/examples/MyFirstTPD_Precovered_local_smart/export_import_library.py
+++ b/examples/MyFirstTPD_Precovered_local_smart/export_import_library.py
@@ -23,7 +23,7 @@ class module_export_import:
with open(self.save_filename, 'wt') as f:
for module_var in module_vars:
module_var_val = getattr(self.module, module_var)
- if type(module_var_val) is str or type(module_var_val) is str:
+ if (type(module_var_val) == type('str')) or (type(module_var_val) == type(b'str')):
# We need to make sure string values get printed as string
# values or they won't be read properly on reload
f.write(module_var + " = '" + str(module_var_val) + "'\n")
@@ -61,7 +61,20 @@ class module_export_import:
module_var_val = module_var_val.strip()
# Convert to an actual Python object
- module_var_val = ast.literal_eval(module_var_val)
+ # Workaround for sets as literal_eval can't handle them in
+ # Python 2.7
+ if 'set' in module_var_val:
+ # Extract the bracketed portion which can be converted into
+ # a list
+ module_var_val = module_var_val[4:-1]
+
+ # Convert to a list
+ module_var_val = ast.literal_eval(module_var_val)
+
+ # Convert list to a set
+ module_var_val = set(module_var_val)
+ else:
+ module_var_val = ast.literal_eval(module_var_val)
# Store it in the module
setattr(self.module, module_var, module_var_val)
diff --git a/examples/MyFirstThrottling/MyFirstThrottling_local_smart/export_import_library.py b/examples/MyFirstThrottling/MyFirstThrottling_local_smart/export_import_library.py
index 8581f870..fe29e884 100644
--- a/examples/MyFirstThrottling/MyFirstThrottling_local_smart/export_import_library.py
+++ b/examples/MyFirstThrottling/MyFirstThrottling_local_smart/export_import_library.py
@@ -23,7 +23,7 @@ class module_export_import:
with open(self.save_filename, 'wt') as f:
for module_var in module_vars:
module_var_val = getattr(self.module, module_var)
- if type(module_var_val) is str or type(module_var_val) is str:
+ if (type(module_var_val) == type('str')) or (type(module_var_val) == type(b'str')):
# We need to make sure string values get printed as string
# values or they won't be read properly on reload
f.write(module_var + " = '" + str(module_var_val) + "'\n")
diff --git a/examples/MyThirdTPR_local_smart/export_import_library.py b/examples/MyThirdTPR_local_smart/export_import_library.py
index 8beb3d77..fe29e884 100644
--- a/examples/MyThirdTPR_local_smart/export_import_library.py
+++ b/examples/MyThirdTPR_local_smart/export_import_library.py
@@ -23,7 +23,7 @@ class module_export_import:
with open(self.save_filename, 'wt') as f:
for module_var in module_vars:
module_var_val = getattr(self.module, module_var)
- if type(module_var_val) is str:
+ if (type(module_var_val) == type('str')) or (type(module_var_val) == type(b'str')):
# We need to make sure string values get printed as string
# values or they won't be read properly on reload
f.write(module_var + " = '" + str(module_var_val) + "'\n")
@@ -61,7 +61,20 @@ class module_export_import:
module_var_val = module_var_val.strip()
# Convert to an actual Python object
- module_var_val = ast.literal_eval(module_var_val)
+ # Workaround for sets as literal_eval can't handle them in
+ # Python 2.7
+ if 'set' in module_var_val:
+ # Extract the bracketed portion which can be converted into
+ # a list
+ module_var_val = module_var_val[4:-1]
+
+ # Convert to a list
+ module_var_val = ast.literal_eval(module_var_val)
+
+ # Convert list to a set
+ module_var_val = set(module_var_val)
+ else:
