From 8c395a1b601c6d872a38d516a1e86f5f433ca9da Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 7 Dec 2012 23:00:25 +0100
Subject: [PATCH] Updated all .h files
The guard "ifndef/define" has been updated so as to also include the
module name. This is important as it will allow files with the same name
to be used in different directories. Modification was done automatically
using header.sh - just run it routinely to keep names consistent
---
src/analysis/Analysis.cpp | 6 ++--
src/analysis/Analysis.h | 4 +--
src/bias/ActionRegister.h | 24 ++++++++++++++
src/bias/Bias.h | 4 +--
src/cltools/CLTool.h | 24 ++++++++++++++
src/cltools/CLToolRegister.h | 24 ++++++++++++++
src/colvar/ActionRegister.h | 24 ++++++++++++++
src/colvar/Colvar.h | 24 ++++++++++++++
src/colvar/ColvarPathMSDBase.h | 5 ++-
src/core/Action.h | 4 +--
src/core/ActionAtomistic.h | 4 +--
src/core/ActionPilot.h | 4 +--
src/core/ActionRegister.h | 4 +--
src/core/ActionSet.h | 4 +--
src/core/ActionSetup.h | 4 +--
src/core/ActionWithArguments.h | 4 +--
src/core/ActionWithValue.h | 4 +--
src/core/ActionWithVirtualAtom.h | 4 +--
src/core/Atoms.h | 4 +--
src/core/CLTool.h | 5 ++-
src/core/CLToolMain.h | 5 ++-
src/core/CLToolRegister.h | 4 +--
src/core/Colvar.h | 4 +--
src/core/CubicInterpolation.h | 4 +--
src/core/ExchangePatterns.h | 4 +--
src/core/FlexibleBin.h | 4 +--
src/core/GREX.h | 4 +--
src/core/MDAtoms.h | 4 +--
src/core/PlumedMain.h | 4 +--
src/core/SetupMolInfo.h | 4 +--
src/core/TargetDist.h | 4 +--
src/core/Value.h | 4 +--
src/core/WithCmd.h | 4 +--
src/function/ActionRegister.h | 24 ++++++++++++++
src/function/Function.h | 4 +--
src/header.sh | 32 +++++++++++++++++++
src/imd/ActionIMD.cpp | 21 ++++++++++++
src/multicolvar/ActionVolume.h | 4 +--
src/multicolvar/MultiColvar.h | 4 +--
.../MultiColvarSecondaryStructureRMSD.h | 4 +--
src/tools/Angle.h | 4 +--
src/tools/AtomNumber.h | 4 +--
src/tools/Citations.h | 4 +--
src/tools/DLLoader.h | 4 +--
src/tools/DRMSD.h | 4 +--
src/tools/DynamicList.h | 4 +--
src/tools/Grid.h | 4 +--
src/tools/HistogramBead.h | 4 +--
src/tools/Kearsley.h | 4 +--
src/tools/KernelFunctions.cpp | 21 ++++++++++++
src/tools/KernelFunctions.h | 12 +++----
src/tools/Keywords.h | 4 +--
src/tools/LatticeReduction.h | 4 +--
src/tools/Log.h | 4 +--
src/tools/Matrix.h | 4 +--
src/tools/MatrixSquareBracketsAccess.h | 4 +--
src/tools/NeighborList.h | 4 +--
src/tools/OptimalAlignment.h | 4 +--
src/tools/PDB.h | 4 +--
src/tools/Pbc.h | 4 +--
src/tools/PlumedCommunicator.h | 4 +--
src/tools/PlumedException.h | 4 +--
src/tools/PlumedFile.h | 4 +--
src/tools/RMSD.h | 4 +--
src/tools/Random.h | 4 +--
src/tools/Stopwatch.h | 4 +--
src/tools/SwitchingFunction.h | 4 +--
src/tools/Tensor.h | 4 +--
src/tools/Tools.h | 4 +--
src/tools/Torsion.h | 4 +--
src/tools/Units.h | 4 +--
src/tools/Vector.h | 4 +--
src/vessel-base/ActionWithVessel.h | 4 +--
src/vessel-base/NormedSumVessel.h | 4 +--
src/vessel-base/SumVessel.h | 4 +--
src/vessel-base/Vessel.h | 4 +--
src/vessel-base/VesselAccumulator.h | 4 +--
src/vessel-base/VesselRegister.h | 4 +--
src/vessel-base/VesselStoreAllValues.h | 4 +--
src/vessel-base/VesselValueAccess.h | 4 +--
src/wrapper/Plumed.h | 4 +--
81 files changed, 367 insertions(+), 152 deletions(-)
diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index d12c7b469..10b3e7204 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -1,11 +1,11 @@
/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Copyright (c) 2012 The plumed team
(see the PEOPLE file at the root of the distribution for a list of names)
-
+
See http://www.plumed-code.org for more information.
-
+
This file is part of plumed, version 2.0.
-
+
plumed is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
diff --git a/src/analysis/Analysis.h b/src/analysis/Analysis.h
index 1c5534ff7..8b59cecca 100644
--- a/src/analysis/Analysis.h
+++ b/src/analysis/Analysis.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Analysis_h
-#define __PLUMED_Colvar_h
+#ifndef __PLUMED_analysis_Analysis_h
+#define __PLUMED_analysis_Analysis_h
#include "core/ActionPilot.h"
#include "core/ActionWithArguments.h"
diff --git a/src/bias/ActionRegister.h b/src/bias/ActionRegister.h
index 732046c8f..c0f89150a 100644
--- a/src/bias/ActionRegister.h
+++ b/src/bias/ActionRegister.h
@@ -1 +1,25 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the 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.
