From b22f79ed0dd8c6c9a22b95ccd296a8e3111a086d Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 20:31:13 -0500
Subject: [PATCH 01/10] Corrected includes

---
 protomol/main.cpp | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/protomol/main.cpp b/protomol/main.cpp
index 6bd5ffa..3878f8c 100644
--- a/protomol/main.cpp
+++ b/protomol/main.cpp
@@ -1,9 +1,11 @@
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/ModuleManager.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/base/Exception.h>
-
-#include <iostream>
+#include <protomol/ProtoMolApp.h>           // for ProtoMolApp
+#include <protomol/base/Exception.h>        // for operator<<, Exception
+#include <protomol/base/ModuleManager.h>    // for ModuleManager
+#include <protomol/module/MainModule.h>     // for InputDebug
+#include <iostream>                         // for cout, operator<<, ostream, basic_ostream, cerr, endl
+#include "protomol/base/Report.h"           // for cerr
+#include "protomol/config/Configuration.h"  // for Configuration
+#include "protomol/config/Value.h"          // for Value
 
 using namespace std;
 using namespace ProtoMol;
@@ -32,4 +34,3 @@ int main(int argc, char *argv[]) {
 
   return 1;
 }
-

From e9675421617e0e5d4eea325069ce71078469e306 Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 20:56:31 -0500
Subject: [PATCH 02/10] Auto applied include header fixes

