Merge branch 'dev' of https://github.com/f0uriest/APC524_FinalProject …

…into dev

GASTOp.py

@@ -1,3 +1,10 @@
+"""GASTOp.py
+This file runs the gastop program
+Authors: Amlan Sinha, Cristian Lacey, Daniel Shaw, Paul Kaneelil, Rory Conlin, Susan Redmond
+Licensed under GNU GPLv3.
+This module implements the GenAlg class.
+
+"""
 import matplotlib.pyplot as plt
 from gastop import GenAlg, utilities
 

docs/config_file_format.rst

@@ -2,4 +2,153 @@
 Config File Formatting and Options
 ==================================
 
+The config file includes all the input parameters used to instantiate a
+GenAlg() object. Certain parameters must be specified by the user, while other
+more advanced parameters can be left blank for simplicity and will default to
+reasonable values.
+
+The config file is parsed as a nested dictionary. Each dictionary is
+indicated by :code:`[dict]`, and nested dictionaries are indicated by nested
+squared brackets, :code:`[[nested dict]]`. Each dictionary contains multiple
+arguments indicated by :code:`key: value`. If the value is an integer, float,
+or string, simply input the value without quotation marks. For instance,
+:code:`key: 3`, :code:`key: 3.14`, or :code:`key: pi`. If the value
+is a numpy array, input the value as an array in list format, within single
+quotes, like :code:`key: '[[3.14 3.14],[3.14 3.14]]'`.
+
+For instance, the config file:
+
+.. code-block:: python
+       
+       [dict1]
+       key1: 3
+       key2: 3.14
+       [[sub_dict1]]
+       sub_key1: apples
+       [[sub_dict2]]
+       sub_key2: None
+       [dict2]
+       key3: '[[3.14 12.8],[6.7 88.9999]]'
+       
+
+would be parsed, forming the dictionary:
+
+.. code-block:: python
+
+       {'dict1':
+              {'key1':3,
+              'key2':3.14,
+              'sub_dict1':{'sub_key1':'apples'},
+              'sub_dict2':{'sub_key2':None}},
+        'dict2':
+              {'key3':array([[3.14 12.8],[6.7 88.9999]])}}
+
+
+Required Parameters
+*******************
+
+General
+=======
+:code:`[general]` contains the following parameters:
+
+:user_spec_nodes: User-specified nodes (nodes with provided loads and displacement boundary conditions) as an nx3 numpy array of floats in the format :code:`'[[x1 y1 z1],[x2 y2 z2],...,[xn yn zn]]'`.
+
+:loads: The forces and moments acting on each user-specified node as an nx6 numpy array of floats in the format :code:`'[[Fx1,Fy1,Fz1,Mx1,My1,Mz1],[Fx2,Fy2,Fz2,Mx2,My2,Mz2],...,[Fxn,Fyn,Fzn,Mxn,Myn,Mzn]]'`.
+
+:fixtures: The translational and rotational displacements for each user-specified node as an nx6 numpy array of integers in the format :code:`'[[transx1,transy1,transz1,rotx1,roty1,rotz1],[transx2,transy2,transz2,rotx2,roty2,rotz2],...,[transxn,transyn,transzn,rotxn,rotyn,rotzn]]'`. Here :code:`transx1` is the translational degree of freedom in the x direction of the first user-specified node, and :code:`rotx1` is the rotational degree of freedom about the x-axis of the first user-specified node. A :code:`1` indicates fixed, while a :code:`0` indicates the node is free to move along or about the corresponding degree of freedom.
+
+:num_rand_nodes: Maximum number of random nodes as an integer.
+
+:num_rand_edges: Maximum number of random edges as an integer.
+
+:properties_path: Path to the properties CSV as a string. For example, :code:`gastop-config/properties.csv`.
+
+:domain: Allowable domain as a 3x2 numpy array of floats in the format :code:`'[[xmin xmax],[ymin ymax],[zmin zmax]]'`.
+
+Fitness Function Parameters
+===========================
+:code:`[fitness_params]` contains the following parameters:
+
+:equation: Method for calculating fitness as a string. *Options: weighted_sum, sphere, rosenbrock, rastrigin.*
+:parameters:
+::
+       goal_fos: 4
+       critical_nodes  '[3]'
+       w_fos = 10000
+       w_mass = 1
+       w_deflection = 100
+
+Evaluator Parameters
+====================
+:code:`[evaluator_params]` contains the following parameters:
+
+:struct_solver: Method for solving truss as a string.
+       - *Options: mat_struct_analysis_DSM*
+:mass_solver: Method of calculating the mass of a truss as a string.
+       - Options: mass_basic
+:interferences_solver: Method of determining interferences as a string. *Options: blank_test, interference_ray_tracing*
+:cost_solver: Method of calculating the cost of a truss as a string. *Options: cost_calc*
+
+Genetic Algorithm Parameters
+============================
+:code:`[ga_params]` contains the following parameters:
+
+:num_threads: Number of threads.
+       -Type: int
+:pop_size: = 1000
+:num_generations: = 30
+:num_elite: =
+:percent_mutation: =
+:percent_crossover: =
+:save_frequency: = 5
+:save_filename_prefix: = Recorded_States_
+
+Progress Monitor Parameters
+===========================
+:code:`[monitor_params]` contains the following parameters:
+
+:progress_display: = 1
+
+
+Advanced Parameters
+*******************
+
 explain different headings and options, with references to API docs
+
+Random Generation Parameters
+============================
+:code:`[random_params]` contains the following parameters:
+
+
+Crossover Parameters
+====================
+:code:`[crossover_params]` contains the following parameters:
+
+:node_crossover_method: =
+:edge_crossover_method: =
+:property_crossover_method: =
+      [[node_crossover_params]]
+      [[edge_crossover_params]]
+      [[property_crossover_params]]
+
+Mutator Parameters
+==================
+:code:`[mutator_params]` contains the following parameters:
+
+:node_mutator_method: =
+:edge_mutator_method: =
+:property_mutator_method: =
+      [[node_mutator_params]]
+      std =
+      [[edge_mutator_params]]
+      proportions =
+      [[property_mutator_params]]
+      proportions =
+
+Selector Parameters
+===================
+:code:`[selector_params]` contains the following parameters:
+
+:method: =
+:tourn_size: = 31 # Must be less than 32
+:tourn_prob: = 0.5

