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Updated the rest of headers and copyright disclaimers.

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commit 294246ee032c8d1b8863634500f62f7beba1324c 1 parent 11d8cb5
@olenz olenz authored
Showing with 428 additions and 352 deletions.
  1. +16 −13 doc/tutorials/01-lennard_jones/scripts/blockfile_read.tcl
  2. +16 −13 doc/tutorials/01-lennard_jones/scripts/lj_functions.tcl
  3. +16 −19 doc/tutorials/01-lennard_jones/scripts/lj_tutorial.tcl
  4. +16 −14 doc/tutorials/01-lennard_jones/scripts/msd.tcl
  5. +16 −13 doc/tutorials/01-lennard_jones/scripts/rdf.tcl
  6. +16 −15 doc/tutorials/01-lennard_jones/scripts/vacf.tcl
  7. +16 −13 doc/tutorials/01-lennard_jones/solutions/blockfile_read.tcl
  8. +16 −13 doc/tutorials/01-lennard_jones/solutions/lj_functions.tcl
  9. +16 −13 doc/tutorials/01-lennard_jones/solutions/lj_tutorial.tcl
  10. +16 −13 doc/tutorials/01-lennard_jones/solutions/msd.tcl
  11. +16 −13 doc/tutorials/01-lennard_jones/solutions/rdf.tcl
  12. +17 −16 doc/tutorials/01-lennard_jones/solutions/vacf.tcl
  13. +16 −15 doc/tutorials/01-lennard_jones/solutions/vacf_vec.tcl
  14. +1 −1  maintainer/espresso-2.1.2j.ebuild
  15. +2 −1  maintainer/files_with_header.sh
  16. +28 −11 maintainer/find_missing_header.sh
  17. +9 −12 maintainer/update_header.sh
  18. +18 −16 packages/mbtools/doc/analysis.html
  19. +18 −18 packages/mbtools/doc/install.html
  20. +18 −18 packages/mbtools/doc/maintcl.html
  21. +18 −18 packages/mbtools/doc/manual.html
  22. +18 −18 packages/mbtools/doc/mmsg.html
  23. +18 −18 packages/mbtools/doc/overview.html
  24. +18 −18 packages/mbtools/doc/system_generation.html
  25. +18 −18 packages/mbtools/doc/utils.html
  26. +17 −0 scripts/dielectrics.tcl
  27. +17 −1 testsuite/dielectric_test.tcl
  28. +1 −1  testsuite/iccp3m.tcl
View
29 doc/tutorials/01-lennard_jones/scripts/blockfile_read.tcl
@@ -1,17 +1,20 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#
# Offline Analysis
#
View
29 doc/tutorials/01-lennard_jones/scripts/lj_functions.tcl
@@ -1,17 +1,20 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#############################################################
# #
# Functions (TCL procedures used in lj_tutorial ) #
View
35 doc/tutorials/01-lennard_jones/scripts/lj_tutorial.tcl
@@ -1,33 +1,30 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#############################################################
# #
# Sample System Lennard Jones Liquid #
# #
-# LJ Tutorial Extented by #
-# SimBio Group, Frankfurt am Main #
-# 2007 June #
-# #
# LJ System Studied in the Book #
# Understanding Molecular Simulations #
# Frankel & Smith , 2nd Edition #
# Chapter 4, Case Study 4 #
# #
#############################################################
-
-
# Source (call) functions to be used
source lj_functions.tcl
View
30 doc/tutorials/01-lennard_jones/scripts/msd.tcl
@@ -1,17 +1,19 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
-#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Offline Analysis for Mean Square Deviation
#
View
29 doc/tutorials/01-lennard_jones/scripts/rdf.tcl
@@ -1,17 +1,20 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#
# Offline Analysis for Radial Distribution Function
#
View
31 doc/tutorials/01-lennard_jones/scripts/vacf.tcl
@@ -1,21 +1,22 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#
# Simple Velocity Auto-Correlation-Function; Direct Method
-# February 2007
-# by m@suzen
#
set filename "data/sim_info.dat"
set in [open "$filename" "r"]
View
29 doc/tutorials/01-lennard_jones/solutions/blockfile_read.tcl
@@ -1,17 +1,20 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#
# Offline Analysis
#
View
29 doc/tutorials/01-lennard_jones/solutions/lj_functions.tcl
@@ -1,17 +1,20 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#############################################################
# #
# Functions (TCL procedures used in lj_tutorial ) #
View
29 doc/tutorials/01-lennard_jones/solutions/lj_tutorial.tcl
@@ -1,17 +1,20 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#############################################################
# #
# Sample System Lennard Jones Liquid #
View
29 doc/tutorials/01-lennard_jones/solutions/msd.tcl