---
 .gitignore                                    |  2 +
 protomol/ProtoMolApp.cpp                      | 62 ++++++++++++-------
 protomol/ProtoMolApp.h                        | 34 +++++-----
 protomol/analysis/Analysis.cpp                |  7 +--
 protomol/analysis/Analysis.h                  |  5 ++
 protomol/analysis/AnalysisCollection.cpp      | 15 ++---
 protomol/analysis/AnalysisDihedral.cpp        | 30 +++++----
 protomol/analysis/AnalysisDihedral.h          |  9 ++-
 protomol/base/FileLocation.h                  |  1 +
 protomol/base/Lapack.cpp                      |  2 -
 protomol/base/Makeable.cpp                    |  3 +
 protomol/base/Makeable.h                      |  8 ++-
 protomol/base/MathUtilities.cpp               |  5 ++
 protomol/base/MathUtilities.h                 |  7 ++-
 protomol/base/Module.h                        |  7 +--
 protomol/base/ModuleManager.cpp               | 14 +++--
 protomol/base/PMConstants.cpp                 |  2 +
 protomol/base/Random.h                        |  5 +-
 protomol/base/Report.cpp                      |  5 +-
 protomol/base/StringUtilities.cpp             | 13 ++--
 protomol/base/StringUtilities.h               |  6 +-
 protomol/base/SystemUtilities.cpp             | 20 +++---
 protomol/base/Timer.cpp                       | 13 ++--
 protomol/base/TimerStatistic.cpp              |  4 ++
 protomol/base/TimerStatistic.h                |  9 ++-
 protomol/config/CommandLine.cpp               | 21 ++++---
 protomol/config/CommandLineOption.cpp         |  2 -
 protomol/config/CommandLineOption.h           |  4 +-
 protomol/config/Configuration.cpp             |  8 ++-
 protomol/config/Configuration.h               |  9 ++-
 protomol/config/ConstraintValueType.h         |  1 +
 protomol/config/Parameter.cpp                 |  7 ++-
 protomol/config/Parameter.h                   |  2 +-
 protomol/config/Value.cpp                     | 10 ++-
 protomol/config/Value.h                       | 14 ++++-
 protomol/config/ValueType.h                   | 22 ++++---
 protomol/factory/AnalysisFactory.cpp          | 17 ++++-
 protomol/factory/AnalysisFactory.h            |  7 ++-
 protomol/factory/ForceFactory.cpp             | 16 ++++-
 protomol/factory/ForceFactory.h               | 11 +++-
 protomol/factory/HelpTextFactory.cpp          |  8 ++-
 protomol/factory/HelpTextFactory.h            |  6 +-
 protomol/factory/IntegratorFactory.cpp        | 24 ++++---
 protomol/factory/IntegratorFactory.h          |  4 ++
 protomol/factory/OutputFactory.cpp            | 19 ++++--
 protomol/factory/OutputFactory.h              |  7 ++-
 protomol/factory/TopologyFactory.cpp          | 13 +++-
 protomol/factory/TopologyFactory.h            |  3 +
 protomol/force/CompareForce.cpp               | 19 +++++-
 protomol/force/CompareForce.h                 |  9 +++
 protomol/force/CoulombForce.h                 | 14 ++++-
 protomol/force/Force.cpp                      |  4 +-
 protomol/force/Force.h                        | 17 +++--
 protomol/force/ForceGroup.cpp                 | 20 +++---
 protomol/force/ForceGroup.h                   | 13 ++--
 protomol/force/GB/GBACEForce.cpp              | 17 ++++-
 protomol/force/GB/GBACEForce.h                | 15 ++++-
 protomol/force/GB/GBBornRadii.cpp             | 16 ++++-
 protomol/force/GB/GBBornRadii.h               | 15 ++++-
 protomol/force/GB/GBForce.cpp                 | 18 +++++-
 protomol/force/GB/GBForce.h                   | 15 ++++-
 protomol/force/GB/GBPartialSum.cpp            | 13 +++-
 protomol/force/GB/GBPartialSum.h              | 15 ++++-
 protomol/force/HarmonicRestraintForce.cpp     |  6 ++
 protomol/force/HarmonicRestraintForce.h       | 20 ++++--
 protomol/force/LennardJonesForce.h            | 19 +++++-
 protomol/force/LennardJonesVDWForce.h         | 21 ++++++-
 protomol/force/MetaForce.h                    |  1 +
 protomol/force/MollyForce.h                   |  4 +-
 protomol/force/ProteinRestraintForce.cpp      |  5 ++
 protomol/force/ProteinRestraintForce.h        | 20 ++++--
 protomol/force/TimeForce.cpp                  | 21 +++++--
 protomol/force/TimeForce.h                    | 10 ++-
 protomol/force/born/BornRadii.cpp             |  5 ++
 protomol/force/born/BornRadii.h               | 24 +++++--
 protomol/force/born/BornSelfForce.cpp         |  6 ++
 protomol/force/born/BornSelfForce.h           | 20 ++++--
 protomol/force/coulomb/CoulombForceDiElec.cpp |  5 ++
 protomol/force/coulomb/CoulombForceDiElec.h   | 15 ++++-
 protomol/force/coulomb/CoulombSCPISMForce.cpp |  5 ++
 protomol/force/coulomb/CoulombSCPISMForce.h   | 24 +++++--
 .../force/extended/ExtendedCompareForce.cpp   | 11 +++-
 .../force/extended/ExtendedCompareForce.h     |  5 ++
 protomol/force/extended/ExtendedForce.cpp     |  6 +-
 protomol/force/extended/ExtendedForce.h       |  7 ++-
 protomol/force/extended/ExtendedTimeForce.cpp | 11 +++-
 protomol/force/extended/ExtendedTimeForce.h   |  5 ++
 protomol/force/hessian/HessDihedral.cpp       |  9 ++-
 protomol/force/hessian/HessDihedral.h         |  6 ++
 protomol/force/hessian/ReducedHessAngle.cpp   |  5 +-
 protomol/force/hessian/ReducedHessAngle.h     |  4 ++
 protomol/force/hessian/ReducedHessBond.cpp    |  4 ++
 protomol/force/hessian/ReducedHessBond.h      |  4 +-
 .../force/hessian/ReducedHessBornSelf.cpp     | 10 ++-
 protomol/force/hessian/ReducedHessBornSelf.h  |  5 +-
 protomol/force/hessian/ReducedHessCoulomb.cpp |  6 ++
 protomol/force/hessian/ReducedHessCoulomb.h   |  5 +-
 .../hessian/ReducedHessCoulombDiElec.cpp      |  6 ++
 .../force/hessian/ReducedHessCoulombDiElec.h  |  5 +-
 .../hessian/ReducedHessCoulombSCPISM.cpp      |  6 ++
 .../force/hessian/ReducedHessCoulombSCPISM.h  |  5 +-
 protomol/force/hessian/ReducedHessGB.cpp      | 10 +--
 protomol/force/hessian/ReducedHessGB.h        |  5 +-
 protomol/force/hessian/ReducedHessGBACE.cpp   | 10 +--
 protomol/force/hessian/ReducedHessGBACE.h     |  5 +-
 .../force/hessian/ReducedHessLennardJones.cpp |  7 +++
 .../force/hessian/ReducedHessLennardJones.h   |  5 +-
 protomol/force/system/SystemCompareForce.cpp  | 11 +++-
 protomol/force/system/SystemCompareForce.h    |  7 ++-
 protomol/force/system/SystemForce.cpp         |  6 +-
 protomol/force/system/SystemTimeForce.cpp     | 11 +++-
 protomol/force/system/SystemTimeForce.h       |  5 ++
 protomol/integrator/Integrator.cpp            | 15 +++--
 protomol/integrator/Integrator.h              |  6 +-
 protomol/integrator/IntegratorDefinition.cpp  |  6 +-
 protomol/integrator/IntegratorDefinition.h    |  2 +
 protomol/integrator/MTSIntegrator.cpp         | 16 +++--
 protomol/integrator/MTSIntegrator.h           | 10 ++-
 protomol/integrator/STSIntegrator.cpp         | 17 ++---
 protomol/integrator/STSIntegrator.h           | 10 ++-
 protomol/integrator/StandardIntegrator.cpp    | 20 +++---
 protomol/integrator/StandardIntegrator.h      |  2 +-
 .../integrator/base/CGMinimizerIntegrator.cpp | 15 +++--
 .../integrator/base/CGMinimizerIntegrator.h   | 10 ++-
 .../base/LangevinImpulseIntegrator.cpp        | 18 ++++--
 .../base/LangevinImpulseIntegrator.h          |  9 ++-
 .../base/LangevinLeapfrogIntegrator.cpp       | 18 ++++--
 .../base/LangevinLeapfrogIntegrator.h         |  9 ++-
 .../LangevinLeapfrogSwitchingIntegrator.cpp   | 17 +++--
 .../LangevinLeapfrogSwitchingIntegrator.h     | 10 ++-
 .../base/LangevinVVVRIntegrator.cpp           | 20 ++++--
 .../integrator/base/LangevinVVVRIntegrator.h  |  9 ++-
 .../base/NumericalDifferentiation.cpp         | 17 +++--
 .../base/NumericalDifferentiation.h           |  9 ++-
 .../base/NumericallyDifferentiatedHessian.cpp | 19 +++---
 .../base/NumericallyDifferentiatedHessian.h   |  9 ++-
 protomol/integrator/base/RMTIntegrator.cpp    | 20 ++++--
 protomol/integrator/base/RMTIntegrator.h      | 11 +++-
 protomol/integrator/hessian/BlockHessian.cpp  | 60 ++++++++----------
 protomol/integrator/hessian/BlockHessian.h    |  8 +++
 .../hessian/BlockHessianDiagonalize.cpp       | 24 ++++---
 .../hessian/BlockHessianDiagonalize.h         | 16 +++--
 protomol/integrator/hessian/Hessian.cpp       | 59 +++++++++++-------
 protomol/integrator/hessian/Hessian.h         |  8 ++-
 protomol/integrator/hessian/HessianInt.cpp    | 36 ++++++++---
 protomol/integrator/hessian/HessianInt.h      | 16 ++++-
 .../leapfrog/DMDLeapfrogIntegrator.cpp        | 19 ++++--
 .../leapfrog/DMDLeapfrogIntegrator.h          |  9 ++-
 protomol/integrator/leapfrog/GPU.cpp          | 32 +++++++---
 protomol/integrator/leapfrog/GPU.h            | 11 +++-
 .../leapfrog/LeapfrogDataAcquisition.cpp      | 18 +++++-
 .../leapfrog/LeapfrogDataAcquisition.h        | 14 ++++-
 .../leapfrog/LeapfrogIntegrator.cpp           | 15 +++--
 .../integrator/leapfrog/LeapfrogIntegrator.h  |  8 ++-
 .../leapfrog/LeapfrogTruncatedShadow.cpp      | 42 ++++++++-----
 .../leapfrog/LeapfrogTruncatedShadow.h        | 16 ++++-
 .../leapfrog/NoseNVTLeapfrogIntegrator.cpp    | 17 +++--
 .../leapfrog/NoseNVTLeapfrogIntegrator.h      |  9 ++-
 .../leapfrog/PLeapfrogIntegrator.cpp          | 14 +++--
 .../integrator/leapfrog/PLeapfrogIntegrator.h |  9 ++-
 .../integrator/normal/NormalModeBrownian.cpp  | 26 +++++---
 .../integrator/normal/NormalModeBrownian.h    | 11 +++-
 .../integrator/normal/NormalModeCompLang.cpp  | 26 +++++---
 .../integrator/normal/NormalModeCompLang.h    | 10 ++-
 .../integrator/normal/NormalModeDamping.cpp   | 25 +++++---
 .../integrator/normal/NormalModeDamping.h     | 13 +++-
 .../normal/NormalModeDiagonalize.cpp          | 29 +++++----
 .../integrator/normal/NormalModeDiagonalize.h | 20 ++++--
 .../integrator/normal/NormalModeLangLf.cpp    | 27 +++++---
 protomol/integrator/normal/NormalModeLangLf.h | 11 +++-
 .../integrator/normal/NormalModeLangevin.cpp  | 20 +++---
 .../integrator/normal/NormalModeLangevin.h    | 11 +++-
 .../NormalModeLangevinLeapfrogSwitching.cpp   | 29 ++++++---
 .../NormalModeLangevinLeapfrogSwitching.h     | 12 +++-
 .../integrator/normal/NormalModeMinimizer.cpp | 24 +++++--
 .../integrator/normal/NormalModeMinimizer.h   |  9 ++-
 protomol/integrator/normal/NormalModeMori.cpp | 24 ++++---
 protomol/integrator/normal/NormalModeMori.h   | 12 +++-
 .../integrator/normal/NormalModeQuadratic.cpp | 28 ++++++---
 .../integrator/normal/NormalModeQuadratic.h   | 13 +++-
 .../integrator/normal/NormalModeRelax.cpp     | 17 +++--
 protomol/integrator/normal/NormalModeRelax.h  | 11 +++-
 .../normal/NormalModeSubspaceSampling.cpp     | 27 +++++---
 .../normal/NormalModeSubspaceSampling.h       | 11 +++-
 .../integrator/normal/NormalModeUtilities.cpp | 20 +++++-
 .../integrator/normal/NormalModeUtilities.h   | 14 +++--
 .../integrator/openMM/NormalModeOpenMM.cpp    | 25 ++++++--
 protomol/integrator/openMM/NormalModeOpenMM.h | 12 +++-
 .../integrator/openMM/OpenMMIntegrator.cpp    | 53 ++++++++++++----
 protomol/integrator/openMM/OpenMMIntegrator.h | 18 +++++-
 protomol/io/CheckpointConfigReader.cpp        | 12 ++--
 protomol/io/CheckpointConfigReader.h          |  8 ++-
 protomol/io/CheckpointConfigWriter.cpp        |  5 ++
 protomol/io/CheckpointConfigWriter.h          |  6 +-
 protomol/io/ConfigurationReader.cpp           |  9 ++-
 protomol/io/ConfigurationReader.h             |  7 ++-
 protomol/io/DCDTrajectoryReader.cpp           | 13 +++-
 protomol/io/DCDTrajectoryReader.h             |  8 ++-
 protomol/io/DCDTrajectoryWriter.cpp           | 13 +++-
 protomol/io/DCDTrajectoryWriter.h             | 12 +++-
 protomol/io/EigenvectorReader.cpp             | 10 +--
 protomol/io/EigenvectorReader.h               |  3 +
 protomol/io/EigenvectorTextReader.cpp         |  8 +--
 protomol/io/EigenvectorTextReader.h           |  5 ++
 protomol/io/File.cpp                          |  9 +--
 protomol/io/File.h                            |  2 +-
 protomol/io/PARReader.cpp                     | 12 +++-
 protomol/io/PARReader.h                       |  1 +
 protomol/io/PDBReader.cpp                     | 14 +++--
 protomol/io/PDBReader.h                       |  5 ++
 protomol/io/PDBWriter.cpp                     | 12 ++--
 protomol/io/PDBWriter.h                       |  4 ++
 protomol/io/PSFReader.cpp                     | 11 +++-
 protomol/io/PSFReader.h                       |  3 +
 protomol/io/PosVelReader.cpp                  | 15 +++--
 protomol/io/PosVelReader.h                    |  6 +-
 protomol/io/PosVelReaderType.h                |  1 +
 protomol/io/Reader.cpp                        |  3 +
 protomol/io/Reader.h                          |  2 +
 protomol/io/SCPISMReader.cpp                  |  7 ++-
 protomol/io/SCPISMReader.h                    |  7 ++-
 protomol/io/Writer.cpp                        |  3 +
 protomol/io/Writer.h                          |  2 +
 protomol/io/XYZBinReader.cpp                  | 13 +++-
 protomol/io/XYZBinReader.h                    |  3 +
 protomol/io/XYZReader.cpp                     | 10 ++-
 protomol/io/XYZReader.h                       |  6 ++
 protomol/io/XYZTrajectoryReader.cpp           |  7 ++-
 protomol/io/XYZTrajectoryReader.h             |  3 +
 protomol/io/XYZTrajectoryWriter.cpp           | 15 +++--
 protomol/io/XYZTrajectoryWriter.h             |  8 ++-
 protomol/io/XYZWriter.cpp                     | 14 +++--
 protomol/io/XYZWriter.h                       |  8 ++-
 .../GromacsBondedParameterFileReader.cpp      | 13 +++-
 .../GromacsBondedParameterFileReader.h        |  4 +-
 .../gromacs/GromacsGBParameterFileReader.cpp  | 11 +++-
 .../io/gromacs/GromacsGBParameterFileReader.h |  4 +-
 .../GromacsNonbondedParameterFileReader.cpp   | 11 +++-
 .../GromacsNonbondedParameterFileReader.h     |  4 +-
 .../io/gromacs/GromacsParameterFileReader.cpp | 12 +++-
 .../io/gromacs/GromacsParameterFileReader.h   |  4 +-
 protomol/io/gromacs/GromacsTopologyReader.cpp | 10 ++-
 protomol/io/gromacs/GromacsTopologyReader.h   |  5 +-
 protomol/io/gromacs/PortGromacsParameters.cpp | 31 ++++++----
 protomol/io/gromacs/PortGromacsParameters.h   |  9 +--
 protomol/main.cpp                             |  4 ++
 protomol/modifier/Modifier.cpp                |  5 +-
 protomol/modifier/Modifier.h                  |  9 +--
 protomol/modifier/ModifierMetaRattle.cpp      | 10 ++-
 protomol/modifier/ModifierMetaRattle.h        |  3 +
 protomol/modifier/ModifierMetaRattleShake.cpp | 10 ++-
 protomol/modifier/ModifierMetaRattleShake.h   |  5 ++
 protomol/modifier/ModifierMetaShake.cpp       | 11 +++-
 protomol/modifier/ModifierMetaShake.h         |  3 +
 protomol/modifier/ModifierRattle.cpp          | 15 +++--
 protomol/modifier/ModifierRattle.h            |  7 +++
 protomol/modifier/ModifierShadow.cpp          | 14 +++--
 protomol/modifier/ModifierShadow.h            |  5 ++
 protomol/modifier/ModifierShake.cpp           | 15 +++--
 protomol/modifier/ModifierShake.h             |  7 +++
 protomol/module/AnalysisModule.cpp            |  7 +--
 protomol/module/AnalysisModule.h              |  3 +-
 protomol/module/BondedForcesModule.cpp        | 23 ++++---
 protomol/module/CheckpointModule.cpp          |  9 ++-
 protomol/module/CheckpointModule.h            |  3 +-
 protomol/module/CommandLineModule.cpp         | 24 +++++--
 protomol/module/ConfigurationModule.cpp       | 17 +++--
 protomol/module/ConfigurationModule.h         |  7 ++-
 protomol/module/HessianIntegratorModule.cpp   |  5 +-
 protomol/module/IOModule.cpp                  | 42 ++++++++-----
 protomol/module/IOModule.h                    |  3 +-
 protomol/module/IntegratorBaseModule.cpp      |  8 +--
 protomol/module/IntegratorOpenMMModule.cpp    |  2 +
 protomol/module/LeapfrogModule.cpp            | 13 ++--
 protomol/module/MainModule.cpp                | 17 +++--
 protomol/module/MainModule.h                  |  3 +
 protomol/module/ModifierModule.cpp            | 25 +++++---
 protomol/module/ModifierModule.h              |  3 +-
 .../module/NonbondedCutoffForceModule.cpp     | 47 +++++++-------
 .../NonbondedFullElectrostaticForceModule.cpp | 22 ++++---
 protomol/module/NonbondedFullForceModule.cpp  | 23 ++++---
 .../NonbondedIntermittentFullForceModule.cpp  | 33 +++++-----
 .../module/NonbondedSimpleFullForceModule.cpp | 42 ++++++-------
 protomol/module/NormalModeModule.cpp          | 34 ++++++----
 protomol/module/NormalModeModule.h            |  3 +-
 protomol/module/OutputModule.cpp              | 17 ++---
 protomol/module/OutputModule.h                |  1 -
 protomol/module/TopologyModule.cpp            | 16 ++---
 protomol/module/TopologyModule.h              |  5 +-
 protomol/output/GUIServer.cpp                 | 28 +++++----
 protomol/output/GUIServer.h                   | 11 +++-
 protomol/output/Output.cpp                    | 13 ++--
 protomol/output/Output.h                      |  5 ++
 protomol/output/OutputCache.cpp               | 28 ++++-----
 protomol/output/OutputCache.h                 | 15 ++---
 protomol/output/OutputCheckpoint.cpp          | 30 +++++----
 protomol/output/OutputCheckpoint.h            |  6 +-
 protomol/output/OutputCollection.cpp          | 18 +++---
 protomol/output/OutputDCDTrajectory.cpp       | 26 ++++++--
 protomol/output/OutputDCDTrajectory.h         |  5 ++
 protomol/output/OutputDCDTrajectoryForces.cpp | 19 +++---
 protomol/output/OutputDCDTrajectoryForces.h   |  5 ++
 protomol/output/OutputDCDTrajectoryVel.cpp    | 18 +++---
 protomol/output/OutputDCDTrajectoryVel.h      |  5 ++
 protomol/output/OutputDihedrals.cpp           | 20 +++---
 protomol/output/OutputDihedrals.h             | 12 ++--
 protomol/output/OutputEnergies.cpp            | 17 ++---
 protomol/output/OutputEnergies.h              |  9 +++
 protomol/output/OutputFAHFile.cpp             | 16 ++++-
 protomol/output/OutputFAHFile.h               |  5 +-
 protomol/output/OutputFinalPDBPos.cpp         | 23 ++++---
 protomol/output/OutputFinalPDBPos.h           |  6 ++
 protomol/output/OutputFinalXYZPos.cpp         | 23 +++++--
 protomol/output/OutputFinalXYZPos.h           |  4 ++
 protomol/output/OutputFinalXYZVel.cpp         | 17 +++--
 protomol/output/OutputFinalXYZVel.h           |  4 ++
 protomol/output/OutputScreen.cpp              | 21 ++++---
 protomol/output/OutputScreen.h                |  6 ++
 protomol/output/OutputXTCTrajectory.cpp       | 22 +++++--
 protomol/output/OutputXTCTrajectory.h         |  8 +++
 protomol/output/OutputXYZTrajectoryForce.cpp  | 18 +++---
 protomol/output/OutputXYZTrajectoryForce.h    |  4 ++
 protomol/output/OutputXYZTrajectoryPos.cpp    | 23 +++++--
 protomol/output/OutputXYZTrajectoryPos.h      |  5 ++
 protomol/output/OutputXYZTrajectoryVel.cpp    | 16 +++--
 protomol/output/OutputXYZTrajectoryVel.h      |  4 ++
 protomol/parallel/FFTComplex.cpp              |  9 +--
 protomol/parallel/Parallel.cpp                | 25 ++++----
 protomol/parallel/ParallelType.h              |  1 +
 protomol/switch/C1SwitchingFunction.cpp       |  7 ++-
 protomol/switch/C1SwitchingFunction.h         | 11 +++-
 protomol/switch/C2SwitchingFunction.cpp       | 10 ++-
 protomol/switch/C2SwitchingFunction.h         | 11 +++-
 protomol/switch/CmpCnCnSwitchingFunction.cpp  |  9 ++-
 protomol/switch/CmpCnCnSwitchingFunction.h    | 12 +++-
 protomol/switch/CnSwitchingFunction.cpp       | 10 ++-
 protomol/switch/CnSwitchingFunction.h         | 11 +++-
 protomol/topology/AngleInfo.cpp               |  2 +
 protomol/topology/ArrayCellListStructure.cpp  | 13 +++-
 protomol/topology/ArrayCellListStructure.h    |  5 +-
 protomol/topology/BuildTopology.cpp           | 39 +++++++++---
 protomol/topology/BuildTopology.h             |  5 +-
 protomol/topology/BuildTopologyFromTpr.cpp    | 36 ++++++++---
 protomol/topology/BuildTopologyFromTpr.h      |  5 +-
 .../topology/CoulombSCPISMParameterTable.cpp  | 14 +++--
 protomol/topology/CubicCellManager.cpp        | 10 ++-
 protomol/topology/CubicCellManager.h          | 10 ++-
 protomol/topology/ExclusionTable.cpp          |  4 ++
 protomol/topology/ExclusionTable.h            |  9 +--
 protomol/topology/ExclusionType.h             |  1 +
 protomol/topology/GenericTopology.cpp         | 14 ++++-
 protomol/topology/GenericTopology.h           | 24 ++++---
 .../topology/LennardJonesParameterTable.cpp   |  6 +-
 .../topology/PeriodicBoundaryConditions.cpp   |  9 ++-
 .../topology/PeriodicBoundaryConditions.h     | 12 +++-
 protomol/topology/TopologyUtilities.cpp       | 26 +++++---
 protomol/topology/TopologyUtilities.h         | 17 ++---
 .../topology/VacuumBoundaryConditions.cpp     |  3 +
 protomol/topology/VacuumBoundaryConditions.h  | 12 +++-
 protomol/type/BlockMatrix.cpp                 |  5 +-
 protomol/type/BlockMatrix.h                   |  4 +-
 protomol/type/EigenvectorInfo.cpp             |  2 +
 protomol/type/Matrix3By3.cpp                  |  7 ++-
 protomol/type/Matrix3By3.h                    |  4 +-
 protomol/type/PAR.cpp                         |  3 +-
 protomol/type/PAR.h                           | 11 ++--
 protomol/type/PDB.cpp                         |  3 +
 protomol/type/PDB.h                           | 11 +++-
 protomol/type/ScalarStructure.cpp             |  3 +
 protomol/type/ScalarStructure.h               |  6 +-
 protomol/type/String.cpp                      |  6 +-
 protomol/type/Vector3DBlock.cpp               |  4 +-
 protomol/type/Vector3DBlock.h                 |  9 ++-
 373 files changed, 3258 insertions(+), 1303 deletions(-)

