added license statements and modified documentation to reflect recent changes

Author: gjkennedy

doc/TMR_user_manual.tex

@@ -255,9 +255,9 @@ \subsection{Quad/octree-level classes}
 \item \texttt{TMROctForest *coarsen()}: Create a new forest object by coarsening all the elements within the mesh by one level, if possible. Does not create new nodes.
 \item \texttt{void refine( const int refinement[] )}: Refine the elements in the node by the specified number of levels. If a negative number is supplied, coarsen the element.
 \item \texttt{void balance( int balance\_corner=0 )}: Balance all the elements in the mesh to achieve a 2:1 balance 
-\item \texttt{void createNodes( int order=2 )}: Create all the nodes within the mesh with the given element order
+\item \texttt{void createNodes()}: Create all the nodes within the mesh
 \item \texttt{TMROctantArray* getOctsWithAttribute( const char *attr )}: Get an array of octants with the desired attribute
-\item \texttt{TMROctantArray* getNodesWithAttribute( const char *attr)}: Get an array of octant nodes with the desired attribute
+\item \texttt{int* getNodesWithAttribute( const char *attr, int *len )}: Get an array of the nodes numbers with the desired attribute
 \item \texttt{void createMeshConn( int **conn, int *nelems )}: Create and return the distributed mesh connectivity using a global ordering
 \item \texttt{void createDepNodeConn()}: Create the dependent (hanging) node connectivity
 \item \texttt{int getDepNodeConn( const int **ptr, const int **conn, const double **weights )}: Retrieve the dependent node connectivity from the octree object
@@ -314,37 +314,34 @@ \subsection{Python-level}
 mesh.mesh(htarget, opts=opts)
 \end{verbatim}
 
-
-\subsection{Mesh refinement algorithms}
+\subsection{Error estimation algorithms}
 
 There are two mesh refinement strategies that are implemented in TMR: the first is based on the strain energy norm, while the second is an adjoint-based refinement technique.
-Currently, both strategies are implemented only for 2D and mapped 2D meshes.
 The strain energy based refinement method is designed to reduce the solution error in the natural strain energy norm.
 This call takes the form:
 %
 \begin{verbatim}
-TacsScalar TMR_StrainEnergyRefine( TACSAssembler *tacs,
-                                   TMRQuadForest *forest,
-                                   double target_err,
-                                   int min_level=0, 
-                                   int max_level=TMR_MAX_LEVEL );
+double TMR_StrainEnergyErrorEst( TMRQuadForest *forest,
+                                 TACSAssembler *tacs,
+                                 TMRQuadForest *forest_refined,
+                                 TACSAssembler *tacs_refined,
+                                 double *error );
 \end{verbatim}
 %
-The forest is automatically refined based on the requested target error and the solution set in TACS.
+The forest can be refined based on the requested target error and the solution set in TACS.
 
 The adjoint-based refinement method requires a \texttt{TACSAssembler} object for both the current level of refinement and a uniformly refined version of the model. 
 The adjoint-based mesh refinement call takes the form
 \begin{verbatim}
-TacsScalar TMR_AdjointRefine( TACSAssembler *tacs,
-                              TACSAssembler *refine,
-                              TACSBVec *adjvec,
-                              TMRQuadForest *forest,
-                              double target_err,
-                              int min_level=0, 
-                              int max_level=TMR_MAX_LEVEL,
-                              TacsScalar *adj_corr=NULL );
+double TMR_AdjointErrorEst( TMRQuadForest *forest,
+                            TACSAssembler *tacs,
+                            TMRQuadForest *forest_refined,
+                            TACSAssembler *tacs_refined,
+                            TACSBVec *adjoint,
+                            double *error,
+                            double *adj_corr );
 \end{verbatim}
-The adjoint vector is supplied in \texttt{adjvec} and the target error is specified by the \texttt{target\_err} argument.
+The adjoint vector is supplied in \texttt{adjvec}.
 