+ module_var_val = ast.literal_eval(module_var_val)
# Store it in the module
setattr(self.module, module_var, module_var_val)
diff --git a/tests/MyFirstThrottling/MyFirstThrottling_local_smart/export_import_library.py b/tests/MyFirstThrottling/MyFirstThrottling_local_smart/export_import_library.py
index 8581f870..fe29e884 100644
--- a/tests/MyFirstThrottling/MyFirstThrottling_local_smart/export_import_library.py
+++ b/tests/MyFirstThrottling/MyFirstThrottling_local_smart/export_import_library.py
@@ -23,7 +23,7 @@ class module_export_import:
with open(self.save_filename, 'wt') as f:
for module_var in module_vars:
module_var_val = getattr(self.module, module_var)
- if type(module_var_val) is str or type(module_var_val) is str:
+ if (type(module_var_val) == type('str')) or (type(module_var_val) == type(b'str')):
# We need to make sure string values get printed as string
# values or they won't be read properly on reload
f.write(module_var + " = '" + str(module_var_val) + "'\n")
diff --git a/tests/SQERTSS_unit_tests/throttling_test_reaction_local_smart/export_import_library.py b/tests/SQERTSS_unit_tests/throttling_test_reaction_local_smart/export_import_library.py
index b9869b27..fe29e884 100644
--- a/tests/SQERTSS_unit_tests/throttling_test_reaction_local_smart/export_import_library.py
+++ b/tests/SQERTSS_unit_tests/throttling_test_reaction_local_smart/export_import_library.py
@@ -23,7 +23,7 @@ class module_export_import:
with open(self.save_filename, 'wt') as f:
for module_var in module_vars:
module_var_val = getattr(self.module, module_var)
- if type(module_var_val) is str or type(module_var_val) is str:
+ if (type(module_var_val) == type('str')) or (type(module_var_val) == type(b'str')):
# We need to make sure string values get printed as string
# values or they won't be read properly on reload
f.write(module_var + " = '" + str(module_var_val) + "'\n")
@@ -61,7 +61,20 @@ class module_export_import:
module_var_val = module_var_val.strip()
# Convert to an actual Python object
- module_var_val = ast.literal_eval(module_var_val)
+ # Workaround for sets as literal_eval can't handle them in
+ # Python 2.7
+ if 'set' in module_var_val:
+ # Extract the bracketed portion which can be converted into
+ # a list
+ module_var_val = module_var_val[4:-1]
+
+ # Convert to a list
+ module_var_val = ast.literal_eval(module_var_val)
+
+ # Convert list to a set
+ module_var_val = set(module_var_val)
+ else:
+ module_var_val = ast.literal_eval(module_var_val)
# Store it in the module
setattr(self.module, module_var, module_var_val)
--
GitLab
From 861e1a394b1cfbfdc4f3def59df196d38f3a5c0e Mon Sep 17 00:00:00 2001
From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com>
Date: Tue, 16 Aug 2022 17:49:04 -0400
Subject: [PATCH 6/8] improving commenting about updating rate constants
---
.../runfile2_TPD_desorptionOnlyWithExportImport.py | 2 +-
examples/MyFirstTPD_Precovered_local_smart/runfile1.py | 2 +-
examples/MyFirstTPD_Precovered_local_smart/runfile1b.py | 2 +-
examples/MyFirstTPD_Precovered_local_smart/runfile2.py | 2 +-
examples/MyFirstTPD_Precovered_local_smart/runfile3.py | 2 +-
examples/MyFirstTPD_Precovered_local_smart/runfile4.py | 4 ++--
examples/MyFirstTPD_Precovered_local_smart/runfile5.py | 2 +-
examples/MyFirstTPD_Precovered_local_smart/runfile6.py | 2 +-
examples/MyThirdTPR_local_smart/runfile.py | 2 +-