diff --git a/.gitignore b/.gitignore
index 865e0e6..1f347af 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,5 @@
 
 test/ProtoMol*
 test/tests/output
+
+*.gch
diff --git a/protomol/ProtoMolApp.cpp b/protomol/ProtoMolApp.cpp
index 6cf5ca9..ca8eff7 100644
--- a/protomol/ProtoMolApp.cpp
+++ b/protomol/ProtoMolApp.cpp
@@ -1,39 +1,53 @@
+#include <ctype.h>
 #include <protomol/ProtoMolApp.h>
-
+#include <protomol/analysis/AnalysisCollection.h>
 #include <protomol/base/ModuleManager.h>
-#include <protomol/base/SystemUtilities.h>
-#include <protomol/base/StringUtilities.h>
 #include <protomol/base/PMConstants.h>
+#include <protomol/base/Report.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/base/SystemUtilities.h>
 #include <protomol/base/TimerStatistic.h>
 #include <protomol/base/Zap.h>
-#include <protomol/base/Report.h>
-
-#include <protomol/module/MainModule.h>
-#include <protomol/module/IOModule.h>
-#include <protomol/module/ConfigurationModule.h>
-#include <protomol/module/AnalysisModule.h>
-
-#include <protomol/type/String.h>
-
 #include <protomol/config/CommandLine.h>
 #include <protomol/config/Configuration.h>
-
-#include <protomol/io/ConfigurationReader.h>
-
-#include <protomol/factory/TopologyFactory.h>
 #include <protomol/factory/OutputFactory.h>
-
-#include <protomol/topology/GenericTopology.h>
+#include <protomol/factory/TopologyFactory.h>
+#include <protomol/module/AnalysisModule.h>
+#include <protomol/module/ConfigurationModule.h>
+#include <protomol/module/IOModule.h>
+#include <protomol/module/MainModule.h>
+#include <protomol/output/OutputCollection.h>
+#include <protomol/parallel/Parallel.h>
 #include <protomol/topology/BuildTopology.h>
 #include <protomol/topology/BuildTopologyFromTpr.h>
+#include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-
-#include <protomol/output/OutputCollection.h>
-#include <protomol/analysis/AnalysisCollection.h>
-
-#include <protomol/parallel/Parallel.h>
-
+#include <stdio.h>
+#include <string.h>
+#include <algorithm>
 #include <iomanip>
+#include <iostream>
+#include <list>
+#include <map>
+
+#include "protomol/analysis/Analysis.h"
+#include "protomol/base/Exception.h"
+#include "protomol/base/Factory.h"
+#include "protomol/base/Timer.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/AnalysisFactory.h"
+#include "protomol/factory/ForceFactory.h"
+#include "protomol/factory/IntegratorFactory.h"
+#include "protomol/force/Force.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/integrator/IntegratorDefinition.h"
+#include "protomol/output/Output.h"
+#include "protomol/output/OutputCache.h"
+#include "protomol/topology/CoulombSCPISMParameterTable.h"
+#include "protomol/topology/CoulombSCPISMParameters.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/ScalarStructure.h"
 #ifdef HAVE_PACKAGE_H
 #include <protomol/package.h>
 #endif
diff --git a/protomol/ProtoMolApp.h b/protomol/ProtoMolApp.h
index 85cafdc..5c47c1d 100644
--- a/protomol/ProtoMolApp.h
+++ b/protomol/ProtoMolApp.h
@@ -1,23 +1,22 @@
 #ifndef PROTOMOLAPP_H
 #define PROTOMOLAPP_H
 
-#include <protomol/factory/TopologyFactory.h>
-#include <protomol/factory/ForceFactory.h>
-#include <protomol/factory/IntegratorFactory.h>
-#include <protomol/factory/OutputFactory.h>
-#include <protomol/factory/AnalysisFactory.h>
-
-#include <protomol/config/Configuration.h>
-#include <protomol/config/CommandLine.h>
-#include <protomol/output/OutputCache.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/type/EigenvectorInfo.h>
-#include <protomol/type/PSF.h>
-#include <protomol/type/PAR.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/CoulombSCPISMParameterTable.h>
-
-#include <ostream>
+#include <protomol/config/CommandLine.h>         // for CommandLine
+#include <protomol/config/Configuration.h>       // for Configuration
+#include <protomol/factory/AnalysisFactory.h>    // for AnalysisFactory
+#include <protomol/factory/ForceFactory.h>       // for ForceFactory
+#include <protomol/factory/IntegratorFactory.h>  // for IntegratorFactory
+#include <protomol/factory/OutputFactory.h>      // for OutputFactory
+#include <protomol/factory/TopologyFactory.h>    // for TopologyFactory
+#include <protomol/output/OutputCache.h>         // for OutputCache
+#include <protomol/type/EigenvectorInfo.h>       // for EigenvectorInfo
+#include <protomol/type/PAR.h>                   // for PAR
+#include <protomol/type/PSF.h>                   // for PSF
+#include <protomol/type/ScalarStructure.h>       // for ScalarStructure
+#include <protomol/type/Vector3DBlock.h>         // for Vector3DBlock
+#include <ostream>                               // for ostream
+#include <string>                                // for string
+#include <vector>                                // for vector
 
 namespace ProtoMol {
   class OutputCollection;
@@ -25,6 +24,7 @@ namespace ProtoMol {
   class Integrator;
   class GenericTopology;
   class ModuleManager;
+  struct CoulombSCPISMParameterTable;
 
   class ProtoMolApp {
   public:
diff --git a/protomol/analysis/Analysis.cpp b/protomol/analysis/Analysis.cpp
index bc2715a..881793b 100644
--- a/protomol/analysis/Analysis.cpp
+++ b/protomol/analysis/Analysis.cpp
@@ -1,9 +1,8 @@
 #include <protomol/analysis/Analysis.h>
 #include <protomol/config/Configuration.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/ProtoMolApp.h>
+
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/analysis/Analysis.h b/protomol/analysis/Analysis.h
index 670bf43..3c5ae39 100644
--- a/protomol/analysis/Analysis.h
+++ b/protomol/analysis/Analysis.h
@@ -2,9 +2,14 @@
 #define PROTOMOL_ANALYSIS_ANALYSIS_H
 