+
+ plumed 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_bias_ActionRegister_h
+#define __PLUMED_bias_ActionRegister_h
#include "core/ActionRegister.h"
+#endif
diff --git a/src/bias/Bias.h b/src/bias/Bias.h
index 68f126135..496205dea 100644
--- a/src/bias/Bias.h
+++ b/src/bias/Bias.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Bias_h
-#define __PLUMED_Bias_h
+#ifndef __PLUMED_bias_Bias_h
+#define __PLUMED_bias_Bias_h
#include "core/ActionPilot.h"
#include "core/ActionWithValue.h"
diff --git a/src/cltools/CLTool.h b/src/cltools/CLTool.h
index ec6cf24fb..b043e98ba 100644
--- a/src/cltools/CLTool.h
+++ b/src/cltools/CLTool.h
@@ -1 +1,25 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the 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.
+
+ plumed 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_cltools_CLTool_h
+#define __PLUMED_cltools_CLTool_h
#include "core/CLTool.h"
+#endif
diff --git a/src/cltools/CLToolRegister.h b/src/cltools/CLToolRegister.h
index 024736faf..f3718481b 100644
--- a/src/cltools/CLToolRegister.h
+++ b/src/cltools/CLToolRegister.h
@@ -1 +1,25 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the 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.
+
+ plumed 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_cltools_CLToolRegister_h
+#define __PLUMED_cltools_CLToolRegister_h
#include "core/CLToolRegister.h"
+#endif
diff --git a/src/colvar/ActionRegister.h b/src/colvar/ActionRegister.h
index 732046c8f..1a7b61b8f 100644
--- a/src/colvar/ActionRegister.h
+++ b/src/colvar/ActionRegister.h
@@ -1 +1,25 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the 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.
+
+ plumed 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_colvar_ActionRegister_h
+#define __PLUMED_colvar_ActionRegister_h
#include "core/ActionRegister.h"
+#endif
diff --git a/src/colvar/Colvar.h b/src/colvar/Colvar.h
index fab079d4d..506299b8e 100644
--- a/src/colvar/Colvar.h
+++ b/src/colvar/Colvar.h
@@ -1 +1,25 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the 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.
+
+ plumed 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_colvar_Colvar_h
+#define __PLUMED_colvar_Colvar_h
#include "core/Colvar.h"
+#endif
diff --git a/src/colvar/ColvarPathMSDBase.h b/src/colvar/ColvarPathMSDBase.h
index eb514bda0..7882e1cb5 100644
--- a/src/colvar/ColvarPathMSDBase.h
+++ b/src/colvar/ColvarPathMSDBase.h
@@ -19,9 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-
-#ifndef __PLUMED_ColvarPathMSDBase
-#define __PLUMED_ColvarPathMSDBase
+#ifndef __PLUMED_colvar_ColvarPathMSDBase_h
+#define __PLUMED_colvar_ColvarPathMSDBase_h
#include <cmath>
diff --git a/src/core/Action.h b/src/core/Action.h
index 2e8328645..3be08dae5 100644
--- a/src/core/Action.h
+++ b/src/core/Action.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Action_h
-#define __PLUMED_Action_h
+#ifndef __PLUMED_core_Action_h
+#define __PLUMED_core_Action_h
#include <vector>
#include <string>
#include <set>
diff --git a/src/core/ActionAtomistic.h b/src/core/ActionAtomistic.h
index f05cfe2d7..48960bacf 100644
--- a/src/core/ActionAtomistic.h
+++ b/src/core/ActionAtomistic.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionAtomistic_h
-#define __PLUMED_ActionAtomistic_h
+#ifndef __PLUMED_core_ActionAtomistic_h
+#define __PLUMED_core_ActionAtomistic_h
#include "Action.h"
#include "tools/Tensor.h"
diff --git a/src/core/ActionPilot.h b/src/core/ActionPilot.h
index 42b337780..ebcf24da8 100644
--- a/src/core/ActionPilot.h
+++ b/src/core/ActionPilot.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionPilot_h
-#define __PLUMED_ActionPilot_h
+#ifndef __PLUMED_core_ActionPilot_h
+#define __PLUMED_core_ActionPilot_h
#include "Action.h"
diff --git a/src/core/ActionRegister.h b/src/core/ActionRegister.h
index 7fab120c8..3734bbd33 100644
--- a/src/core/ActionRegister.h
+++ b/src/core/ActionRegister.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionRegister_h
-#define __PLUMED_ActionRegister_h
+#ifndef __PLUMED_core_ActionRegister_h
+#define __PLUMED_core_ActionRegister_h
#include <string>
#include <map>
diff --git a/src/core/ActionSet.h b/src/core/ActionSet.h
index c997d9c51..0e9aceeae 100644
--- a/src/core/ActionSet.h
+++ b/src/core/ActionSet.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionSet_h
-#define __PLUMED_ActionSet_h
+#ifndef __PLUMED_core_ActionSet_h
+#define __PLUMED_core_ActionSet_h