9 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/examples/MyFirstTPD_DesorptionOnly_local_smart/runfile2_TPD_desorptionOnlyWithExportImport.py b/examples/MyFirstTPD_DesorptionOnly_local_smart/runfile2_TPD_desorptionOnlyWithExportImport.py
index 5c41d856..8487056c 100644
--- a/examples/MyFirstTPD_DesorptionOnly_local_smart/runfile2_TPD_desorptionOnlyWithExportImport.py
+++ b/examples/MyFirstTPD_DesorptionOnly_local_smart/runfile2_TPD_desorptionOnlyWithExportImport.py
@@ -166,7 +166,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = T_initial + T_ramp * (kmc_time - kmc_time_tpdinit)
diff --git a/examples/MyFirstTPD_Precovered_local_smart/runfile1.py b/examples/MyFirstTPD_Precovered_local_smart/runfile1.py
index 8a0dc9f8..f1b1b864 100644
--- a/examples/MyFirstTPD_Precovered_local_smart/runfile1.py
+++ b/examples/MyFirstTPD_Precovered_local_smart/runfile1.py
@@ -64,7 +64,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = Ti + beta * (sg.kmc_time)
diff --git a/examples/MyFirstTPD_Precovered_local_smart/runfile1b.py b/examples/MyFirstTPD_Precovered_local_smart/runfile1b.py
index 472f34f1..35e2197b 100644
--- a/examples/MyFirstTPD_Precovered_local_smart/runfile1b.py
+++ b/examples/MyFirstTPD_Precovered_local_smart/runfile1b.py
@@ -64,7 +64,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = Ti + beta * (sg.kmc_time)
diff --git a/examples/MyFirstTPD_Precovered_local_smart/runfile2.py b/examples/MyFirstTPD_Precovered_local_smart/runfile2.py
index 02f10e7b..f107f48d 100644
--- a/examples/MyFirstTPD_Precovered_local_smart/runfile2.py
+++ b/examples/MyFirstTPD_Precovered_local_smart/runfile2.py
@@ -63,7 +63,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = Ti + beta * (sg.kmc_time)
diff --git a/examples/MyFirstTPD_Precovered_local_smart/runfile3.py b/examples/MyFirstTPD_Precovered_local_smart/runfile3.py
index 70dccede..ddf40a88 100644
--- a/examples/MyFirstTPD_Precovered_local_smart/runfile3.py
+++ b/examples/MyFirstTPD_Precovered_local_smart/runfile3.py
@@ -64,7 +64,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = Ti + beta * (sg.kmc_time)
diff --git a/examples/MyFirstTPD_Precovered_local_smart/runfile4.py b/examples/MyFirstTPD_Precovered_local_smart/runfile4.py
index 5bdba992..b23d86f4 100644
--- a/examples/MyFirstTPD_Precovered_local_smart/runfile4.py
+++ b/examples/MyFirstTPD_Precovered_local_smart/runfile4.py
@@ -63,7 +63,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = Ti + beta * (sg.kmc_time)
@@ -131,7 +131,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = Ti + beta * (sg.kmc_time)
diff --git a/examples/MyFirstTPD_Precovered_local_smart/runfile5.py b/examples/MyFirstTPD_Precovered_local_smart/runfile5.py
index 0eafe9d1..25e7b0c7 100644
--- a/examples/MyFirstTPD_Precovered_local_smart/runfile5.py
+++ b/examples/MyFirstTPD_Precovered_local_smart/runfile5.py
@@ -64,7 +64,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = Ti + beta * (sg.kmc_time)
diff --git a/examples/MyFirstTPD_Precovered_local_smart/runfile6.py b/examples/MyFirstTPD_Precovered_local_smart/runfile6.py
index 30c23446..664c683e 100644
--- a/examples/MyFirstTPD_Precovered_local_smart/runfile6.py
+++ b/examples/MyFirstTPD_Precovered_local_smart/runfile6.py
@@ -64,7 +64,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = Ti + beta * (sg.kmc_time)
diff --git a/examples/MyThirdTPR_local_smart/runfile.py b/examples/MyThirdTPR_local_smart/runfile.py
index 5c41d856..8487056c 100644
--- a/examples/MyThirdTPR_local_smart/runfile.py
+++ b/examples/MyThirdTPR_local_smart/runfile.py
@@ -166,7 +166,7 @@ if load_simulation_state:
# The following assignment (and similar assignments elsewhere) is *magical*.
# It invokes a hidden __setattr__ method of the Model_Parameters class that
# calls the set_rate_constants() function to update the values of the rate
- # constants in the Fortran base module. Any other kind of assignment will
+ # constants in the Fortran base module. Any other syntax of assignment will
# require an explicit call to set_rate_constants(). *Failure to update the
# rate constants in the Fortran module will result in wrong results!*
T = T_initial + T_ramp * (kmc_time - kmc_time_tpdinit)
--
GitLab
From 0d14c01ba19790bd7e2e4caa5ce875bf7b4b274f Mon Sep 17 00:00:00 2001
From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com>
Date: Tue, 16 Aug 2022 20:18:46 -0400
Subject: [PATCH 7/8] Create runfile7.py
---
.../runfile7.py | 122 ++++++++++++++++++
1 file changed, 122 insertions(+)
create mode 100644 examples/MyFirstTPD_Precovered_local_smart/runfile7.py
diff --git a/examples/MyFirstTPD_Precovered_local_smart/runfile7.py b/examples/MyFirstTPD_Precovered_local_smart/runfile7.py
new file mode 100644
index 00000000..6a075e6f
--- /dev/null
+++ b/examples/MyFirstTPD_Precovered_local_smart/runfile7.py
@@ -0,0 +1,122 @@
+from kmcos.snapshots import *
+import kmcos.snapshots_globals as sg
+import kmcos.snapshots as snapshots
+import kmcos.throttling_globals as tg
+import kmcos.throttling as throttling
+import os; import sys
+import export_import_library as eil
+
+
+##### SOME LINES THAT SHOULD NOT NORMALLY BE CHANGED####
+
+# File names for loading/saving parameters (related to the export import module and throttling module)
+# These will not really be used for this example, but are good lines to have.
+# In the future, this may be done automatically within kmcos.
+tg_load_file = sg.simulation_name + 'throttling_parameters.txt'
+tg_save_file = sg.simulation_name + 'throttling_parameters.txt'
+sg_load_file = sg.simulation_name + 'snapshots_parameters.txt'
+sg_save_file = sg.simulation_name + 'snapshots_parameters.txt'
+
+# Export/import module objects for saving/loading data
+tg_module = eil.module_export_import(tg_save_file, tg_load_file, tg)
+sg_module = eil.module_export_import(sg_save_file, sg_load_file, sg)
+
+
+#### LOADING AND INITIALIZING #####
+# Random seed
+random_seed = -731543673 #can be any integer. only used if not loading a simulation. The PRNG_state that will be generated is a list, unlike the seed, which is an integer.
+
+load_simulation_state = False #This is a user setting that will affect what happens below. It is for continuing a simulation from where one left off.
+
+if load_simulation_state == False: #initialize the seed.
+ snapshots.seed_PRNG(restart=False, state=random_seed)
+elif load_simulation_state == True: #load everything and set the SEED to be what it was before.
+ # Load modules
+ sg_module.load_params()
+ tg_module.load_params()
+
+ # Reset number of steps and time
+ sg.model.base.set_kmc_time(sg.kmc_time)
+ sg.model.base.set_kmc_step(sg.steps_so_far)
+ sg.atoms.kmc_step = sg.steps_so_far
+
+ # Load the lattice
+ sg.model._set_configuration(np.array(sg.config))
+ sg.model._adjust_database()
+
+ # Read the PRNG state, if available, and set it in the model
+ snapshots.seed_PRNG(restart=True, state=sg.PRNG_state)
+ # Update the snapshot number
+ tg.current_snapshot += 1
+
+
+##### GETTING SETTINGS READY FOR THE SIMULATION ####
+
+#Snapshots module options.
+sg.parameters_of_interest = ['T'] #['T','R'] #<-- put the parameters you want exported with each snapshot here. Can also put activation energy etc.