gastop-config/boolean_parse_test_init.txt

@@ -32,6 +32,8 @@ num_generations = 30
 num_elite =
 percent_mutation =
 percent_crossover =
+save_frequency = 5
+save_filename_prefix = Recorded_States_
 
 [monitor_params]
 progress_display = 1
@@ -43,6 +45,7 @@ progress_display = 1
 # optional stuff
 
 [random_params]
+rng_seed = 
 
 
 [crossover_params]
@@ -67,5 +70,6 @@ property_mutator_method =
 
 [selector_params]
 method =
-tourn_size = 31 # Must be less than 32
-tourn_prob = 0.5
+       [[method_params]]
+       tourn_size = 
+       tourn_prob = 

gastop-config/error_config.txt

@@ -29,6 +29,8 @@ num_generations = 30
 num_elite =
 percent_mutation = .7
 percent_crossover = .8
+save_frequency = 5
+save_filename_prefix = Recorded_States_
 
 [monitor_params]
 progress_display = 1
@@ -40,7 +42,7 @@ progress_display = 1
 # optional stuff
 
 [random_params]
-
+rng_seed = 
 
 [crossover_params]
 node_crossover_method =
@@ -62,7 +64,9 @@ property_mutator_method =
       [[property_mutator_params]]
       proportions =
 
+
 [selector_params]
 method =
-tourn_size = 31 # Must be less than 32
-tourn_prob = 0.5
+       [[method_params]]
+       tourn_size = 
+       tourn_prob = 

gastop-config/init.txt

@@ -11,6 +11,8 @@ num_generations = 30
 num_elite = 1 # int, ~10 (the whole truss that get passed)
 percent_crossover = 0.4 # float between 0 and 1
 percent_mutation = 0.4 # float between 0 and 1
+save_frequency = 5
+save_filename_prefix = Recorded_States_
 
 [random_params]
 num_rand_nodes = 1 # int

gastop-config/main_test.txt

@@ -29,6 +29,8 @@ num_generations = 5
 num_elite =
 percent_mutation =
 percent_crossover =
+save_frequency = 5
+save_filename_prefix = Recorded_States_
 
 [monitor_params]
 progress_display = 1
@@ -40,7 +42,7 @@ progress_display = 1
 # optional stuff
 