#include "Action.h"
diff --git a/src/core/ActionSetup.h b/src/core/ActionSetup.h
index 565c90539..725fb2fa0 100644
--- a/src/core/ActionSetup.h
+++ b/src/core/ActionSetup.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionSetup_h
-#define __PLUMED_ActionSetup_h
+#ifndef __PLUMED_core_ActionSetup_h
+#define __PLUMED_core_ActionSetup_h
#include "Action.h"
diff --git a/src/core/ActionWithArguments.h b/src/core/ActionWithArguments.h
index 85d9e0b78..891769fdd 100644
--- a/src/core/ActionWithArguments.h
+++ b/src/core/ActionWithArguments.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionWithArguments_h
-#define __PLUMED_ActionWithArguments_h
+#ifndef __PLUMED_core_ActionWithArguments_h
+#define __PLUMED_core_ActionWithArguments_h
#include "Action.h"
#include "Value.h"
diff --git a/src/core/ActionWithValue.h b/src/core/ActionWithValue.h
index 95e0fffa6..2bb744a9a 100644
--- a/src/core/ActionWithValue.h
+++ b/src/core/ActionWithValue.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionWithValue_h
-#define __PLUMED_ActionWithValue_h
+#ifndef __PLUMED_core_ActionWithValue_h
+#define __PLUMED_core_ActionWithValue_h
#include "Action.h"
#include "Value.h"
diff --git a/src/core/ActionWithVirtualAtom.h b/src/core/ActionWithVirtualAtom.h
index 5e008467d..cbff60063 100644
--- a/src/core/ActionWithVirtualAtom.h
+++ b/src/core/ActionWithVirtualAtom.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionWithVirtualAtom_h
-#define __PLUMED_ActionWithVirtualAtom_h
+#ifndef __PLUMED_core_ActionWithVirtualAtom_h
+#define __PLUMED_core_ActionWithVirtualAtom_h
#include "ActionAtomistic.h"
#include "tools/AtomNumber.h"
diff --git a/src/core/Atoms.h b/src/core/Atoms.h
index be61dc562..b048b7619 100644
--- a/src/core/Atoms.h
+++ b/src/core/Atoms.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Atoms_h
-#define __PLUMED_Atoms_h
+#ifndef __PLUMED_core_Atoms_h
+#define __PLUMED_core_Atoms_h
#include "tools/PlumedCommunicator.h"
#include "tools/Tensor.h"
diff --git a/src/core/CLTool.h b/src/core/CLTool.h
index 16ca6b166..abe404a31 100644
--- a/src/core/CLTool.h
+++ b/src/core/CLTool.h
@@ -19,9 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-
-#ifndef __PLUMED_CLTool_h
-#define __PLUMED_CLTool_h
+#ifndef __PLUMED_core_CLTool_h
+#define __PLUMED_core_CLTool_h
#include <cstdio>
#include <vector>
#include <string>
diff --git a/src/core/CLToolMain.h b/src/core/CLToolMain.h
index 405d735b3..279d388f8 100644
--- a/src/core/CLToolMain.h
+++ b/src/core/CLToolMain.h
@@ -19,9 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-
-#ifndef __PLUMED_CLToolMain_h
-#define __PLUMED_CLToolMain_h
+#ifndef __PLUMED_core_CLToolMain_h
+#define __PLUMED_core_CLToolMain_h
#include <cstdio>
#include <vector>
#include <string>
diff --git a/src/core/CLToolRegister.h b/src/core/CLToolRegister.h
index 739acb19e..d4e676295 100644
--- a/src/core/CLToolRegister.h
+++ b/src/core/CLToolRegister.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_CLToolRegister_h
-#define __PLUMED_CLToolRegister_h
+#ifndef __PLUMED_core_CLToolRegister_h
+#define __PLUMED_core_CLToolRegister_h
#include <string>
#include <map>
diff --git a/src/core/Colvar.h b/src/core/Colvar.h
index a2988eacf..31758b156 100644
--- a/src/core/Colvar.h
+++ b/src/core/Colvar.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Colvar_h
-#define __PLUMED_Colvar_h
+#ifndef __PLUMED_core_Colvar_h
+#define __PLUMED_core_Colvar_h
#include "ActionAtomistic.h"
#include "ActionWithValue.h"
diff --git a/src/core/CubicInterpolation.h b/src/core/CubicInterpolation.h
index 9a42d9eb2..d952ead36 100644
--- a/src/core/CubicInterpolation.h
+++ b/src/core/CubicInterpolation.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_CubitInterpolation_h
-#define __PLUMED_CubitInterpolation_h
+#ifndef __PLUMED_core_CubicInterpolation_h
+#define __PLUMED_core_CubicInterpolation_h
#include <vector>
#include "tools/Matrix.h"
diff --git a/src/core/ExchangePatterns.h b/src/core/ExchangePatterns.h
index 292cdb54d..0795cd190 100644
--- a/src/core/ExchangePatterns.h
+++ b/src/core/ExchangePatterns.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ExchangePatterns_h
-#define __PLUMED_ExchangePatterns_h
+#ifndef __PLUMED_core_ExchangePatterns_h
+#define __PLUMED_core_ExchangePatterns_h
namespace PLMD {
class Random;
diff --git a/src/core/FlexibleBin.h b/src/core/FlexibleBin.h
index da5ef6c14..9ee167890 100644
--- a/src/core/FlexibleBin.h
+++ b/src/core/FlexibleBin.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_FlexibleBin_h