@@ -1,17 +1,20 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#
# Offline Analysis for Mean Square Deviation
#
View
29 doc/tutorials/01-lennard_jones/solutions/rdf.tcl
@@ -1,17 +1,20 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#
# Offline Analysis for Radial Distribution Function
#
View
33 doc/tutorials/01-lennard_jones/solutions/vacf.tcl
@@ -1,21 +1,22 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
-#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
#
# Simple Velocity Auto-Correlation-Function; Direct Method
-# February 2007
-# by m@suzen
#
set filename "data/sim_info.dat"
set in [open "$filename" "r"]
View
31 doc/tutorials/01-lennard_jones/solutions/vacf_vec.tcl
@@ -1,21 +1,22 @@
-#!/bin/sh
-# tricking... the line after a these comments are interpreted as standard shell script \
-exec $ESPRESSO_SOURCE/Espresso $0 $*
+# Copyright (C) 2010,2011,2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-# This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
-# It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
-# and by which you are legally bound while utilizing this file in any form or way.
-# There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# You should have received a copy of that license along with this program;
-# if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
-# write to
-# Max-Planck-Institute for Polymer Research, Theory Group.
-# Copyright (C) 2012 The ESPResSo project
-# Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
#
# Simple Velocity Auto-Correlation-Function; Direct Method
-# February 2007
-# by m@suzen
#
set filename "data/sim_info.dat"
set in [open "$filename" "r"]
View
2  maintainer/espresso-2.1.2j.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2010,2011 The ESPResSo project
+# Copyright 2010,2011,2012 The ESPResSo project
# Copyright 1999-2009 Gentoo Foundation
#
# This file is part of ESPResSo.
View
3  maintainer/files_with_header.sh
@@ -22,4 +22,5 @@ egrep -v '^testsuite/configs/|^old/' |
egrep -v '(ChangeLog|AUTHORS|COPYING|bootstrap\.sh)' |
egrep -v '(\.gitignore|pkgIndex\.tcl)' |
egrep -v '(config\.guess|config\.sub|install-sh)' |
-egrep -v '(Doxyfile|latexmk\.1|latexmkrc|assemble_quickref\.awk)'
+egrep -v '(Doxyfile|latexmk\.1|latexmkrc|assemble_quickref\.awk|doc/misc/homepage/palette.html)' |
+egrep -v '(featurelist)'
View
39 maintainer/find_missing_header.sh
@@ -1,3 +1,4 @@
+#! /bin/bash -x
# Copyright (C) 2012 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
@@ -21,24 +22,40 @@
files=`sh maintainer/files_with_header.sh`
num_files=`echo $files | wc -w`
+current_year=`date +%Y`
echo "Examining $num_files files."
+echo
-current_year=`date +%Y`
-echo "Checking for copyright disclaimer missing the current year $current_year"
-echo "-------------------------------------------------------------------"
-egrep -L "Copyright.*$current_year" $files
+missing_current_copyright=`egrep -IL "Copyright.*$current_year" $files`
+
+echo "Copyright disclaimer missing the current year $current_year"
+echo "--------------------------------------------------"
+if [ -n "$missing_current_copyright" ]; then
+ egrep -Il "Copyright" $missing_current_copyright
+else
+ echo "NONE"
+fi
echo
-echo "Checking for missing copyright disclaimer"
-echo "-----------------------------------------"
-egrep -L "Copyright" $files
+echo "Missing copyright disclaimer"
+echo "----------------------------"
+if [ -n "$missing_current_copyright" ]; then
+ egrep -IL "Copyright" $missing_current_copyright
+else
+ echo "NONE"
+fi
echo
-echo "Checking for missing GPL/simple header"
-echo "--------------------------------------"
-no_gpl_files=`egrep -L "(ESPResSo|This program) is free software" $files`
-egrep -L "Copying and distribution of this file" $no_gpl_files
+echo "Missing GPL/simple header"
+echo "-------------------------"
+nolicense=`egrep -IL "((ESPResSo|This program) is free software|Copying and distribution of this file)" $files`
+if [ -n "$nolicense" ]; then
+ echo $nolicense
+else
+ echo "NONE"
+fi
echo
+
View
21 maintainer/update_header.sh
@@ -35,27 +35,24 @@ files=`egrep -l "Copyright" $files`
num_files=`echo $files | wc -w`
echo " $num_files files."