 [random_params]
-
+rng_seed = 1138
 
 [crossover_params]
 node_crossover_method =
@@ -64,5 +66,6 @@ property_mutator_method =
 
 [selector_params]
 method =
-tourn_size = 31 # Must be less than 32
-tourn_prob = 0.5
+       [[method_params]]
+       tourn_size = 
+       tourn_prob = 

gastop-config/struct_making_test_init.txt

@@ -26,23 +26,20 @@ cost_solver = cost_calc
 num_threads = 4
 pop_size = 1000
 num_generations = 30
-num_elite =
+num_elite = 1
 percent_mutation =
 percent_crossover =
 save_frequency = 5
-save_filenames = 'save'
+save_filename_prefix = Recorded_States_
 
 [monitor_params]
 progress_display = 1
 
 
-
-
-
 # optional stuff
 
 [random_params]
-
+rng_seed = 
 
 [crossover_params]
 node_crossover_method =
@@ -66,5 +63,6 @@ property_mutator_method =
 
 [selector_params]
 method =
-tourn_size = 31 # Must be less than 32
-tourn_prob = 0.5
+       [[method_params]]
+       tourn_size = 
+       tourn_prob = 

gastop-config/struct_making_test_init2.txt

@@ -29,6 +29,8 @@ num_generations = 30
 num_elite =
 percent_mutation =
 percent_crossover =
+save_frequency = 5
+save_filename_prefix = Recorded_States_
 
 [monitor_params]
 progress_display = 1
@@ -40,7 +42,7 @@ progress_display = 1
 # optional stuff
 
 [random_params]
-
+rng_seed = 
 
 [crossover_params]
 node_crossover_method =
@@ -64,5 +66,6 @@ property_mutator_method =
 
 [selector_params]
 method =
-tourn_size = 31 # Must be less than 32
-tourn_prob = 0.5
+       [[method_params]]
+       tourn_size = 
+       tourn_prob = 

gastop-config/struct_making_test_init_sfr.txt

@@ -29,6 +29,8 @@ num_generations = 5
 num_elite =
 percent_mutation =
 percent_crossover =
+save_frequency = 5
+save_filename_prefix = Recorded_States_
 
 [monitor_params]
 progress_display = 1
@@ -40,7 +42,7 @@ progress_display = 1
 # optional stuff
 
 [random_params]
-
+rng_seed = 
 
 [crossover_params]
 node_crossover_method =
@@ -64,5 +66,6 @@ property_mutator_method =
 
 [selector_params]
 method =
-tourn_size = 31 # Must be less than 32
-tourn_prob = 0.5
+       [[method_params]]
+       tourn_size = 
+       tourn_prob = 

gastop/__init__.py

@@ -1,3 +1,11 @@
+"""__init__.py
+This file is a part of GASTOp
+Authors: Amlan Sinha, Cristian Lacey, Daniel Shaw, Paul Kaneelil, Rory Conlin, Susan Redmond
+Licensed under GNU GPLv3.
+This module imports the main classes so they are available at the top level of the package.
+
+"""
+
 from gastop.truss import Truss
 from gastop.evaluator import Evaluator
 from gastop.crossover import Crossover

gastop/__main__.py

@@ -1,6 +1,11 @@
+"""Runs the gastop program
+This file runs scripts for GASTOp
+Authors: Amlan Sinha, Cristian Lacey, Daniel Shaw, Paul Kaneelil, Rory Conlin, Susan Redmond
+Licensed under GNU GPLv3.
+
+"""
 import argparse
 import sys
-from matplotlib import pyplot as plt
 from gastop import GenAlg, utilities
 
 
@@ -32,6 +37,11 @@ def parse_args(args):
 
 
 def main(args=sys.argv[1:]):
+    """Runs the main GASTOp script, from the command line.
+
+    Reads and parses user input from command line, runs the code,
+    and prints and plots the resulting best truss.
+    """
 
     args = parse_args(args)
     config = utilities.init_file_parser(args.config_path)
@@ -72,7 +82,6 @@ def main(args=sys.argv[1:]):
                   loads=config['evaluator_params']['boundary_conditions']['loads'],
                   fixtures=config['evaluator_params']['boundary_conditions']['fixtures'],
                   deflection=True)
-        plt.show()
 
 
 if __name__ == '__main__':