-#define __PLUMED_FlexibleBin_h
+#ifndef __PLUMED_core_FlexibleBin_h
+#define __PLUMED_core_FlexibleBin_h
#include<vector>
using namespace std;
diff --git a/src/core/GREX.h b/src/core/GREX.h
index 73f304c57..4cc6a517a 100644
--- a/src/core/GREX.h
+++ b/src/core/GREX.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Grex_h
-#define __PLUMED_Grex_h
+#ifndef __PLUMED_core_GREX_h
+#define __PLUMED_core_GREX_h
#include "WithCmd.h"
#include <string>
diff --git a/src/core/MDAtoms.h b/src/core/MDAtoms.h
index 758f7a5ba..e3b9b6ccf 100644
--- a/src/core/MDAtoms.h
+++ b/src/core/MDAtoms.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_MDAtoms_h
-#define __PLUMED_MDAtoms_h
+#ifndef __PLUMED_core_MDAtoms_h
+#define __PLUMED_core_MDAtoms_h
#include "tools/Tensor.h"
#include "tools/Vector.h"
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index d182f56eb..a99ccdd7f 100644
--- a/src/core/PlumedMain.h
+++ b/src/core/PlumedMain.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_PlumedMain_h
-#define __PLUMED_PlumedMain_h
+#ifndef __PLUMED_core_PlumedMain_h
+#define __PLUMED_core_PlumedMain_h
#include "WithCmd.h"
#include <cstdio>
diff --git a/src/core/SetupMolInfo.h b/src/core/SetupMolInfo.h
index 57e793c10..09ec12602 100644
--- a/src/core/SetupMolInfo.h
+++ b/src/core/SetupMolInfo.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_MolInfo_h
-#define __PLUMED_MolInfo_h
+#ifndef __PLUMED_core_SetupMolInfo_h
+#define __PLUMED_core_SetupMolInfo_h
#include "ActionSetup.h"
#include "ActionAtomistic.h"
diff --git a/src/core/TargetDist.h b/src/core/TargetDist.h
index c926de917..1f8b409b9 100644
--- a/src/core/TargetDist.h
+++ b/src/core/TargetDist.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_TargetDist_h
-#define __PLUMED_TargetDist_h
+#ifndef __PLUMED_core_TargetDist_h
+#define __PLUMED_core_TargetDist_h
#include <vector>
#include <string>
diff --git a/src/core/Value.h b/src/core/Value.h
index 23c07eec8..49ed49585 100644
--- a/src/core/Value.h
+++ b/src/core/Value.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Value_h
-#define __PLUMED_Value_h
+#ifndef __PLUMED_core_Value_h
+#define __PLUMED_core_Value_h
#include <vector>
#include <string>
diff --git a/src/core/WithCmd.h b/src/core/WithCmd.h
index c1fc2a480..e6ab41022 100644
--- a/src/core/WithCmd.h
+++ b/src/core/WithCmd.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_WithCmd_h
-#define __PLUMED_WithCmd_h
+#ifndef __PLUMED_core_WithCmd_h
+#define __PLUMED_core_WithCmd_h
#include <string>
diff --git a/src/function/ActionRegister.h b/src/function/ActionRegister.h
index 732046c8f..923749a5b 100644
--- a/src/function/ActionRegister.h
+++ b/src/function/ActionRegister.h
@@ -1 +1,25 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the 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.
+
+ plumed 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_function_ActionRegister_h
+#define __PLUMED_function_ActionRegister_h
#include "core/ActionRegister.h"
+#endif
diff --git a/src/function/Function.h b/src/function/Function.h
index 2ed50420a..f7e7445d2 100644
--- a/src/function/Function.h
+++ b/src/function/Function.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Function_h
-#define __PLUMED_Function_h
+#ifndef __PLUMED_function_Function_h
+#define __PLUMED_function_Function_h
#include "core/ActionWithValue.h"
#include "core/ActionWithArguments.h"
diff --git a/src/header.sh b/src/header.sh
index ec032aef9..15421719f 100755
--- a/src/header.sh
+++ b/src/header.sh
@@ -50,6 +50,38 @@ awk -v plus=$plus 'BEGIN{
} > $file.tmp
+case "$file" in
+(*h)
+guard="${file//\//_}"
+guard="${guard//./_}"
+guard="__PLUMED_${guard//-/_}"
+
+awk -v plus=$plus -v guard=$guard '
+{
+ if(past==1){
+ if($1=="#ifndef"){
+ line=-10;
+ } else if($1=="#define" && line==-9){
+ found=1;
+ }
+ else if(found!=1 && NF==0);
+ else past=2;
+ }
+ if(past==0 || past==2) print $0;
+ if(past==0 && $1==plus && $2=="*/") {
+ past=1;
+ print "#ifndef "guard
+ print "#define "guard
+ }
+ if(NF>0)line++;
+}END{
+if(!found) print "#endif"
+}' $file.tmp > $file.tmp2
+mv $file.tmp2 $file.tmp
+
+esac
+
+
cmp -s $file $file.tmp || cp $file.tmp $file
rm $file.tmp
diff --git a/src/imd/ActionIMD.cpp b/src/imd/ActionIMD.cpp
index b57bd5bdc..c71f5ac38 100644
--- a/src/imd/ActionIMD.cpp
+++ b/src/imd/ActionIMD.cpp
@@ -1,3 +1,24 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the 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.