-echo "Files that are missing the project and the current year..."
-files=`egrep -L "Copyright.*$current_year.*The ESPResSo project" $files`
-num_files=`echo $files | wc -w`
-echo " $num_files files."
+echo "Files that are missing the current year ($current_year) in the copyright disclaimer(s)..."
+files=`egrep -L "Copyright.*$current_year" $files`
+for file in $files; do
+ echo " $file"
+done
-noproject_files=`egrep -L "Copyright.*The ESPResSo project" $files`
noyear_files=`egrep -l "Copyright.*The ESPResSo project" $files`
-
-echo "Files that are missing the current year..."
-num_files=`echo $noyear_files | wc -w`
-echo " $num_files files."
-echo " Adding year to copyright disclaimer..."
+echo " Adding current year to project copyright disclaimer..."
echo " \"$current_year\""
tmpfile=`mktemp`
for file in $noyear_files; do
echo " $file"
- perl -pe "if (!\$done) { s/(Copyright\s+(?:\(C\)\s+)\d+(?:\s*,\s*\d+)*)(\s+The ESPResSo project)/\1,2012\2/ and \$done=1; }" $file > $tmpfile
+ perl -pe "if (!\$done) { s/(Copyright\s+(?:\(C\)\s+)?\d+(?:\s*,\s*\d+)*)(\s+The ESPResSo project)/\1,2012\2/ and \$done=1; }" $file > $tmpfile
cat $tmpfile > $file
done
-echo "Files that are missing the project..."
+noproject_files=`egrep -L "Copyright.*The ESPResSo project" $files`
+echo "Files that are missing the project copyright disclaimer..."
num_files=`echo $noproject_files | wc -w`
echo " $num_files files."
echo " Adding project copyright disclaimer..."
View
34 packages/mbtools/doc/analysis.html
@@ -1,4 +1,22 @@
<head>
+<!--
+Copyright (C) 2010,2011,2012 The ESPResSo project
+
+This file is part of ESPResSo.
+
+ESPResSo 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.
+
+ESPResSo 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.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
<link href="./docustyle.css" rel="stylesheet" type="text/css">
</head>
<title> mbtools analysis Documentation</title>
@@ -288,19 +306,3 @@ <h2 class=center > mbtools Analysis </h2>
</body>
-<!--
-This file is part of ESPResSo.
-
-ESPResSo 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.
-
-ESPResSo 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.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
--->
View
36 packages/mbtools/doc/install.html
@@ -1,4 +1,22 @@
<head>
+<!--
+Copyright (C) 2010,2011,2012 The ESPResSo project
+
+This file is part of ESPResSo.
+
+ESPResSo 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.
+
+ESPResSo 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.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
<link href="./docustyle.css" rel="stylesheet" type="text/css">
</head>
<title> mbtools Installation Guide</title>
@@ -90,21 +108,3 @@ <h2 class=center > Getting Started</h2>
</body>
-
-
-<!--
-This file is part of ESPResSo.
-
-ESPResSo 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.
-
-ESPResSo 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.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
--->
View
36 packages/mbtools/doc/maintcl.html
@@ -1,4 +1,22 @@
<head>
+<!--
+Copyright (C) 2010,2011,2012 The ESPResSo project
+
+This file is part of ESPResSo.
+
+ESPResSo 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.