 #include <protomol/base/Makeable.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
 	class ProtoMolApp;
+	class Configuration;
+	class Value;
+	struct Parameter;
 
 	class Analysis : public Makeable<Analysis> {
 		public:
diff --git a/protomol/analysis/AnalysisCollection.cpp b/protomol/analysis/AnalysisCollection.cpp
index 1f6eee5..27b29bb 100644
--- a/protomol/analysis/AnalysisCollection.cpp
+++ b/protomol/analysis/AnalysisCollection.cpp
@@ -1,15 +1,10 @@
-#include <protomol/analysis/AnalysisCollection.h>
-#include <protomol/analysis/Analysis.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/integrator/Integrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
-#include <protomol/topology/TopologyUtilities.h>
 #include <protomol/ProtoMolApp.h>
+#include <protomol/analysis/Analysis.h>
+#include <protomol/analysis/AnalysisCollection.h>
 #include <protomol/base/Exception.h>
+#include <string>
+
+#include "protomol/output/OutputCache.h"
 
 using namespace ProtoMol;
 
diff --git a/protomol/analysis/AnalysisDihedral.cpp b/protomol/analysis/AnalysisDihedral.cpp
index edd3a7a..c4183e6 100644
--- a/protomol/analysis/AnalysisDihedral.cpp
+++ b/protomol/analysis/AnalysisDihedral.cpp
@@ -1,18 +1,24 @@
-#include <protomol/analysis/AnalysisDihedral.h>
-
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/module/MainModule.h>
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
-
+#include <protomol/analysis/AnalysisDihedral.h>
 #include <protomol/base/MathUtilities.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/SystemUtilities.h>
-
-#include <protomol/io/XYZWriter.h>
-#include <protomol/io/CheckpointConfigWriter.h>
-
-#include <sstream>
+#include <stdio.h>
 #include <iostream>
+#include <limits>
+#include <map>
+
+#include "protomol/analysis/Analysis.h"
+#include "protomol/base/Report.h"
+#include "protomol/config/Configuration.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/topology/RBTorsion.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/analysis/AnalysisDihedral.h b/protomol/analysis/AnalysisDihedral.h
index 0d3c579..55fdfb3 100644
--- a/protomol/analysis/AnalysisDihedral.h
+++ b/protomol/analysis/AnalysisDihedral.h
@@ -1,13 +1,18 @@
 #ifndef PROTOMOL_ANALYSIS_DIHEDRAL_H
 #define PROTOMOL_ANALYSIS_DIHEDRAL_H
 
-#include <protomol/base/StringUtilities.h>
 #include <protomol/analysis/Analysis.h>
-
+#include <protomol/base/StringUtilities.h>
 #include <map>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
 	class Configuration;
+class Value;
+struct Parameter;
 
 	class AnalysisDihedral : public Analysis {
 		public:
diff --git a/protomol/base/FileLocation.h b/protomol/base/FileLocation.h
index 0041abd..535b1fe 100644
--- a/protomol/base/FileLocation.h
+++ b/protomol/base/FileLocation.h
@@ -26,6 +26,7 @@
 #ifndef FILELOCATION_H
 #define FILELOCATION_H
 
+#include <iosfwd>
 #include <string>
 
 namespace ProtoMol {
diff --git a/protomol/base/Lapack.cpp b/protomol/base/Lapack.cpp
index b23305c..4addde5 100755
--- a/protomol/base/Lapack.cpp
+++ b/protomol/base/Lapack.cpp
@@ -1,7 +1,5 @@
 #include "Lapack.h"
 
-#include <protomol/base/Exception.h>
-
 #if defined(HAVE_LAPACK)
 #include <protomol/integrator/hessian/LapackProtomol.h>
 #elif defined(HAVE_SIMTK_LAPACK)
diff --git a/protomol/base/Makeable.cpp b/protomol/base/Makeable.cpp
index 5aea0b4..66e365b 100644
--- a/protomol/base/Makeable.cpp
+++ b/protomol/base/Makeable.cpp
@@ -2,6 +2,9 @@
 
 #include <protomol/base/StringUtilities.h>
 #include <protomol/base/Exception.h>
+#include <iostream>
+
+#include "protomol/base/MakeableDefinition.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/base/Makeable.h b/protomol/base/Makeable.h
index 278a291..0b0a817 100644
--- a/protomol/base/Makeable.h
+++ b/protomol/base/Makeable.h
@@ -3,8 +3,14 @@
 #define PROTOMOL_MAKEABLE_H
 
 #include <protomol/base/MakeableDefinition.h>
-
+#include <stddef.h>
 #include <iostream>
+#include <string>
+#include <vector>
+
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+
 using namespace std;
 
 namespace ProtoMol {
diff --git a/protomol/base/MathUtilities.cpp b/protomol/base/MathUtilities.cpp
index e46e35a..22283b9 100644
--- a/protomol/base/MathUtilities.cpp
+++ b/protomol/base/MathUtilities.cpp
@@ -1,5 +1,10 @@
 #include <protomol/base/MathUtilities.h>
 #include <protomol/base/Timer.h>
+#include <stdlib.h>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/base/Random.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 
diff --git a/protomol/base/MathUtilities.h b/protomol/base/MathUtilities.h
index de3c8b6..41a8f9c 100644
--- a/protomol/base/MathUtilities.h
+++ b/protomol/base/MathUtilities.h
@@ -3,14 +3,15 @@
 #define MATHUTILITIES_H
 
 #include <protomol/base/PMConstants.h>
-#include <protomol/type/SimpleTypes.h>
 #include <protomol/base/Random.h>
-
-#include <cmath>
+#include <protomol/type/SimpleTypes.h>
 #include <algorithm>
+#include <cmath>
 #include <queue>
 #include <vector>
 
+#include "protomol/type/Real.h"
+
 #ifndef M_PI
 #define M_PI 3.14159265358979323846
 #endif
diff --git a/protomol/base/Module.h b/protomol/base/Module.h
index 47e2411..873e098 100644
--- a/protomol/base/Module.h
+++ b/protomol/base/Module.h
@@ -2,14 +2,13 @@
 #define MODULE_H
 
 #include <protomol/base/Exception.h>
-
-#include <string>
 #include <set>
+#include <string>
 
 namespace ProtoMol {
-  class ProtoMolApp;
-  class GenericTopology;
   class ForceFactory;
+  class GenericTopology;
+  class ProtoMolApp;
 
   class Module {
   public:
diff --git a/protomol/base/ModuleManager.cpp b/protomol/base/ModuleManager.cpp
index 9c3c1ad..83f0643 100644
--- a/protomol/base/ModuleManager.cpp
+++ b/protomol/base/ModuleManager.cpp
@@ -1,12 +1,14 @@
-#include <protomol/base/ModuleManager.h>
-#include <protomol/base/Module.h>
-
-#include <protomol/base/Exception.h>
 #include <protomol/ProtoMolApp.h>
-#include <protomol/config/CommandLine.h>
+#include <protomol/base/Exception.h>
+#include <protomol/base/Module.h>
+#include <protomol/base/ModuleManager.h>
 #include <protomol/base/StringUtilities.h>
-
+#include <protomol/config/CommandLine.h>
 #include <iostream>
+#include <vector>
+
+#include "protomol/base/SmartPointer.h"
+#include "protomol/config/CommandLineOption.h"
 
 using namespace ProtoMol;
 using namespace std;
diff --git a/protomol/base/PMConstants.cpp b/protomol/base/PMConstants.cpp
index 015f06e..c8c0dd7 100644
--- a/protomol/base/PMConstants.cpp
+++ b/protomol/base/PMConstants.cpp
@@ -10,6 +10,8 @@
 
 #include <protomol/base/StringUtilities.h>
 
+#include "protomol/type/Real.h"
+
 using namespace std;
 
 namespace ProtoMol {
diff --git a/protomol/base/Random.h b/protomol/base/Random.h
index 58b1e32..23934ec 100644
--- a/protomol/base/Random.h
+++ b/protomol/base/Random.h
@@ -1,12 +1,11 @@
 #ifndef RANDOM_H
 #define RANDOM_H
 
-#include <protomol/type/Real.h>
 #include <protomol/base/Singleton.h>
-
-#include <vector>
+#include <protomol/type/Real.h>
 #include <fstream>
 #include <iostream>
+#include <vector>
 
 namespace ProtoMol {
 
diff --git a/protomol/base/Report.cpp b/protomol/base/Report.cpp
index b21c5bf..03d406e 100644
--- a/protomol/base/Report.cpp
+++ b/protomol/base/Report.cpp
@@ -1,8 +1,7 @@
 #include <protomol/base/Report.h>
-
-#include <iomanip>
-
 #include <protomol/base/SystemUtilities.h>
+#include <stddef.h>
+#include <algorithm>
 
 using namespace std;
 
diff --git a/protomol/base/StringUtilities.cpp b/protomol/base/StringUtilities.cpp
index 0b38a17..dc49dec 100644
--- a/protomol/base/StringUtilities.cpp
+++ b/protomol/base/StringUtilities.cpp
@@ -1,11 +1,14 @@
+#include <ctype.h>
+#include <math.h>
 #include <protomol/base/StringUtilities.h>
-#include <protomol/base/MathUtilities.h>
-
-#include <algorithm>
 #include <stdlib.h>
-#include <errno.h>
+#include <sys/errno.h>
+#include <algorithm>
+#include <cstring>
+#include <ostream>
 
-#include <protomol/base/Report.h>
+#include "protomol/base/PMConstants.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/base/StringUtilities.h b/protomol/base/StringUtilities.h
index 3c709f9..f04d5a5 100644
--- a/protomol/base/StringUtilities.h
+++ b/protomol/base/StringUtilities.h
@@ -2,8 +2,8 @@
 #ifndef STRINGUTILITIES_H
 #define STRINGUTILITIES_H
 
-#include <string>
 #include <cstring>
+#include <string>
 
 #ifdef HAVE_NO_SSTREAM
 #include <protomol/base/sstream_local.h>
@@ -12,8 +12,10 @@
 #endif
 
 #include <protomol/type/Vector3D.h>
-#include <vector>
 #include <ostream>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   //__________________________________________________________________ uppercase
diff --git a/protomol/base/SystemUtilities.cpp b/protomol/base/SystemUtilities.cpp
index ed982e0..0ace4a3 100644
--- a/protomol/base/SystemUtilities.cpp
+++ b/protomol/base/SystemUtilities.cpp
@@ -1,21 +1,23 @@
 #include <protomol/base/SystemUtilities.h>
-
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/Exception.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/errno.h>
+#include <sys/unistd.h>
 