+
+ plumed 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "../core/ActionRegister.h"
#include "../core/ActionAtomistic.h"
#include "../core/ActionPilot.h"
diff --git a/src/multicolvar/ActionVolume.h b/src/multicolvar/ActionVolume.h
index 89bb57d2f..834fe6c15 100644
--- a/src/multicolvar/ActionVolume.h
+++ b/src/multicolvar/ActionVolume.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionVolume_h
-#define __PLUMED_ActionVolume_h
+#ifndef __PLUMED_multicolvar_ActionVolume_h
+#define __PLUMED_multicolvar_ActionVolume_h
#include "core/ActionAtomistic.h"
#include "tools/HistogramBead.h"
diff --git a/src/multicolvar/MultiColvar.h b/src/multicolvar/MultiColvar.h
index c4249ca1d..6ab9a5a0a 100644
--- a/src/multicolvar/MultiColvar.h
+++ b/src/multicolvar/MultiColvar.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_MultiColvar_h
-#define __PLUMED_MultiColvar_h
+#ifndef __PLUMED_multicolvar_MultiColvar_h
+#define __PLUMED_multicolvar_MultiColvar_h
#include "core/ActionAtomistic.h"
#include "core/ActionWithValue.h"
diff --git a/src/multicolvar/MultiColvarSecondaryStructureRMSD.h b/src/multicolvar/MultiColvarSecondaryStructureRMSD.h
index dc469bb3c..5685aa8bb 100644
--- a/src/multicolvar/MultiColvarSecondaryStructureRMSD.h
+++ b/src/multicolvar/MultiColvarSecondaryStructureRMSD.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_MultiColvarSecondaryStructureRMSD_h
-#define __PLUMED_MultiColvarSecondaryStructureRMSD_h
+#ifndef __PLUMED_multicolvar_MultiColvarSecondaryStructureRMSD_h
+#define __PLUMED_multicolvar_MultiColvarSecondaryStructureRMSD_h
#include "MultiColvar.h"
#include <vector>
diff --git a/src/tools/Angle.h b/src/tools/Angle.h
index 9f0784dbd..d6e81319c 100644
--- a/src/tools/Angle.h
+++ b/src/tools/Angle.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Angle_h
-#define __PLUMED_Angle_h
+#ifndef __PLUMED_tools_Angle_h
+#define __PLUMED_tools_Angle_h
#include "Vector.h"
diff --git a/src/tools/AtomNumber.h b/src/tools/AtomNumber.h
index fdcac2e70..f72990a5b 100644
--- a/src/tools/AtomNumber.h
+++ b/src/tools/AtomNumber.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_AtomNumber_h
-#define __PLUMED_AtomNumber_h
+#ifndef __PLUMED_tools_AtomNumber_h
+#define __PLUMED_tools_AtomNumber_h
#include "PlumedException.h"
#include <limits>
diff --git a/src/tools/Citations.h b/src/tools/Citations.h
index 79fb95a4e..8f2d0a228 100644
--- a/src/tools/Citations.h
+++ b/src/tools/Citations.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Citations_h
-#define __PLUMED_Citations_h
+#ifndef __PLUMED_tools_Citations_h
+#define __PLUMED_tools_Citations_h
#include <vector>
#include <string>
diff --git a/src/tools/DLLoader.h b/src/tools/DLLoader.h
index dbb07fdae..a61b6732d 100644
--- a/src/tools/DLLoader.h
+++ b/src/tools/DLLoader.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_DLLoader_h
-#define __PLUMED_DLLoader_h
+#ifndef __PLUMED_tools_DLLoader_h
+#define __PLUMED_tools_DLLoader_h
#include <stack>
#include <string>
diff --git a/src/tools/DRMSD.h b/src/tools/DRMSD.h
index b9ce260d5..e0dfbabbe 100644
--- a/src/tools/DRMSD.h
+++ b/src/tools/DRMSD.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_DRMSD_h
-#define __PLUMED_DRMSD_h
+#ifndef __PLUMED_tools_DRMSD_h
+#define __PLUMED_tools_DRMSD_h
#include "Tensor.h"
#include "Vector.h"
diff --git a/src/tools/DynamicList.h b/src/tools/DynamicList.h
index 1fc824047..26fe9d22c 100644
--- a/src/tools/DynamicList.h
+++ b/src/tools/DynamicList.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_DynamicList_h
-#define __PLUMED_DynamicList_h
+#ifndef __PLUMED_tools_DynamicList_h
+#define __PLUMED_tools_DynamicList_h
#include "PlumedCommunicator.h"
diff --git a/src/tools/Grid.h b/src/tools/Grid.h
index 474937207..d3999f17a 100644
--- a/src/tools/Grid.h
+++ b/src/tools/Grid.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Grid_h
-#define __PLUMED_Grid_h
+#ifndef __PLUMED_tools_Grid_h
+#define __PLUMED_tools_Grid_h
#include <vector>
#include <string>
diff --git a/src/tools/HistogramBead.h b/src/tools/HistogramBead.h
index 5568be77f..5cbe75cf5 100644
--- a/src/tools/HistogramBead.h
+++ b/src/tools/HistogramBead.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_HistogramBead_h
-#define __PLUMED_HistogramBead_h
+#ifndef __PLUMED_tools_HistogramBead_h
+#define __PLUMED_tools_HistogramBead_h
#include <cassert>
#include <cmath>
diff --git a/src/tools/Kearsley.h b/src/tools/Kearsley.h
index 68e9f1d06..4ed16e664 100644
--- a/src/tools/Kearsley.h
+++ b/src/tools/Kearsley.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Kearsley_h
-#define __PLUMED_Kearsley_h
+#ifndef __PLUMED_tools_Kearsley_h
+#define __PLUMED_tools_Kearsley_h
#include "Vector.h"
#include "Tensor.h"
diff --git a/src/tools/KernelFunctions.cpp b/src/tools/KernelFunctions.cpp
index 395014e06..3cc37830c 100644
--- a/src/tools/KernelFunctions.cpp
+++ b/src/tools/KernelFunctions.cpp
@@ -1,3 +1,24 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the 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.
