update license to L-GPL and add user_doc/Maze.md

regtest/.gitignore

@@ -13,6 +13,7 @@
 !/drr
 !/logmfd
 !/mapping
+!/maze
 !/multicolvar
 !/python
 !/secondarystructure

src/.gitignore

@@ -29,6 +29,7 @@
 !/maketools
 !/mapping
 !/manyrestraints
+!/maze
 !/molfile
 !/multicolvar
 !/python

src/maze/COPYRIGHT

@@ -1,17 +1,19 @@
 Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
 
+See http://www.maze-code.github.io for more information.
+
 This file is part of maze.
 
 maze is free software: you can redistribute it and/or modify it under the
-terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
-version.
+terms of the GNU Lesser General Public License as published by the Free 
+Software Foundation, either version 3 of the License, or (at your option) 
+any later version.
 
 maze is distributed in the hope that it will be useful, but WITHOUT ANY
 WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 FOR A PARTICULAR PURPOSE.
 
-See the GNU General Public License for more details.
+See the GNU Lesser General Public License for more details.
 
-You should have received a copy of the GNU General Public License along with
-maze. If not, see <https://www.gnu.org/licenses/>.
+You should have received a copy of the GNU Lesser General Public License 
+along with maze. If not, see <https://www.gnu.org/licenses/>.

src/maze/Core.cpp

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Core.cpp

src/maze/Core.h

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Core.h

src/maze/Loss.cpp

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Loss.cpp

src/maze/Loss.h

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Loss.h

src/maze/Member.cpp

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Member.cpp

src/maze/Member.h

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Member.h

src/maze/Memetic.cpp

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Memetic.cpp

src/maze/Memetic.h

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Memetic.h

src/maze/Optimizer.cpp

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Optimizer.cpp

src/maze/Optimizer.h

@@ -1,24 +1,25 @@
 /*
- *
  * Copyright (c) 2019 Jakub Rydzewski ([email protected]). All rights reserved.
  *
+ * See http://www.maze-code.github.io for more information.
+ *
  * This file is part of maze.
  *
  * maze is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
+ * terms of the GNU Lesser General Public License as published by the Free 
+ * Software Foundation, either version 3 of the License, or (at your option) 
+ * any later version.
  *
  * maze is distributed in the hope that it will be useful, but WITHOUT ANY
  * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  * FOR A PARTICULAR PURPOSE.
  *
- * See the GNU General Public License for more details.
+ * See the GNU Lesser General Public License for more details.
  *
- * You should have received a copy of the GNU General Public License along with
- * maze. If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License 
+ * along with maze. If not, see <https://www.gnu.org/licenses/>.
  *
- */
+ */ 
 
 /**
  * @file Optimizer.h