+sps = 1000 # <-- the kmc steps per snapshot. Defining this variable now is optional, and also the value can be changed later.
+n_snapshots = 1 # <-- The total number of snapshots to do. Defining this variable now is optional, and also the value can be changed later.
+tps = 1.0 #this sets the maximum amount of time per snapshot.
+
+#Generally, if a user needs to change a parameter after each snapshot, only do 1 snapshot at a time with n_snapshots=1.
+#This example is a temperature programmed reaction example, so n_snapshots=1 makes sense, since we need to change the temperature after each snapshot.
+
+#Some simulation settings.
+Ti = 300 #initial temperature
+Tf = 345 #final temperature
+beta = 5 #beta, heating rate in Kelvin per second.
+
+
+
+# Update the cutoff time
+tg.cutoff_time = 1E6 #the throttling module's cutoff time is in seconds. We are not using that feature in this simulation, but it could be set here, for example.
+
+
+if load_simulation_state == False:
+ sg.model.parameters.T = 300 #set the initial temperature.
+ T = Ti
+ sys.stdout.write("Starting a fresh simulation. Current temperature is " +
+ str(T) + " K. Current time is " + str(sg.kmc_time) + " s.\n")
+ #The kmcos Model is initialized in create_headers
+ create_headers()
+ #If it is desired to run snapshots without writing output to a file, set sg.write_output = 'False'.
+ #If you want to start writing again, set sg.write_output = 'True' before running
+ #more snapshots.
+elif load_simulation_state == True:
+ #The temperatures will have been loaded already, but we need to set our runfile's variable.
+ T = sg.model.parameters.T
+ sys.stdout.write("Restarting from old simulation. Current temperature is " +
+ str(T) + " K. Current time is " + str(sg.kmc_time) + " s.\n")
+
+
+# The following assignment (and similar assignments elsewhere) is *magical*.
+# It invokes a hidden __setattr__ method of the Model_Parameters class that
+# calls the set_rate_constants() function to update the values of the rate
+# constants in the Fortran base module. Any other kind of assignment will
+# require an explicit call to set_rate_constants(). *Failure to update the
+# rate constants in the Fortran module will result in wrong results!*
+sg.model.parameters.T = T
+
+#### SIMULATING AFTER ALL INITIALIZING IS DONE ####
+
+#Here is the TPD/TPR loop.
+while T < Tf:
+ #Set the 'previous' Temperature and time variables before running any steps.
+ last_T = T
+ last_t = sg.atoms.kmc_time
+ #Run some steps as snapshots.
+ # Note that the below command will try to run n_snapshots with a certain 'steps per snapshot'
+ # but for any given snapshot, if thte time per snapshot (tps) is reached, the snapshot will be stopped.
+ # in this way, no snapshot will be greater than 1 second.
+
+ do_snapshots(sps=sps, n_snapshots=n_snapshots, tps=tps)
+ #update the time and temperature for after the snaphsot is over.
+ t = sg.atoms.kmc_time
+ Tincr = beta*(t-last_t) # calculate the value to increment the temperature by
+ T = T + Tincr
+ sg.model.parameters.T = T
+ print("Snapshot taken. New temperature:", T)
+
+
+#The final command below writes the simulation details to the logfile
+create_log()
--
GitLab
From ad06b07da3f58dcefd02d8b6999ed239c8330e50 Mon Sep 17 00:00:00 2001
From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com>
Date: Tue, 16 Aug 2022 20:45:23 -0400
Subject: [PATCH 8/8] Update __init__.py
---
kmcos/__init__.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/kmcos/__init__.py b/kmcos/__init__.py
index b4c04ebb..2abc59a0 100644
--- a/kmcos/__init__.py
+++ b/kmcos/__init__.py
@@ -50,7 +50,7 @@ from __future__ import print_function
-__version__ = "0.0.76"
+__version__ = "1.0.0"
VERSION = __version__
def evaluate_param_expression(param, parameters={}):
--
GitLab