+
+ plumed 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 Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "KernelFunctions.h"
namespace PLMD {
diff --git a/src/tools/KernelFunctions.h b/src/tools/KernelFunctions.h
index 1c13c3e47..3a7b7e728 100644
--- a/src/tools/KernelFunctions.h
+++ b/src/tools/KernelFunctions.h
@@ -3,24 +3,24 @@
(see the PEOPLE file at the root of the distribution for a list of names)
See http://www.plumed-code.org for more information.
-
+
This file is part of plumed, version 2.0.
-
+
plumed is free software: you can redistribute it and/or modify
it under the 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.
-
+
plumed 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 Lesser General Public License for more details.
-
+
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_KernelFunctions_h
-#define __PLUMED_KernelFunctions_h
+#ifndef __PLUMED_tools_KernelFunctions_h
+#define __PLUMED_tools_KernelFunctions_h
#include "Tools.h"
#include "Matrix.h"
diff --git a/src/tools/Keywords.h b/src/tools/Keywords.h
index 05c57a7cc..6c3f428ed 100644
--- a/src/tools/Keywords.h
+++ b/src/tools/Keywords.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Keywords_h
-#define __PLUMED_Keywords_h
+#ifndef __PLUMED_tools_Keywords_h
+#define __PLUMED_tools_Keywords_h
#include <vector>
#include <string>
#include <set>
diff --git a/src/tools/LatticeReduction.h b/src/tools/LatticeReduction.h
index e3104d5eb..21dba0bba 100644
--- a/src/tools/LatticeReduction.h
+++ b/src/tools/LatticeReduction.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_LatticeReduction_h
-#define __PLUMED_LatticeReduction_h
+#ifndef __PLUMED_tools_LatticeReduction_h
+#define __PLUMED_tools_LatticeReduction_h
#include "Vector.h"
#include "Tensor.h"
diff --git a/src/tools/Log.h b/src/tools/Log.h
index b112c0164..cdd6b6e79 100644
--- a/src/tools/Log.h
+++ b/src/tools/Log.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Log_h
-#define __PLUMED_Log_h
+#ifndef __PLUMED_tools_Log_h
+#define __PLUMED_tools_Log_h
#include <cstdio>
#include <string>
diff --git a/src/tools/Matrix.h b/src/tools/Matrix.h
index 253de806d..680cb5b94 100644
--- a/src/tools/Matrix.h
+++ b/src/tools/Matrix.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Matrix_h
-#define __PLUMED_Matrix_h
+#ifndef __PLUMED_tools_Matrix_h
+#define __PLUMED_tools_Matrix_h
#include <vector>
#include <string>
#include <set>
diff --git a/src/tools/MatrixSquareBracketsAccess.h b/src/tools/MatrixSquareBracketsAccess.h
index 5a25af165..593606927 100644
--- a/src/tools/MatrixSquareBracketsAccess.h
+++ b/src/tools/MatrixSquareBracketsAccess.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_MatrixSquareBracketsAccess_h
-#define __PLUMED_MatrixSquareBracketsAccess_h
+#ifndef __PLUMED_tools_MatrixSquareBracketsAccess_h
+#define __PLUMED_tools_MatrixSquareBracketsAccess_h
namespace PLMD{
diff --git a/src/tools/NeighborList.h b/src/tools/NeighborList.h
index 42a99c52c..e169e0be2 100644
--- a/src/tools/NeighborList.h
+++ b/src/tools/NeighborList.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_NeighborList_h
-#define __PLUMED_NeighborList_h
+#ifndef __PLUMED_tools_NeighborList_h
+#define __PLUMED_tools_NeighborList_h
#include "Vector.h"
#include "AtomNumber.h"
diff --git a/src/tools/OptimalAlignment.h b/src/tools/OptimalAlignment.h
index 89cfa7e3c..1051a2181 100644
--- a/src/tools/OptimalAlignment.h
+++ b/src/tools/OptimalAlignment.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_OptimalAlignment_h
-#define __PLUMED_OptimalAlignment_h
+#ifndef __PLUMED_tools_OptimalAlignment_h
+#define __PLUMED_tools_OptimalAlignment_h
#include "Vector.h"
#include "Tensor.h"
diff --git a/src/tools/PDB.h b/src/tools/PDB.h
index 4482b0e34..fcf0b052b 100644
--- a/src/tools/PDB.h
+++ b/src/tools/PDB.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_PDB_h
-#define __PLUMED_PDB_h
+#ifndef __PLUMED_tools_PDB_h
+#define __PLUMED_tools_PDB_h
#include "AtomNumber.h"
#include "Vector.h"
diff --git a/src/tools/Pbc.h b/src/tools/Pbc.h
index 4d9762ada..bb193146d 100644
--- a/src/tools/Pbc.h