 #ifdef _WIN32
 
 #define WIN32_LEAN_AND_MEAN
-#include <windows.h> // for GetFullPathName
-
 //____ Define the missing symbols from <unistd.h> for M$ ....
 #include <direct.h>
+#include <windows.h> // for GetFullPathName
+
 #define CHDIR _chdir
 #define PATHSEP '\\'
 #define PATHSEPSTR "\\"
 #define access _access
 #include <fcntl.h>
 #include <io.h>
+
 #define F_OK 0
 #define W_OK 2
 #define R_OK 4
@@ -26,15 +28,17 @@
 
 #include <libgen.h>
 #include <unistd.h>
+
 #define CHDIR chdir
 #define PATHSEP '/'
 #define PATHSEPSTR "/"
 #endif
 
-#include <fstream>
-#include <sys/stat.h>
 #include <string.h>
-#include <errno.h>
+#include <sys/stat.h>
+#include <fstream>
+
+#include "/Users/Omegaice/Documents/Code/ProtoMol/protomol/base/Exception.h"
 
 #ifdef HAVE_LIBFAH
 #include <fah/checksum/overrides.h>
diff --git a/protomol/base/Timer.cpp b/protomol/base/Timer.cpp
index 813a980..a6dc38e 100644
--- a/protomol/base/Timer.cpp
+++ b/protomol/base/Timer.cpp
@@ -19,23 +19,26 @@
  */
 
 #ifdef SVR4
-#include <unistd.h>
+#include <sys/param.h>
 #include <sys/time.h>
 #include <sys/times.h>
-#include <sys/param.h>
+#include <unistd.h>
 #elif defined (_WIN32)
+#include <mmsystem.h> // timeGetTime()
 #include <time.h>
 #include <windows.h>  // mmsystem.h cannot exist without this.
-#include <mmsystem.h> // timeGetTime()
 #else
-#include <unistd.h>
-#include <sys/time.h>
 #include <sys/resource.h>
+#include <sys/time.h>
 #endif
 
 #include <protomol/base/Timer.h>
+#include <stddef.h>
+#include <sys/_types/_timeval.h>
 #include <iostream>
 
+#include "protomol/base/Report.h"
+
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
 using namespace std;
diff --git a/protomol/base/TimerStatistic.cpp b/protomol/base/TimerStatistic.cpp
index a32385e..2eee0d7 100644
--- a/protomol/base/TimerStatistic.cpp
+++ b/protomol/base/TimerStatistic.cpp
@@ -1,4 +1,8 @@
 #include <protomol/base/TimerStatistic.h>
+#include <iostream>
+
+#include "protomol/base/Report.h"
+#include "protomol/base/Timer.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/base/TimerStatistic.h b/protomol/base/TimerStatistic.h
index 36cdae9..8996ca5 100644
--- a/protomol/base/TimerStatistic.h
+++ b/protomol/base/TimerStatistic.h
@@ -2,10 +2,9 @@
 #ifndef TIMERSTATISTIC_H
 #define TIMERSTATISTIC_H
 
-#include <string>
-
-#include <protomol/base/Timer.h>
 #include <protomol/base/Report.h>
+#include <protomol/base/Timer.h>
+#include <string>
 
 namespace ProtoMol {
   //____________________________________________________________ TimerStatistic
@@ -16,6 +15,10 @@ namespace ProtoMol {
    * TimerStatistic::timer[TimerStatistic::RUN].stop();@n
    * TimerStatistic::timer[TimerStatistic::RUN].reset();@n
    */
+namespace Report {
+class MyStreamer;
+}  // namespace Report
+
   class TimerStatistic {
 public:
     enum Enum {
diff --git a/protomol/config/CommandLine.cpp b/protomol/config/CommandLine.cpp
index 85176d9..3505a3c 100644
--- a/protomol/config/CommandLine.cpp
+++ b/protomol/config/CommandLine.cpp
@@ -1,14 +1,17 @@
-#include <protomol/config/CommandLine.h>
-
+#include <protomol/ProtoMolApp.h>
 #include <protomol/base/Exception.h>
-#include <protomol/type/String.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/module/ConfigurationModule.h>
 #include <protomol/base/StringUtilities.h>
-#include <protomol/base/SystemUtilities.h>
-#include <protomol/ProtoMolApp.h>
-
-#include <stdlib.h>
+#include <protomol/config/CommandLine.h>
+#include <protomol/config/Configuration.h>
+#include <iostream>
+#include <set>
+#include <utility>
+
+#include "protomol/base/Report.h"
+#include "protomol/base/SmartPointer.h"
+#include "protomol/config/CommandLineOption.h"
+#include "protomol/config/Value.h"
+#include "protomol/config/ValueType.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/config/CommandLineOption.cpp b/protomol/config/CommandLineOption.cpp
index 75ceee0..dfa8e96 100644
--- a/protomol/config/CommandLineOption.cpp
+++ b/protomol/config/CommandLineOption.cpp
@@ -1,7 +1,5 @@
 #include <protomol/config/CommandLineOption.h>
 
-#include <ctype.h>
-
 using namespace ProtoMol;
 using namespace std;
 
diff --git a/protomol/config/CommandLineOption.h b/protomol/config/CommandLineOption.h
index b52473f..8c239cd 100644
--- a/protomol/config/CommandLineOption.h
+++ b/protomol/config/CommandLineOption.h
@@ -1,10 +1,10 @@
 #ifndef COMMAND_LINE_OPTION_H
 #define COMMAND_LINE_OPTION_H
 
-#include <string>
+#include <ostream>
 #include <set>
+#include <string>
 #include <vector>
-#include <ostream>
 
 namespace ProtoMol {
   class CommandLineOption {
diff --git a/protomol/config/Configuration.cpp b/protomol/config/Configuration.cpp
index 07b102c..6d641b1 100644
--- a/protomol/config/Configuration.cpp
+++ b/protomol/config/Configuration.cpp
@@ -1,7 +1,11 @@
+#include <protomol/base/Exception.h>
+#include <protomol/base/Report.h>
 #include <protomol/config/Configuration.h>
+#include <utility>
 
-#include <protomol/base/Report.h>
-#include <protomol/base/Exception.h>
+#include "protomol/base/PMConstants.h"
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/Parameter.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/config/Configuration.h b/protomol/config/Configuration.h
index 8f5b896..a9cbef5 100644
--- a/protomol/config/Configuration.h
+++ b/protomol/config/Configuration.h
@@ -2,11 +2,14 @@
 #ifndef CONFIGURATION_H
 #define CONFIGURATION_H
 
-#include <protomol/config/Parameter.h>
 #include <protomol/base/StringUtilities.h>
+#include <protomol/config/Parameter.h>
+#include <map>
 #include <ostream>
+#include <string>
 #include <vector>
-#include <map>
+
+#include "protomol/config/Value.h"
 
 namespace ProtoMol {
   
@@ -16,6 +19,8 @@ namespace ProtoMol {
    * with the value and an optional help text.  The value uses Value, which
    * comes with additional information about the type and constraints.
    */
+struct Parameter;
+
   class Configuration {
     typedef std::map<std::string, Value, ltstrNocase>       ValueMapType;
     typedef std::map<std::string, std::string, ltstrNocase> AliasMapType;
diff --git a/protomol/config/ConstraintValueType.h b/protomol/config/ConstraintValueType.h
index 0317aa1..5a12cb4 100644
--- a/protomol/config/ConstraintValueType.h
+++ b/protomol/config/ConstraintValueType.h
@@ -3,6 +3,7 @@
 #define CONSTRAINTVALUETYPE_H
 
 #include <protomol/type/AbstractEnumType.h>
+#include <string>
 
 namespace ProtoMol {
   //_____________________________________________________ ConstraintValueEnum
diff --git a/protomol/config/Parameter.cpp b/protomol/config/Parameter.cpp
index 93ffed9..a292b4c 100644
--- a/protomol/config/Parameter.cpp
+++ b/protomol/config/Parameter.cpp
@@ -1,8 +1,11 @@
-#include <protomol/config/Parameter.h>
 #include <protomol/base/StringUtilities.h>
-
+#include <protomol/config/Parameter.h>
 #include <iomanip>
 
+#include "protomol/base/PMConstants.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+
 using namespace std;
 using namespace ProtoMol;
 
diff --git a/protomol/config/Parameter.h b/protomol/config/Parameter.h
index 40b1009..07fbf9e 100644
--- a/protomol/config/Parameter.h
+++ b/protomol/config/Parameter.h
@@ -4,8 +4,8 @@
 
 #include <protomol/config/Value.h>
 #include <protomol/type/SimpleTypes.h>
-
 #include <ostream>
+#include <string>
 
 namespace ProtoMol {
   //________________________________________________________ Parameter
diff --git a/protomol/config/Value.cpp b/protomol/config/Value.cpp
index a48a219..b67889c 100644
--- a/protomol/config/Value.cpp
+++ b/protomol/config/Value.cpp
@@ -1,7 +1,13 @@
 #include <protomol/config/Value.h>
+#include <algorithm>
 
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/MathUtilities.h>
+#include "protomol/base/Report.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/ValueType.h"
+
+namespace ProtoMol {
+template <typename T> struct ValueTraits;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/config/Value.h b/protomol/config/Value.h
index 12ed13a..8455003 100644
--- a/protomol/config/Value.h
+++ b/protomol/config/Value.h
@@ -2,9 +2,16 @@
 #ifndef VALUE_H
 #define VALUE_H
 
-#include <protomol/config/ValueType.h>
 #include <protomol/config/ConstraintValueType.h>
+#include <protomol/config/ValueType.h>
+#include <stddef.h>
+#include <iosfwd>
+#include <string>
 #include <typeinfo>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //________________________________________________________ Value
@@ -23,6 +30,11 @@ namespace ProtoMol {
    * - Special, extended types; acts like string with a type (ValueType),
    *   i.e., integrator, force etc.
    */
+namespace Report {
+class MyStreamer;
+}  // namespace Report
+template <typename T> struct ValueTraits;
+
   class Value {
     //________________________________________________________ PlaceHolder
     /**
diff --git a/protomol/config/ValueType.h b/protomol/config/ValueType.h
index e3e7c4f..149a8c1 100644
--- a/protomol/config/ValueType.h
+++ b/protomol/config/ValueType.h
@@ -2,10 +2,15 @@
 #ifndef VALUETYPE_H
 #define VALUETYPE_H
 
+#include <protomol/config/ConstraintValueType.h>
 #include <protomol/type/AbstractEnumType.h>
 #include <protomol/type/Vector3D.h>
+#include <istream>
+#include <string>
+#include <vector>
 
-#include <protomol/config/ConstraintValueType.h>
+#include "protomol/base/StringUtilities.h"
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   //_____________________________________________________ ValueEnum
@@ -64,14 +69,6 @@ namespace ProtoMol {
   //_____________________________________________________ ValueType
   typedef AbstractEnumType<ValueEnum> ValueType;
 
