Merge pull request #3 from pcarruscag/develop

update master
pcarruscag · Dec 8, 2021 · d4dfa56 · d4dfa56
2 parents f098f47 + 750a100
commit d4dfa56
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diff --git a/AUTHORS.md b/AUTHORS.md
@@ -0,0 +1,20 @@
+# FADO Authors #
+
+FADO is developed by a community of voluntary contributors who contribute code, bug reports, documentation, support, etc.
+
+## Original Authors ##
+
+```
+Pedro Gomes (Imperial College London)
+```
+
+## Individual Contributors ##
+
+(extracted using `git shortlog -s --no-merges`, alphabetical order).
+Copyright holders might be the individual person or their respective employer. If no real name is available, the Github user name is listed.
+
+```
+Pedro Gomes
+Tobias Kattmann
+```
+
diff --git a/documentation.py b/documentation.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #

diff --git a/drivers/base_driver.py b/drivers/base_driver.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #
@@ -232,7 +232,7 @@ def setStorageMode(self,keepDesigns=False,dirPrefix="DSN_"):
 
     def setFailureMode(self,mode):
         """
-        Set the failure behavior, for "HARD" (default) an exeption is throw if function evaluations fail,
+        Set the failure behavior, for "HARD" (default) an exception is throw if function evaluations fail,
         for "SOFT" the driver catches exceptions and uses default function values (if they have them).
         The "SOFT" mode is useful if the optimizer does not handle exceptions.
         """

diff --git a/drivers/constrained_optim_driver.py b/drivers/constrained_optim_driver.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #

diff --git a/drivers/exterior_penalty.py b/drivers/exterior_penalty.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #

diff --git a/drivers/ipopt_driver.py b/drivers/ipopt_driver.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #

diff --git a/drivers/parallel_eval_driver.py b/drivers/parallel_eval_driver.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #
@@ -187,7 +187,7 @@ def _runAction(self, action):
         #end
     #end
 
-    # Evaluate all functions (objectives and constraints), imediately
+    # Evaluate all functions (objectives and constraints), immediately
     # retrieves and stores the results after shifting and scaling.
     def _evaluateFunctions(self, x):
         self._handleVariableChange(x)

diff --git a/drivers/scipy_driver.py b/drivers/scipy_driver.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #

diff --git a/evaluation.py b/evaluation.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #
@@ -34,6 +34,7 @@ class ExternalRun:
     """
     def __init__(self,dir,command,useSymLinks=False):
         self._dataFiles = []
+        self._dataFilesDestination = []
         self._confFiles = []
         self._expectedFiles = []
         self._workDir = dir
@@ -54,17 +55,22 @@ def _addAbsoluteFile(self,file,flist):
             raise ValueError("File '"+file+"' not found.")
         flist.append(file)
 
-    def addData(self,file,location="auto"):
+    def addData(self,file,location="auto",destination=None):
         """
         Adds a "data" file to the run, an immutable dependency of the process.
 
         Parameters
         ----------
-        file     : Path to the file.
-        location : Type of path, "relative" (to the parent of "dir"), "absolute" (the path
-                   is immediately converted to an absolute path, the file must exist),
-                   or "auto" (tries "absolute" first, reverts to "relative"). 
+        file        : Path to the file.
+        location    : Type of path, "relative" (to the parent of "dir"), "absolute" (the path
+                     is immediately converted to an absolute path, the file must exist),
+                     or "auto" (tries "absolute" first, falls back to "relative").
+        destination : Filename to be set at the destination. Discards any additional file path.
+                      The default destination is the regular filename (i.e. "file").
         """
+        if destination is None: destination = file
+        self._dataFilesDestination.append(os.path.basename(destination))
+
         if location == "relative":
             self._dataFiles.append(file)
         else:
@@ -119,8 +125,8 @@ def initialize(self):
 
         try:
             os.mkdir(self._workDir)
-            for file in self._dataFiles:
-                target = os.path.join(self._workDir,os.path.basename(file))
+            for file, destination in zip(self._dataFiles, self._dataFilesDestination):
+                target = os.path.join(self._workDir,destination)
                 (shutil.copy,os.symlink)[self._symLinks](os.path.abspath(file),target)
 
             for file in self._confFiles:

diff --git a/examples/example3_SU2/example.py b/examples/example3_SU2/example.py
@@ -20,9 +20,6 @@
 # two load cases
 load_horizontal = Parameter(["1.0,  0.0"],LabelReplacer("__LOAD_DIR__"))
 load_vertical   = Parameter(["0.0, -1.0"],LabelReplacer("__LOAD_DIR__"))
-# for deformation the input mesh is different
-mesh_deform = Parameter(["MESH_FILENAME= mesh_ffd.su2"],\
-           LabelReplacer("MESH_FILENAME= mesh_def.su2"))
 # this is a meta-parameter, for SU2_GEO the FFD variables are the FD step sizes
 vars_geometry = Parameter(["DV_VALUE=0.001"+",0.001"*(ffd.getSize()-1)],\
              LabelReplacer("DV_VALUE= 0"+",0"*(ffd.getSize()-1)))
@@ -37,7 +34,6 @@
 deform = ExternalRun("DEFORM","SU2_DEF settings.cfg",True)
 deform.addConfig("settings.cfg")
 deform.addData("mesh_ffd.su2")
-deform.addParameter(mesh_deform)
 # these parameters are not relevant but are needed to make a valid config
 deform.addParameter(load_vertical)
 deform.addParameter(filter_type)
@@ -47,7 +43,7 @@
 # geometric properties
 geometry = ExternalRun("GEOMETRY","SU2_GEO settings.cfg",True)
 geometry.addConfig("settings.cfg")
-geometry.addData("DEFORM/mesh_def.su2")
+geometry.addData("DEFORM/mesh_def.su2",destination="mesh_ffd.su2")
 geometry.addParameter(vars_geometry)
 # these parameters are not relevant but are needed to make a valid config
 geometry.addParameter(load_vertical)
@@ -59,7 +55,7 @@
 hload_dir = ExternalRun("HLOAD","SU2_CFD -t 2 settings.cfg",True)
 hload_dir.addConfig("settings.cfg")
 hload_dir.addConfig("element_properties.dat")
-hload_dir.addData("DEFORM/mesh_def.su2")
+hload_dir.addData("DEFORM/mesh_def.su2",destination="mesh_ffd.su2")
 hload_dir.addParameter(load_horizontal)
 hload_dir.addParameter(filter_type)
 hload_dir.addParameter(filter_radius)
@@ -69,7 +65,7 @@
 vload_dir = ExternalRun("VLOAD","SU2_CFD -t 2 settings.cfg",True)
 vload_dir.addConfig("settings.cfg")
 vload_dir.addConfig("element_properties.dat")
-vload_dir.addData("DEFORM/mesh_def.su2")
+vload_dir.addData("DEFORM/mesh_def.su2",destination="mesh_ffd.su2")
 vload_dir.addParameter(load_vertical)
 vload_dir.addParameter(filter_type)
 vload_dir.addParameter(filter_radius)
@@ -83,7 +79,7 @@
 volume = ExternalRun("VOLUME",adj_command.replace("FUN","volfrac"),True)
 volume.addConfig("settings.cfg")
 volume.addConfig("element_properties.dat")
-volume.addData("DEFORM/mesh_def.su2")
+volume.addData("DEFORM/mesh_def.su2",destination="mesh_ffd.su2")
 volume.addData("direct.dat") # dummy solution file
 volume.addParameter(func_constraint)
 volume.addParameter(iter_constraint)
@@ -97,7 +93,7 @@
 hload_adj = ExternalRun("HLOAD_ADJ",adj_command.replace("FUN","refnode"),True)
 hload_adj.addConfig("settings.cfg")
 hload_adj.addConfig("element_properties.dat")
-hload_adj.addData("DEFORM/mesh_def.su2")
+hload_adj.addData("DEFORM/mesh_def.su2",destination="mesh_ffd.su2")
 hload_adj.addData("HLOAD/direct.dat")
 hload_adj.addParameter(load_horizontal)
 hload_adj.addParameter(filter_type)
@@ -108,7 +104,7 @@
 vload_adj = ExternalRun("VLOAD_ADJ",adj_command.replace("FUN","refnode"),True)
 vload_adj.addConfig("settings.cfg")
 vload_adj.addConfig("element_properties.dat")
-vload_adj.addData("DEFORM/mesh_def.su2")
+vload_adj.addData("DEFORM/mesh_def.su2",destination="mesh_ffd.su2")
 vload_adj.addData("VLOAD/direct.dat")
 vload_adj.addParameter(load_vertical)
 vload_adj.addParameter(filter_type)

diff --git a/examples/example3_SU2/settings.cfg b/examples/example3_SU2/settings.cfg
@@ -66,7 +66,7 @@ DISCADJ_LIN_SOLVER= CONJUGATE_GRADIENT
 DISCADJ_LIN_PREC= ILU
 %
 % In/Out
-MESH_FILENAME= mesh_def.su2
+MESH_FILENAME= mesh_ffd.su2
 MESH_OUT_FILENAME= mesh_def.su2
 MESH_FORMAT= SU2
 SOLUTION_FILENAME= direct.dat

diff --git a/function.py b/function.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #
@@ -20,7 +20,7 @@
 
 
 class FunctionBase(abc.ABC):
-    """Abstract base class to define the essencial interface of Function objects."""
+    """Abstract base class to define the essential interface of Function objects."""
     def __init__(self,name):
         self._name = name
         # inputs

diff --git a/optimizers/fletcher_reeves.py b/optimizers/fletcher_reeves.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #

diff --git a/optimizers/line_searches.py b/optimizers/line_searches.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #

diff --git a/tools/file_parser.py b/tools/file_parser.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #
@@ -85,7 +85,7 @@ class PreStringHandler:
     Read or write "delim"-separated values in front of a label (prefix-string),
     which must start the line. Both label and delimiter are passed to __init__.
     When reading the class can only handle the first occurrence of the label,
-    when writing every occurence will be handled.
+    when writing every occurrence will be handled.
 
     Example
     -------

diff --git a/tools/variable_transformation.py b/tools/variable_transformation.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #

diff --git a/variable.py b/variable.py
@@ -1,4 +1,4 @@
-#  Copyright 2019-2020, Pedro Gomes.
+#  Copyright 2019-2020, FADO Contributors (cf. AUTHORS.md)
 #
 #  This file is part of FADO.
 #