+++ b/src/tools/Pbc.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Pbc_h
-#define __PLUMED_Pbc_h
+#ifndef __PLUMED_tools_Pbc_h
+#define __PLUMED_tools_Pbc_h
#include "Vector.h"
#include "Tensor.h"
diff --git a/src/tools/PlumedCommunicator.h b/src/tools/PlumedCommunicator.h
index 664ded8c3..0b2fb8d5e 100644
--- a/src/tools/PlumedCommunicator.h
+++ b/src/tools/PlumedCommunicator.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_PlumedCommunicator_h
-#define __PLUMED_PlumedCommunicator_h
+#ifndef __PLUMED_tools_PlumedCommunicator_h
+#define __PLUMED_tools_PlumedCommunicator_h
#ifdef __PLUMED_MPI
#include <mpi.h>
#endif
diff --git a/src/tools/PlumedException.h b/src/tools/PlumedException.h
index 855572ccd..a7b85a9b2 100644
--- a/src/tools/PlumedException.h
+++ b/src/tools/PlumedException.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_PlumedException_h
-#define __PLUMED_PlumedException_h
+#ifndef __PLUMED_tools_PlumedException_h
+#define __PLUMED_tools_PlumedException_h
#include <string>
#include <stdexcept>
diff --git a/src/tools/PlumedFile.h b/src/tools/PlumedFile.h
index 430553be8..c40ee3713 100644
--- a/src/tools/PlumedFile.h
+++ b/src/tools/PlumedFile.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_PlumedFile_h
-#define __PLUMED_PlumedFile_h
+#ifndef __PLUMED_tools_PlumedFile_h
+#define __PLUMED_tools_PlumedFile_h
#include <cstdio>
#include <vector>
diff --git a/src/tools/RMSD.h b/src/tools/RMSD.h
index 8ed72c97f..64f4e3f77 100644
--- a/src/tools/RMSD.h
+++ b/src/tools/RMSD.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_RMSD_h
-#define __PLUMED_RMSD_h
+#ifndef __PLUMED_tools_RMSD_h
+#define __PLUMED_tools_RMSD_h
#include "Vector.h"
#include <vector>
diff --git a/src/tools/Random.h b/src/tools/Random.h
index 3cf1a7d96..70ef22a4d 100644
--- a/src/tools/Random.h
+++ b/src/tools/Random.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __RANDOM_H
-#define __RANDOM_H
+#ifndef __PLUMED_tools_Random_h
+#define __PLUMED_tools_Random_h
#include <string>
#include <iosfwd>
diff --git a/src/tools/Stopwatch.h b/src/tools/Stopwatch.h
index ec9d0032a..7b87dd6de 100644
--- a/src/tools/Stopwatch.h
+++ b/src/tools/Stopwatch.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Stopwatch_h
-#define __PLUMED_Stopwatch_h
+#ifndef __PLUMED_tools_Stopwatch_h
+#define __PLUMED_tools_Stopwatch_h
#include <string>
#include <map>
diff --git a/src/tools/SwitchingFunction.h b/src/tools/SwitchingFunction.h
index 6ea12ca00..410107a5b 100644
--- a/src/tools/SwitchingFunction.h
+++ b/src/tools/SwitchingFunction.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_SwitchingFunction_h
-#define __PLUMED_SwitchingFunction_h
+#ifndef __PLUMED_tools_SwitchingFunction_h
+#define __PLUMED_tools_SwitchingFunction_h
#include <string>
diff --git a/src/tools/Tensor.h b/src/tools/Tensor.h
index 895d352ff..bfd87772b 100644
--- a/src/tools/Tensor.h
+++ b/src/tools/Tensor.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Tensor_h
-#define __PLUMED_Tensor_h
+#ifndef __PLUMED_tools_Tensor_h
+#define __PLUMED_tools_Tensor_h
#include "MatrixSquareBracketsAccess.h"
#include "Vector.h"
diff --git a/src/tools/Tools.h b/src/tools/Tools.h
index c7ef12112..b8a9c2c94 100644
--- a/src/tools/Tools.h
+++ b/src/tools/Tools.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Tools_h
-#define __PLUMED_Tools_h
+#ifndef __PLUMED_tools_Tools_h
+#define __PLUMED_tools_Tools_h
#include "AtomNumber.h"
#include <vector>
diff --git a/src/tools/Torsion.h b/src/tools/Torsion.h
index 82bbb97e3..69199730f 100644
--- a/src/tools/Torsion.h
+++ b/src/tools/Torsion.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Torsion_h
-#define __PLUMED_Torsion_h
+#ifndef __PLUMED_tools_Torsion_h
+#define __PLUMED_tools_Torsion_h
#include "Vector.h"
diff --git a/src/tools/Units.h b/src/tools/Units.h
index be025f328..f2027e4ce 100644
--- a/src/tools/Units.h
+++ b/src/tools/Units.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Units_h
-#define __PLUMED_Units_h
+#ifndef __PLUMED_tools_Units_h
+#define __PLUMED_tools_Units_h
#include <string>
diff --git a/src/tools/Vector.h b/src/tools/Vector.h
index 6ba047722..1e8a25175 100644