-  //_____________________________________________ ValueTraits & Enum2ValueTraits
-  /**
-   * ValueTraits and Enum2ValueTraits define mapping and type implementation
-   * behavior used by Value.
-   */
-  template<typename T>
-  struct ValueTraits;
-
   /**
    * Trait class defining the actual type, enum value, the representation type,
    * possible constraints, and implements the conversions.@n
@@ -81,6 +78,13 @@ namespace ProtoMol {
    */
   template<ValueType::Enum e>
   struct Enum2ValueTraits;
+  //_____________________________________________ ValueTraits & Enum2ValueTraits
+  /**
+   * ValueTraits and Enum2ValueTraits define mapping and type implementation
+   * behavior used by Value.
+   */
+  template<typename T>
+  struct ValueTraits;
 
   /// STRING
   template<>
diff --git a/protomol/factory/AnalysisFactory.cpp b/protomol/factory/AnalysisFactory.cpp
index 868b1d6..80841ce 100644
--- a/protomol/factory/AnalysisFactory.cpp
+++ b/protomol/factory/AnalysisFactory.cpp
@@ -1,9 +1,20 @@
-#include <protomol/factory/AnalysisFactory.h>
 #include <protomol/analysis/AnalysisCollection.h>
-#include <protomol/config/Configuration.h>
 #include <protomol/base/StringUtilities.h>
+#include <protomol/config/Configuration.h>
+#include <protomol/factory/AnalysisFactory.h>
 #include <protomol/factory/HelpTextFactory.h>
-#include <algorithm>
+#include <stddef.h>
+#include <map>
+#include <ostream>
+#include <set>
+#include <utility>
+
+#include "protomol/analysis/Analysis.h"
+#include "protomol/base/Exception.h"
+#include "protomol/base/Factory.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/factory/AnalysisFactory.h b/protomol/factory/AnalysisFactory.h
index 3449886..7b94440 100644
--- a/protomol/factory/AnalysisFactory.h
+++ b/protomol/factory/AnalysisFactory.h
@@ -2,13 +2,16 @@
 #ifndef ANALYSIS_FACTORY_H
 #define ANALYSIS_FACTORY_H
 
-#include <protomol/base/Factory.h>
-
 #include <protomol/analysis/Analysis.h>
+#include <protomol/base/Factory.h>
 #include <protomol/config/Value.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
 	class AnalysisCollection;
+class Configuration;
+class Value;
 
 	class AnalysisFactory : public Factory<Analysis> {
 		public:
diff --git a/protomol/factory/ForceFactory.cpp b/protomol/factory/ForceFactory.cpp
index 3f4a546..3add3a6 100644
--- a/protomol/factory/ForceFactory.cpp
+++ b/protomol/factory/ForceFactory.cpp
@@ -1,12 +1,22 @@
-#include <protomol/factory/ForceFactory.h>
-#include <protomol/base/StringUtilities.h>
+#include <ctype.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/SimpleTypes.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/factory/ForceFactory.h>
 #include <protomol/force/CompareForce.h>
 #include <protomol/force/TimeForce.h>
 #include <protomol/parallel/Parallel.h>
+#include <protomol/type/SimpleTypes.h>
+#include <stddef.h>
 #include <algorithm>
 #include <sstream>
+#include <utility>
+
+#include "protomol/base/Exception.h"
+#include "protomol/base/Factory.h"
+#include "protomol/base/PMConstants.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/force/Force.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/factory/ForceFactory.h b/protomol/factory/ForceFactory.h
index 1ed931f..598b16f 100644
--- a/protomol/factory/ForceFactory.h
+++ b/protomol/factory/ForceFactory.h
@@ -3,11 +3,20 @@
 #define FORCE_FACTORY_H
 
 #include <protomol/base/Factory.h>
-#include <protomol/force/Force.h>
 #include <protomol/config/Value.h>
+#include <protomol/force/Force.h>
+#include <iosfwd>
+#include <map>
+#include <set>
+#include <string>
+#include <vector>
+
+#include "protomol/base/StringUtilities.h"
 
 namespace ProtoMol {
   //________________________________________ ForceFactory
+class CompareForce;
+
   class ForceFactory : public Factory<Force> {
     typedef std::set<std::string, ltstrNocase> policy_t;
     typedef std::map<std::string, std::string, ltstrNocase> policiesSorted_t;
diff --git a/protomol/factory/HelpTextFactory.cpp b/protomol/factory/HelpTextFactory.cpp
index 8c2376c..5b8807e 100644
--- a/protomol/factory/HelpTextFactory.cpp
+++ b/protomol/factory/HelpTextFactory.cpp
@@ -1,5 +1,11 @@
-#include <protomol/factory/HelpTextFactory.h>
 #include <protomol/config/Configuration.h>
+#include <protomol/factory/HelpTextFactory.h>
+#include <stdlib.h>
+#include <utility>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/factory/HelpTextFactory.h b/protomol/factory/HelpTextFactory.h
index 486292b..7d992a6 100644
--- a/protomol/factory/HelpTextFactory.h
+++ b/protomol/factory/HelpTextFactory.h
@@ -3,9 +3,13 @@
 #define HELPTEXTFACTORY_H
 
 #include <protomol/config/Parameter.h>
-#include <vector>
 #include <map>
 #include <set>
+#include <string>
+#include <vector>
+
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/Value.h"
 
 namespace ProtoMol {
   class Configuration;
diff --git a/protomol/factory/IntegratorFactory.cpp b/protomol/factory/IntegratorFactory.cpp
index a6a3a4a..927c6ec 100644
--- a/protomol/factory/IntegratorFactory.cpp
+++ b/protomol/factory/IntegratorFactory.cpp
@@ -1,13 +1,23 @@
-#include <protomol/factory/IntegratorFactory.h>
-
-#include <protomol/integrator/STSIntegrator.h>
-#include <protomol/integrator/MTSIntegrator.h>
-#include <protomol/integrator/NonStandardIntegrator.h>
 #include <protomol/base/StringUtilities.h>
 #include <protomol/factory/ForceFactory.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/base/Report.h>
 #include <protomol/factory/HelpTextFactory.h>
+#include <protomol/factory/IntegratorFactory.h>
+#include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/MTSIntegrator.h>
+#include <protomol/integrator/NonStandardIntegrator.h>
+#include <protomol/integrator/STSIntegrator.h>
+#include <stddef.h>
+#include <istream>
+#include <map>
+#include <utility>
+
+#include "protomol/base/Exception.h"
+#include "protomol/base/Factory.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/ValueType.h"
+#include "protomol/force/Force.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/factory/IntegratorFactory.h b/protomol/factory/IntegratorFactory.h
index 188f76d..8706061 100644
--- a/protomol/factory/IntegratorFactory.h
+++ b/protomol/factory/IntegratorFactory.h
@@ -4,6 +4,10 @@
 
 #include <protomol/base/Factory.h>
 #include <protomol/integrator/Integrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/config/Value.h"
 
 namespace ProtoMol {
   class ForceFactory;
diff --git a/protomol/factory/OutputFactory.cpp b/protomol/factory/OutputFactory.cpp
index 10dbf27..f64e3f1 100644
--- a/protomol/factory/OutputFactory.cpp
+++ b/protomol/factory/OutputFactory.cpp
@@ -1,9 +1,20 @@
-#include <protomol/factory/OutputFactory.h>
-#include <protomol/output/OutputCollection.h>
-#include <protomol/config/Configuration.h>
 #include <protomol/base/StringUtilities.h>
+#include <protomol/config/Configuration.h>
 #include <protomol/factory/HelpTextFactory.h>
-#include <algorithm>
+#include <protomol/factory/OutputFactory.h>
+#include <protomol/output/OutputCollection.h>
+#include <stddef.h>
+#include <map>
+#include <ostream>
+#include <set>
+#include <utility>
+
+#include "protomol/base/Exception.h"
+#include "protomol/base/Factory.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/factory/OutputFactory.h b/protomol/factory/OutputFactory.h
index f723bbf..8b1885f 100644
--- a/protomol/factory/OutputFactory.h
+++ b/protomol/factory/OutputFactory.h
@@ -3,12 +3,15 @@
 #define OUTPUT_FACTORY_H
 
 #include <protomol/base/Factory.h>
-
-#include <protomol/output/Output.h>
 #include <protomol/config/Value.h>
+#include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class OutputCollection;
+class Configuration;
+class Value;
 
   //____ OutputFactory
   class OutputFactory : public Factory<Output> {
diff --git a/protomol/factory/TopologyFactory.cpp b/protomol/factory/TopologyFactory.cpp
index 9475e4a..1436408 100644
--- a/protomol/factory/TopologyFactory.cpp
+++ b/protomol/factory/TopologyFactory.cpp
@@ -1,7 +1,16 @@
-#include <protomol/factory/TopologyFactory.h>
-
 #include <protomol/config/Configuration.h>
 #include <protomol/factory/HelpTextFactory.h>
+#include <protomol/factory/TopologyFactory.h>
+#include <map>
+#include <ostream>
+#include <utility>
+
+#include "protomol/base/Exception.h"
+#include "protomol/base/Factory.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/topology/GenericTopology.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/factory/TopologyFactory.h b/protomol/factory/TopologyFactory.h
index f6a70d4..0c64089 100644
--- a/protomol/factory/TopologyFactory.h
+++ b/protomol/factory/TopologyFactory.h
@@ -4,9 +4,12 @@
 
 #include <protomol/base/Factory.h>
 #include <protomol/topology/GenericTopology.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class Configuration;
+class Value;
 
   //________________________________________ TopologyFactory
   class TopologyFactory : public Factory<GenericTopology> {
diff --git a/protomol/force/CompareForce.cpp b/protomol/force/CompareForce.cpp
index e8b0514..8642c49 100644
--- a/protomol/force/CompareForce.cpp
+++ b/protomol/force/CompareForce.cpp
@@ -1,9 +1,22 @@
+#include <math.h>
+#include <protomol/base/MathUtilities.h>
 #include <protomol/force/CompareForce.h>
+#include <protomol/parallel/Parallel.h>
+#include <protomol/topology/GenericTopology.h>
 #include <protomol/type/ScalarStructure.h>
-#include <protomol/base/MathUtilities.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/parallel/Parallel.h>
+#include <stddef.h>
+
+#include "protomol/base/Report.h"
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/Value.h"
+#include "protomol/force/Force.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Vector3D.h"
+
+namespace ProtoMol {
+struct Parameter;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/force/CompareForce.h b/protomol/force/CompareForce.h
index a67249b..10d370e 100644
--- a/protomol/force/CompareForce.h
+++ b/protomol/force/CompareForce.h
@@ -3,11 +3,20 @@
 #define COMPAREFORCE_H
 
 #include <protomol/force/Force.h>
+#include <string>
 #include <vector>
 
+#include "protomol/type/Real.h"
+
 namespace ProtoMol {
   //________________________________________ CompareForce
 