+
+ESPResSo 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.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
<link href="./docustyle.css" rel="stylesheet" type="text/css">
</head>
<title> the main.tcl file</title>
@@ -72,21 +90,3 @@ <h2 class=center > The main.tcl file</h2>
</body>
-
-
-<!--
-This file is part of ESPResSo.
-
-ESPResSo 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.
-
-ESPResSo 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.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
--->
View
36 packages/mbtools/doc/manual.html
@@ -1,4 +1,22 @@
<head>
+<!--
+Copyright (C) 2010,2011,2012 The ESPResSo project
+
+This file is part of ESPResSo.
+
+ESPResSo 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.
+
+ESPResSo 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.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
<link href="./style.css" rel="stylesheet" type="text/css">
</head>
<title> mbtools manual </title>
@@ -41,21 +59,3 @@ <h2 class = center> mbtools Manual </h2>
</body>
-
-
-<!--
-This file is part of ESPResSo.
-
-ESPResSo 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.
-
-ESPResSo 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.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
--->
View
36 packages/mbtools/doc/mmsg.html
@@ -1,4 +1,22 @@
<head>
+<!--
+Copyright (C) 2010,2011,2012 The ESPResSo project
+
+This file is part of ESPResSo.
+
+ESPResSo 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.
+
+ESPResSo 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.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
<link href="./docustyle.css" rel="stylesheet" type="text/css">
</head>
<title> mmsg Documentation</title>
@@ -121,21 +139,3 @@ <h2 class=center > mmsg </h2>
</li>
</ul>
</body>
-
-
-<!--
-This file is part of ESPResSo.
-
-ESPResSo 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.
-
-ESPResSo 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.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
--->
View
36 packages/mbtools/doc/overview.html
@@ -1,4 +1,22 @@
<head>
+<!--
+Copyright (C) 2010,2011,2012 The ESPResSo project
+
+This file is part of ESPResSo.
+
+ESPResSo 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.
+
+ESPResSo 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.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
<link href="./style.css" rel="stylesheet" type="text/css">
</head>
<title> mbtools overview</title>
@@ -82,21 +100,3 @@
</body>
-
-
-<!--
-This file is part of ESPResSo.
-
-ESPResSo 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.
-
-ESPResSo 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.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
--->
View
36 packages/mbtools/doc/system_generation.html
@@ -1,4 +1,22 @@
<head>
+<!--
+Copyright (C) 2010,2011,2012 The ESPResSo project
+
+This file is part of ESPResSo.
+
+ESPResSo 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.
+
+ESPResSo 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.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
<link href="./docustyle.css" rel="stylesheet" type="text/css">
</head>
<title> mbtools system_generation Documentation </title>
@@ -402,21 +420,3 @@ <h2 class=center > mbtools system_generation </h2>
</ul>
</body>
-
-
-<!--
-This file is part of ESPResSo.
-
-ESPResSo 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.
-
-ESPResSo 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.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
--->
View
36 packages/mbtools/doc/utils.html
@@ -1,4 +1,22 @@
<head>
+<!--
+Copyright (C) 2010,2011,2012 The ESPResSo project
+
+This file is part of ESPResSo.
+
+ESPResSo 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.
+
+ESPResSo 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.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+-->
<link href="./docustyle.css" rel="stylesheet" type="text/css">
</head>
<title> mbtools utils documentation </title>
@@ -410,21 +428,3 @@ <h2 class=center > mbtools utils </h2>
</div>
</li>
</ul>
-
-
-<!--
-This file is part of ESPResSo.
-
-ESPResSo 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.
-
-ESPResSo 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.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
--->
View
17 scripts/dielectrics.tcl
@@ -1,3 +1,20 @@
+# Copyright (C) 2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+#
proc dielectric_wall { args } {
global n_induced_charges icc_areas icc_normals icc_epsilons icc_sigmas
View
18 testsuite/dielectric_test.tcl
@@ -1,4 +1,20 @@
-
+# Copyright (C) 2012 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo 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.
+#
+# ESPResSo 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+#
source "tests_common.tcl"
require_feature "CONSTRAINTS"
View
2  testsuite/iccp3m.tcl
@@ -1,4 +1,4 @@
-# Copyright (C) 2010,2011 The ESPResSo project
+# Copyright (C) 2010,2011,2012 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
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