--- a/src/tools/Vector.h
+++ b/src/tools/Vector.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Vector_h
-#define __PLUMED_Vector_h
+#ifndef __PLUMED_tools_Vector_h
+#define __PLUMED_tools_Vector_h
#include <cmath>
diff --git a/src/vessel-base/ActionWithVessel.h b/src/vessel-base/ActionWithVessel.h
index 744ffd168..fcf19aa06 100644
--- a/src/vessel-base/ActionWithVessel.h
+++ b/src/vessel-base/ActionWithVessel.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_ActionWithVessel_h
-#define __PLUMED_ActionWithVessel_h
+#ifndef __PLUMED_vessel_base_ActionWithVessel_h
+#define __PLUMED_vessel_base_ActionWithVessel_h
#include "core/ActionWithValue.h"
#include "core/ActionAtomistic.h"
diff --git a/src/vessel-base/NormedSumVessel.h b/src/vessel-base/NormedSumVessel.h
index a8f6f82f8..3af883a8d 100644
--- a/src/vessel-base/NormedSumVessel.h
+++ b/src/vessel-base/NormedSumVessel.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_NormedSumVessel_h
-#define __PLUMED_NormedSumVessel_h
+#ifndef __PLUMED_vessel_base_NormedSumVessel_h
+#define __PLUMED_vessel_base_NormedSumVessel_h
#include <string>
#include <cstring>
diff --git a/src/vessel-base/SumVessel.h b/src/vessel-base/SumVessel.h
index 55fecf72e..e4b0306dc 100644
--- a/src/vessel-base/SumVessel.h
+++ b/src/vessel-base/SumVessel.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_SumVessel_h
-#define __PLUMED_SumVessel_h
+#ifndef __PLUMED_vessel_base_SumVessel_h
+#define __PLUMED_vessel_base_SumVessel_h
#include <string>
#include <cstring>
diff --git a/src/vessel-base/Vessel.h b/src/vessel-base/Vessel.h
index 9bf23f2a5..1ab1ddeaf 100644
--- a/src/vessel-base/Vessel.h
+++ b/src/vessel-base/Vessel.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Vessel_h
-#define __PLUMED_Vessel_h
+#ifndef __PLUMED_vessel_base_Vessel_h
+#define __PLUMED_vessel_base_Vessel_h
#include <string>
#include <cstring>
diff --git a/src/vessel-base/VesselAccumulator.h b/src/vessel-base/VesselAccumulator.h
index 8f5b97a10..465e8e498 100644
--- a/src/vessel-base/VesselAccumulator.h
+++ b/src/vessel-base/VesselAccumulator.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_VesselAccumulator_h
-#define __PLUMED_VesselAccumulator_h
+#ifndef __PLUMED_vessel_base_VesselAccumulator_h
+#define __PLUMED_vessel_base_VesselAccumulator_h
#include <string>
#include <cstring>
diff --git a/src/vessel-base/VesselRegister.h b/src/vessel-base/VesselRegister.h
index 585f3ed59..84a7aaaf4 100644
--- a/src/vessel-base/VesselRegister.h
+++ b/src/vessel-base/VesselRegister.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_VesselRegister_h
-#define __PLUMED_VesselRegister_h
+#ifndef __PLUMED_vessel_base_VesselRegister_h
+#define __PLUMED_vessel_base_VesselRegister_h
#include <string>
#include <cstring>
diff --git a/src/vessel-base/VesselStoreAllValues.h b/src/vessel-base/VesselStoreAllValues.h
index e0a93ca26..cd3bccc50 100644
--- a/src/vessel-base/VesselStoreAllValues.h
+++ b/src/vessel-base/VesselStoreAllValues.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_VesselStoreAllValues_h
-#define __PLUMED_VesselStoreAllValues_h
+#ifndef __PLUMED_vessel_base_VesselStoreAllValues_h
+#define __PLUMED_vessel_base_VesselStoreAllValues_h
#include <string>
#include <cstring>
diff --git a/src/vessel-base/VesselValueAccess.h b/src/vessel-base/VesselValueAccess.h
index 16211398a..a89a9983b 100644
--- a/src/vessel-base/VesselValueAccess.h
+++ b/src/vessel-base/VesselValueAccess.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_VesselValueAccess_h
-#define __PLUMED_VesselValueAccess_h
+#ifndef __PLUMED_vessel_base_VesselValueAccess_h
+#define __PLUMED_vessel_base_VesselValueAccess_h
#include <string>
#include <cstring>
diff --git a/src/wrapper/Plumed.h b/src/wrapper/Plumed.h
index 2d477314a..77f93716d 100644
--- a/src/wrapper/Plumed.h
+++ b/src/wrapper/Plumed.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_Plumed_h
-#define __PLUMED_Plumed_h
+#ifndef __PLUMED_wrapper_Plumed_h
+#define __PLUMED_wrapper_Plumed_h
/**
\page ReferencePlumedH Reference for interfacing MD codes with PLUMED
--
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