+class GenericTopology;
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class CompareForce : virtual public Force {
     // This class contains the definition of one force
 
diff --git a/protomol/force/CoulombForce.h b/protomol/force/CoulombForce.h
index fb2ef83..43e0693 100644
--- a/protomol/force/CoulombForce.h
+++ b/protomol/force/CoulombForce.h
@@ -2,14 +2,24 @@
 #ifndef COULOMBFORCE_H
 #define COULOMBFORCE_H
 
+#include <math.h>
+#include <protomol/config/Parameter.h>
+#include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/ExclusionTable.h>
-#include <protomol/config/Parameter.h>
 #include <string>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //____ CoulombForce
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class CoulombForce {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // This uses the weighted charges on each atom, so the Coulomb
diff --git a/protomol/force/Force.cpp b/protomol/force/Force.cpp
index dca666a..424f47f 100644
--- a/protomol/force/Force.cpp
+++ b/protomol/force/Force.cpp
@@ -1,7 +1,7 @@
+#include <protomol/force/CompareForce.h>
 #include <protomol/force/Force.h>
 
-#include <protomol/force/CompareForce.h>
-#include <protomol/base/Exception.h>
+#include "protomol/base/Report.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/force/Force.h b/protomol/force/Force.h
index 869e15c..901e557 100644
--- a/protomol/force/Force.h
+++ b/protomol/force/Force.h
@@ -2,20 +2,25 @@
 #ifndef FORCE_H
 #define FORCE_H
 
+#include <protomol/base/Exception.h>
 #include <protomol/base/Makeable.h>
 #include <protomol/base/MakeableDefinition.h>
-#include <protomol/base/Exception.h>
-
+#include <stddef.h>
+#include <string>
 #include <vector>
 
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+
 namespace ProtoMol {
+  class CompareForce;
+  class ForceGroup;
   class ForceGroup;
-  class ScalarStructure;
   class GenericTopology;
-  class Vector3DBlock;
-  class CompareForce;
+  class ScalarStructure;
   class TimeForce;
-  class ForceGroup;
+  class Vector3DBlock;
   //________________________________________ Force
 
   class Force : public Makeable<Force> {
diff --git a/protomol/force/ForceGroup.cpp b/protomol/force/ForceGroup.cpp
index eaadcb0..ae16b70 100644
--- a/protomol/force/ForceGroup.cpp
+++ b/protomol/force/ForceGroup.cpp
@@ -1,15 +1,17 @@
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/TimerStatistic.h>
 #include <protomol/force/ForceGroup.h>
-
-#include <protomol/force/system/SystemForce.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/force/extended/ExtendedForce.h>
-#include <protomol/force/MollyForce.h>
 #include <protomol/force/MetaForce.h>
-#include <protomol/base/TimerStatistic.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/force/MollyForce.h>
+#include <protomol/force/extended/ExtendedForce.h>
+#include <protomol/force/system/SystemForce.h>
 #include <protomol/parallel/Parallel.h>
+#include <protomol/topology/GenericTopology.h>
+#include <stddef.h>
+
+#include "protomol/base/MakeableDefinition.h"
+#include "protomol/base/Timer.h"
+#include "protomol/force/Force.h"
 
 //____#define DEBUG_OUTSTANDING_MSG
 
diff --git a/protomol/force/ForceGroup.h b/protomol/force/ForceGroup.h
index a086e1c..78d58d3 100644
--- a/protomol/force/ForceGroup.h
+++ b/protomol/force/ForceGroup.h
@@ -2,21 +2,22 @@
 #ifndef FORCEGROUP_H
 #define FORCEGROUP_H
 
+#include <protomol/base/MakeableDefinition.h>
 #include <list>
 #include <vector>
 
-#include <protomol/base/MakeableDefinition.h>
 namespace ProtoMol {
+  class ExtendedForce;
   class Force;
+  class GenericTopology;
   class MetaForce;
   class MollyForce;
+  class ProtoMolApp;
+  class ReducedHessAngle;
+  class ScalarStructure;
   class SystemForce;
-  class ExtendedForce;
-  class GenericTopology;
   class Vector3DBlock;
-  class ScalarStructure;
-  class ReducedHessAngle;
-  class ProtoMolApp;
+struct MakeableDefinition;
 
   //________________________________________ ForceGroup
 
diff --git a/protomol/force/GB/GBACEForce.cpp b/protomol/force/GB/GBACEForce.cpp
index 24a8c74..d77c4ab 100644
--- a/protomol/force/GB/GBACEForce.cpp
+++ b/protomol/force/GB/GBACEForce.cpp
@@ -1,7 +1,20 @@
 #include <protomol/force/GB/GBACEForce.h>
-
-#include <protomol/base/Report.h>
 #include <protomol/parallel/Parallel.h>
+#include <cmath>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/ScalarStructure.h"
+#include "protomol/type/SimpleTypes.h"
+
+namespace ProtoMol {
+class Vector3DBlock;
+}  // namespace ProtoMol
 
 using namespace ProtoMol;
 using namespace ProtoMol::Report;
diff --git a/protomol/force/GB/GBACEForce.h b/protomol/force/GB/GBACEForce.h
index d5596f5..c536bfc 100644
--- a/protomol/force/GB/GBACEForce.h
+++ b/protomol/force/GB/GBACEForce.h
@@ -2,13 +2,22 @@
 #ifndef GBACEFORCE_H
 #define GBACEFORCE_H
 
-#include <string>
-
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/GenericTopology.h>
+#include <protomol/type/ScalarStructure.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class GBACEForce {
     public:
       enum {DIST_R2 = 1};
diff --git a/protomol/force/GB/GBBornRadii.cpp b/protomol/force/GB/GBBornRadii.cpp
index b8ab35e..c61595f 100644
--- a/protomol/force/GB/GBBornRadii.cpp
+++ b/protomol/force/GB/GBBornRadii.cpp
@@ -1,8 +1,20 @@
-#include <protomol/force/GB/GBBornRadii.h>
-
+#include <math.h>
 #include <protomol/base/Report.h>
+#include <protomol/force/GB/GBBornRadii.h>
 #include <protomol/parallel/Parallel.h>
 
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/topology/Molecule.h"
+
+namespace ProtoMol {
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+}  // namespace ProtoMol
+
 using namespace ProtoMol;
 using namespace ProtoMol::Report;
 
diff --git a/protomol/force/GB/GBBornRadii.h b/protomol/force/GB/GBBornRadii.h
index 11f8dcd..3c445f5 100644
--- a/protomol/force/GB/GBBornRadii.h
+++ b/protomol/force/GB/GBBornRadii.h
@@ -2,13 +2,22 @@
 #ifndef GBBORNRADII_H
 #define GBBORNRADII_H
 
-#include <string>
-
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/GenericTopology.h>
+#include <protomol/type/ScalarStructure.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class GBBornRadii {
     public:
       enum {DIST_R2 = 1};
diff --git a/protomol/force/GB/GBForce.cpp b/protomol/force/GB/GBForce.cpp
index c8d5ddc..7f97af0 100644
--- a/protomol/force/GB/GBForce.cpp
+++ b/protomol/force/GB/GBForce.cpp
@@ -1,7 +1,21 @@
-#include <protomol/force/GB/GBForce.h>
-
 #include <protomol/base/Report.h>
+#include <protomol/force/GB/GBForce.h>
 #include <protomol/parallel/Parallel.h>
+#include <cmath>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/ScalarStructure.h"
+#include "protomol/type/SimpleTypes.h"
+
+namespace ProtoMol {
+class Vector3DBlock;
+}  // namespace ProtoMol
 
 using namespace ProtoMol;
 using namespace ProtoMol::Report;
diff --git a/protomol/force/GB/GBForce.h b/protomol/force/GB/GBForce.h
index 43a54ab..984f396 100644
--- a/protomol/force/GB/GBForce.h
+++ b/protomol/force/GB/GBForce.h
@@ -2,13 +2,22 @@
 #ifndef GBFORCE_H
 #define GBFORCE_H
 
-#include <string>
-
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/GenericTopology.h>
+#include <protomol/type/ScalarStructure.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class GBForce {
     public:
       enum {DIST_R2 = 1};
diff --git a/protomol/force/GB/GBPartialSum.cpp b/protomol/force/GB/GBPartialSum.cpp
index 698bc97..1d8fe48 100644
--- a/protomol/force/GB/GBPartialSum.cpp
+++ b/protomol/force/GB/GBPartialSum.cpp
@@ -1,6 +1,17 @@
 #include <protomol/force/GB/GBPartialSum.h>
-
 #include <protomol/parallel/Parallel.h>
+#include <cmath>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/GenericTopology.h"
+
+namespace ProtoMol {
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+}  // namespace ProtoMol
 
 using namespace ProtoMol;
 
diff --git a/protomol/force/GB/GBPartialSum.h b/protomol/force/GB/GBPartialSum.h
index f3d4d43..a548de4 100644
--- a/protomol/force/GB/GBPartialSum.h
+++ b/protomol/force/GB/GBPartialSum.h
@@ -2,13 +2,22 @@
 #ifndef GBPARTIALSUM_H
 #define GBPARTIALSUM_H
 
-#include <string>
-
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/GenericTopology.h>
+#include <protomol/type/ScalarStructure.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class GBPartialSum {
     public:
       enum {DIST_R2 = 1};
diff --git a/protomol/force/HarmonicRestraintForce.cpp b/protomol/force/HarmonicRestraintForce.cpp
index b357797..58b7fde 100644
--- a/protomol/force/HarmonicRestraintForce.cpp
+++ b/protomol/force/HarmonicRestraintForce.cpp
@@ -1,5 +1,11 @@
 #include <protomol/force/HarmonicRestraintForce.h>
 
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+
 using namespace std;
 
 //____ HarmonicRestraintForce
diff --git a/protomol/force/HarmonicRestraintForce.h b/protomol/force/HarmonicRestraintForce.h
index c5e6d10..8afaa68 100644
--- a/protomol/force/HarmonicRestraintForce.h
+++ b/protomol/force/HarmonicRestraintForce.h
@@ -2,13 +2,25 @@
 #ifndef HARMONICRESTRAINTFORCE_H
 #define HARMONICRESTRAINTFORCE_H
 
-#include <protomol/topology/Topology.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
+#include <protomol/base/Report.h>
 #include <protomol/config/Parameter.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/topology/Topology.h>
 #include <protomol/topology/TopologyUtilities.h>
+#include <protomol/type/ScalarStructure.h>
 #include <string>
-#include <protomol/base/Report.h>
+#include <vector>
+
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+
+namespace ProtoMol {
+class GenericTopology;
+class Value;
+struct Parameter;
+}  // namespace ProtoMol
 
 using namespace ProtoMol::Report;
 
diff --git a/protomol/force/LennardJonesForce.h b/protomol/force/LennardJonesForce.h
index 4d1a0dd..27b5fd0 100644
--- a/protomol/force/LennardJonesForce.h
+++ b/protomol/force/LennardJonesForce.h
@@ -2,13 +2,26 @@
 #ifndef LENNARDJONESFORCE_H
 #define LENNARDJONESFORCE_H
 