 \bibliographystyle{abbrvnat}
 \bibliography{refs}

license.txt

@@ -0,0 +1,177 @@
+Apache License
+
+Version 2.0, January 2004
+
+http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
+"License" shall mean the terms and conditions for use, reproduction,
+and distribution as defined by Sections 1 through 9 of this document.
+
+"Licensor" shall mean the copyright owner or entity authorized by the
+copyright owner that is granting the License.
+
+"Legal Entity" shall mean the union of the acting entity and all other
+entities that control, are controlled by, or are under common control
+with that entity. For the purposes of this definition, "control" means
+(i) the power, direct or indirect, to cause the direction or
+management of such entity, whether by contract or otherwise, or (ii)
+ownership of fifty percent (50%) or more of the outstanding shares, or
+(iii) beneficial ownership of such entity.
+
+"You" (or "Your") shall mean an individual or Legal Entity exercising
+permissions granted by this License.
+
+"Source" form shall mean the preferred form for making modifications,
+including but not limited to software source code, documentation
+source, and configuration files.
+
+"Object" form shall mean any form resulting from mechanical
+transformation or translation of a Source form, including but not
+limited to compiled object code, generated documentation, and
+conversions to other media types.
+
+"Work" shall mean the work of authorship, whether in Source or Object
+form, made available under the License, as indicated by a copyright
+notice that is included in or attached to the work (an example is
+provided in the Appendix below).
+
+"Derivative Works" shall mean any work, whether in Source or Object
+form, that is based on (or derived from) the Work and for which the
+editorial revisions, annotations, elaborations, or other modifications
+represent, as a whole, an original work of authorship. For the
+purposes of this License, Derivative Works shall not include works
+that remain separable from, or merely link (or bind by name) to the
+interfaces of, the Work and Derivative Works thereof.
+
+"Contribution" shall mean any work of authorship, including the
+original version of the Work and any modifications or additions to
+that Work or Derivative Works thereof, that is intentionally submitted
+to Licensor for inclusion in the Work by the copyright owner or by an
+individual or Legal Entity authorized to submit on behalf of the
+copyright owner. For the purposes of this definition, "submitted"
+means any form of electronic, verbal, or written communication sent to
+the Licensor or its representatives, including but not limited to
+communication on electronic mailing lists, source code control
+systems, and issue tracking systems that are managed by, or on behalf
+of, the Licensor for the purpose of discussing and improving the Work,
+but excluding communication that is conspicuously marked or otherwise
+designated in writing by the copyright owner as "Not a Contribution."
+
+"Contributor" shall mean Licensor and any individual or Legal Entity
+on behalf of whom a Contribution has been received by Licensor and
+subsequently incorporated within the Work.
+
+2. Grant of Copyright License. Subject to the terms and conditions of
+this License, each Contributor hereby grants to You a perpetual,
+worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+copyright license to reproduce, prepare Derivative Works of, publicly
+display, publicly perform, sublicense, and distribute the Work and
+such Derivative Works in Source or Object form.
+
+3. Grant of Patent License. Subject to the terms and conditions of
+this License, each Contributor hereby grants to You a perpetual,
+worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except
+as stated in this section) patent license to make, have made, use,
+offer to sell, sell, import, and otherwise transfer the Work, where
+such license applies only to those patent claims licensable by such
+Contributor that are necessarily infringed by their Contribution(s)
+alone or by combination of their Contribution(s) with the Work to
+which such Contribution(s) was submitted. If You institute patent
+litigation against any entity (including a cross-claim or counterclaim
+in a lawsuit) alleging that the Work or a Contribution incorporated
+within the Work constitutes direct or contributory patent
+infringement, then any patent licenses granted to You under this
+License for that Work shall terminate as of the date such litigation
+is filed.
+
+4. Redistribution. You may reproduce and distribute copies of the Work
+or Derivative Works thereof in any medium, with or without
+modifications, and in Source or Object form, provided that You meet
+the following conditions:
+
+    You must give any other recipients of the Work or Derivative Works
+    a copy of this License; and
+
+    You must cause any modified files to carry prominent notices
+    stating that You changed the files; and
+
+    You must retain, in the Source form of any Derivative Works that
+    You distribute, all copyright, patent, trademark, and attribution
+    notices from the Source form of the Work, excluding those notices
+    that do not pertain to any part of the Derivative Works; and
+
+    If the Work includes a "NOTICE" text file as part of its
+    distribution, then any Derivative Works that You distribute must
+    include a readable copy of the attribution notices contained
+    within such NOTICE file, excluding those notices that do not
+    pertain to any part of the Derivative Works, in at least one of
+    the following places: within a NOTICE text file distributed as
+    part of the Derivative Works; within the Source form or
+    documentation, if provided along with the Derivative Works; or,
+    within a display generated by the Derivative Works, if and
+    wherever such third-party notices normally appear. The contents of
+    the NOTICE file are for informational purposes only and do not
+    modify the License. You may add Your own attribution notices
+    within Derivative Works that You distribute, alongside or as an
+    addendum to the NOTICE text from the Work, provided that such
+    additional attribution notices cannot be construed as modifying
+    the License.
+
+    You may add Your own copyright statement to Your modifications and
+    may provide additional or different license terms and conditions
+    for use, reproduction, or distribution of Your modifications, or
+    for any such Derivative Works as a whole, provided Your use,
+    reproduction, and distribution of the Work otherwise complies with
+    the conditions stated in this License.
+
+5. Submission of Contributions. Unless You explicitly state otherwise,
+any Contribution intentionally submitted for inclusion in the Work by
+You to the Licensor shall be under the terms and conditions of this
+License, without any additional terms or conditions. Notwithstanding
+the above, nothing herein shall supersede or modify the terms of any
+separate license agreement you may have executed with Licensor
+regarding such Contributions.
+
+6. Trademarks. This License does not grant permission to use the trade
+names, trademarks, service marks, or product names of the Licensor,
+except as required for reasonable and customary use in describing the
+origin of the Work and reproducing the content of the NOTICE file.
+
+7. Disclaimer of Warranty. Unless required by applicable law or agreed
+to in writing, Licensor provides the Work (and each Contributor
+provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied, including, without
+limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT,
+MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely
+responsible for determining the appropriateness of using or
+redistributing the Work and assume any risks associated with Your
+exercise of permissions under this License.
+
+8. Limitation of Liability. In no event and under no legal theory,
+whether in tort (including negligence), contract, or otherwise, unless
+required by applicable law (such as deliberate and grossly negligent
+acts) or agreed to in writing, shall any Contributor be liable to You
+for damages, including any direct, indirect, special, incidental, or
+consequential damages of any character arising as a result of this
+License or out of the use or inability to use the Work (including but
+not limited to damages for loss of goodwill, work stoppage, computer
+failure or malfunction, or any and all other commercial damages or
+losses), even if such Contributor has been advised of the possibility
+of such damages.
+
+9. Accepting Warranty or Additional Liability. While redistributing
+the Work or Derivative Works thereof, You may choose to offer, and
+charge a fee for, acceptance of support, warranty, indemnity, or other
+liability obligations and/or rights consistent with this
+License. However, in accepting such obligations, You may act only on
+Your own behalf and on Your sole responsibility, not on behalf of any
+other Contributor, and only if You agree to indemnify, defend, and
+hold each Contributor harmless for any liability incurred by, or
+claims asserted against, such Contributor by reason of your accepting
+any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS

src/TMRBase.cpp

@@ -1,13 +1,29 @@
+/*
+  This file is part of the package TMR for adaptive mesh refinement.
+
+  Copyright (C) 2015 Georgia Tech Research Corporation.
+  Additional copyright (C) 2015 Graeme Kennedy.
+  All rights reserved.
+
+  TMR is licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this software except in compliance with the License.
+  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+  
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+*/
+
 #include "TMRBase.h"
 #include "TMRQuadrant.h"
 #include "TMROctant.h"
 #include <stddef.h>
 #include <string.h>
 
-/*
-  Copyright (c) 2016 Graeme Kennedy. All rights reserved. 
-*/
-
 // Static flag to test if TMR is initialized or not
 static int TMR_is_initialized = 0;
 

src/TMRBase.h

@@ -1,10 +1,26 @@
-#ifndef TMR_BASE_H
-#define TMR_BASE_H
-
 /*
-  Copyright (c) 2016 Graeme Kennedy. All rights reserved. 
+  This file is part of the package TMR for adaptive mesh refinement.
+
+  Copyright (C) 2015 Georgia Tech Research Corporation.
+  Additional copyright (C) 2015 Graeme Kennedy.
+  All rights reserved.
+
+  TMR is licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this software except in compliance with the License.
+  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+  
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
 */
 
+#ifndef TMR_BASE_H
+#define TMR_BASE_H
+
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>

src/TMRBspline.cpp

@@ -1,3 +1,23 @@
+/*
+  This file is part of the package TMR for adaptive mesh refinement.
+
+  Copyright (C) 2015 Georgia Tech Research Corporation.
+  Additional copyright (C) 2015 Graeme Kennedy.
+  All rights reserved.
+
+  TMR is licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this software except in compliance with the License.
+  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+  
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+*/
+
 #include "TMRBspline.h"
 #include "tmrlapack.h"
 #include <math.h>

src/TMRBspline.h

@@ -1,3 +1,23 @@
+/*
+  This file is part of the package TMR for adaptive mesh refinement.
+
+  Copyright (C) 2015 Georgia Tech Research Corporation.
+  Additional copyright (C) 2015 Graeme Kennedy.
+  All rights reserved.
+
+  TMR is licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this software except in compliance with the License.
+  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+  
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+*/
+
 #ifndef TMR_BSPLINE_H
 #define TMR_BSPLINE_H
 

src/TMRGeometry.cpp

@@ -1,3 +1,23 @@
+/*
+  This file is part of the package TMR for adaptive mesh refinement.
+
+  Copyright (C) 2015 Georgia Tech Research Corporation.
+  Additional copyright (C) 2015 Graeme Kennedy.
+  All rights reserved.
+
+  TMR is licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this software except in compliance with the License.
+  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+  
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+*/
+
 #include "TMRGeometry.h"
 #include "TMRMesh.h"
 #include <math.h>