+#include <protomol/base/Report.h>
+#include <protomol/config/Parameter.h>
+#include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/LennardJonesParameters.h>
 #include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/ExclusionTable.h>
-#include <protomol/config/Parameter.h>
 #include <string>
-#include <protomol/base/Report.h>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/LennardJonesParameterTable.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+
+namespace ProtoMol {
+class Value;
+class Vector3DBlock;
+struct Parameter;
+}  // namespace ProtoMol
+
 using namespace ProtoMol::Report;
 
 namespace ProtoMol {
diff --git a/protomol/force/LennardJonesVDWForce.h b/protomol/force/LennardJonesVDWForce.h
index e0da2a6..a581965 100644
--- a/protomol/force/LennardJonesVDWForce.h
+++ b/protomol/force/LennardJonesVDWForce.h
@@ -2,13 +2,28 @@
 #ifndef LENNARDJONESVDWFORCE_H
 #define LENNARDJONESVDWFORCE_H
 
+#include <protomol/base/Report.h>
+#include <protomol/config/Parameter.h>
+#include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/LennardJonesParameters.h>
 #include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/ExclusionTable.h>
-#include <protomol/config/Parameter.h>
+#include <stddef.h>
 #include <string>
-#include <protomol/base/Report.h>
+#include <vector>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Value.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/LennardJonesParameterTable.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+
+namespace ProtoMol {
+class Vector3DBlock;
+}  // namespace ProtoMol
+
 using namespace ProtoMol::Report;
 
 namespace ProtoMol {
diff --git a/protomol/force/MetaForce.h b/protomol/force/MetaForce.h
index 9e4bd5c..e7ae9d0 100644
--- a/protomol/force/MetaForce.h
+++ b/protomol/force/MetaForce.h
@@ -3,6 +3,7 @@
 #define METAFORCE_H
 
 #include <protomol/force/Force.h>
+#include <vector>
 
 namespace ProtoMol {
   class ForceGroup;
diff --git a/protomol/force/MollyForce.h b/protomol/force/MollyForce.h
index 459ac89..069d8fa 100644
--- a/protomol/force/MollyForce.h
+++ b/protomol/force/MollyForce.h
@@ -8,9 +8,9 @@
 namespace ProtoMol {
   class ForceGroup;
   class GenericTopology;
-  class Vector3DBlock;
-  class ScalarStructure;
   class ReducedHessAngle;
+  class ScalarStructure;
+  class Vector3DBlock;
 
   //________________________________________ MollyForce
 
diff --git a/protomol/force/ProteinRestraintForce.cpp b/protomol/force/ProteinRestraintForce.cpp
index 82a5021..43530c7 100644
--- a/protomol/force/ProteinRestraintForce.cpp
+++ b/protomol/force/ProteinRestraintForce.cpp
@@ -1,5 +1,10 @@
 #include <protomol/force/ProteinRestraintForce.h>
 
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+
 using namespace std;
 
 //____ ProteinRestraintForce
diff --git a/protomol/force/ProteinRestraintForce.h b/protomol/force/ProteinRestraintForce.h
index d363c76..6daf5f3 100644
--- a/protomol/force/ProteinRestraintForce.h
+++ b/protomol/force/ProteinRestraintForce.h
@@ -2,13 +2,25 @@
 #ifndef PROTEINRESTRAINTFORCE_H
 #define PROTEINRESTRAINTFORCE_H
 
-#include <protomol/topology/Topology.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
+#include <protomol/base/Report.h>
 #include <protomol/config/Parameter.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/topology/Topology.h>
 #include <protomol/topology/TopologyUtilities.h>
+#include <protomol/type/ScalarStructure.h>
 #include <string>
-#include <protomol/base/Report.h>
+#include <vector>
+
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+
+namespace ProtoMol {
+class GenericTopology;
+class Value;
+struct Parameter;
+}  // namespace ProtoMol
 
 using namespace ProtoMol::Report;
 
diff --git a/protomol/force/TimeForce.cpp b/protomol/force/TimeForce.cpp
index 06e66cd..9b1eb04 100644
--- a/protomol/force/TimeForce.cpp
+++ b/protomol/force/TimeForce.cpp
@@ -1,9 +1,22 @@
-#include <protomol/force/TimeForce.h>
-#include <protomol/type/ScalarStructure.h>
+#include <math.h>
 #include <protomol/base/MathUtilities.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
+#include <protomol/force/TimeForce.h>
 #include <protomol/parallel/Parallel.h>
+#include <stddef.h>
+#include <iostream>
+
+#include "protomol/base/Report.h"
+#include "protomol/base/StringUtilities.h"
+#include "protomol/base/Timer.h"
+#include "protomol/config/Value.h"
+#include "protomol/force/Force.h"
+
+namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+class Vector3DBlock;
+struct Parameter;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/force/TimeForce.h b/protomol/force/TimeForce.h
index b331fea..9036a19 100644
--- a/protomol/force/TimeForce.h
+++ b/protomol/force/TimeForce.h
@@ -2,12 +2,20 @@
 #ifndef TIMEFORCE_H
 #define TIMEFORCE_H
 
-#include <protomol/force/Force.h>
 #include <protomol/base/Timer.h>
+#include <protomol/force/Force.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   //________________________________________ TimeForce
 
+class GenericTopology;
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class TimeForce : virtual public Force {
     // This class contains the definition of one force
 
diff --git a/protomol/force/born/BornRadii.cpp b/protomol/force/born/BornRadii.cpp
index 8e39d8f..a31e682 100644
--- a/protomol/force/born/BornRadii.cpp
+++ b/protomol/force/born/BornRadii.cpp
@@ -1,5 +1,10 @@
 #include <protomol/force/born/BornRadii.h>
 
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+
 using namespace std;
 using namespace ProtoMol;
 //____ Born Radii calculation only
diff --git a/protomol/force/born/BornRadii.h b/protomol/force/born/BornRadii.h
index e045f71..63e8865 100644
--- a/protomol/force/born/BornRadii.h
+++ b/protomol/force/born/BornRadii.h
@@ -2,17 +2,29 @@
 #ifndef BORNRADII_H
 #define BORNRADII_H
 
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/ExclusionTable.h>
-#include <protomol/type/Real.h>
-#include <protomol/type/Vector3D.h>
+#include <math.h>
+#include <protomol/base/Report.h>
 #include <protomol/config/Parameter.h>
 #include <protomol/force/born/BornSwitch.h>
 #include <protomol/parallel/Parallel.h>
+#include <protomol/topology/ExclusionTable.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/type/Real.h>
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3D.h>
 #include <string>
+#include <vector>
 
-#include <protomol/base/Report.h>
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/topology/Molecule.h"
+
+namespace ProtoMol {
+class ScalarStructure;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+}  // namespace ProtoMol
 
 using namespace ProtoMol::Report;
 
diff --git a/protomol/force/born/BornSelfForce.cpp b/protomol/force/born/BornSelfForce.cpp
index d04f3a3..ebe9409 100644
--- a/protomol/force/born/BornSelfForce.cpp
+++ b/protomol/force/born/BornSelfForce.cpp
@@ -1,4 +1,10 @@
 #include <protomol/force/born/BornSelfForce.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+
 using namespace std;
 using namespace ProtoMol;
 //____ BornSelfForce
diff --git a/protomol/force/born/BornSelfForce.h b/protomol/force/born/BornSelfForce.h
index bb50e01..3e0ebab 100644
--- a/protomol/force/born/BornSelfForce.h
+++ b/protomol/force/born/BornSelfForce.h
@@ -2,15 +2,27 @@
 #ifndef BORNSELFFORCE_H
 #define BORNSELFFORCE_H
 
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/ExclusionTable.h>
+#include <math.h>
+#include <protomol/base/Report.h>
 #include <protomol/config/Parameter.h>
 #include <protomol/force/born/BornSwitch.h>
 #include <protomol/parallel/Parallel.h>
+#include <protomol/topology/ExclusionTable.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/type/ScalarStructure.h>
 #include <string>
+#include <vector>
 
-#include <protomol/base/Report.h>
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+
+namespace ProtoMol {
+class Value;
+class Vector3DBlock;
+struct Parameter;
+}  // namespace ProtoMol
 
 using namespace ProtoMol::Report;
 
diff --git a/protomol/force/coulomb/CoulombForceDiElec.cpp b/protomol/force/coulomb/CoulombForceDiElec.cpp
index e278cf3..4b52118 100644
--- a/protomol/force/coulomb/CoulombForceDiElec.cpp
+++ b/protomol/force/coulomb/CoulombForceDiElec.cpp
@@ -1,5 +1,10 @@
 #include <protomol/force/coulomb/CoulombForceDiElec.h>
 
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+
 using namespace std;
 using namespace ProtoMol;
 
diff --git a/protomol/force/coulomb/CoulombForceDiElec.h b/protomol/force/coulomb/CoulombForceDiElec.h
index 573a5dd..e2daaae 100644
--- a/protomol/force/coulomb/CoulombForceDiElec.h
+++ b/protomol/force/coulomb/CoulombForceDiElec.h
@@ -2,15 +2,24 @@
 #ifndef COULOMBFORCEDIELEC_H
 #define COULOMBFORCEDIELEC_H
 
+#include <math.h>
+#include <protomol/config/Parameter.h>
+#include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/ExclusionTable.h>
-#include <protomol/config/Parameter.h>
 #include <string>
-#include <math.h>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //____ CoulombForce
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class CoulombForceDiElec {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // This uses the weighted charges on each atom.
diff --git a/protomol/force/coulomb/CoulombSCPISMForce.cpp b/protomol/force/coulomb/CoulombSCPISMForce.cpp
index 7e838aa..f872b28 100644
--- a/protomol/force/coulomb/CoulombSCPISMForce.cpp
+++ b/protomol/force/coulomb/CoulombSCPISMForce.cpp
@@ -1,5 +1,10 @@
 #include <protomol/force/coulomb/CoulombSCPISMForce.h>
 
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+
 using namespace std;
 using namespace ProtoMol;
 
diff --git a/protomol/force/coulomb/CoulombSCPISMForce.h b/protomol/force/coulomb/CoulombSCPISMForce.h
index 16088f4..e67e0f0 100644
--- a/protomol/force/coulomb/CoulombSCPISMForce.h
+++ b/protomol/force/coulomb/CoulombSCPISMForce.h
@@ -2,16 +2,28 @@
 #ifndef COULOMBSCPISMFORCE_H
 #define COULOMBSCPISMFORCE_H
 
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/ExclusionTable.h>
-#include <protomol/config/Parameter.h>
+#include <math.h>
 #include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
+#include <protomol/config/Parameter.h>
+#include <protomol/topology/ExclusionTable.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/type/ScalarStructure.h>
+#include <iostream>
 #include <string>
-#include <math.h>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Molecule.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+
+namespace ProtoMol {
+class Value;
+class Vector3DBlock;
+struct Parameter;
+}  // namespace ProtoMol
 
-#include <iostream>
 using namespace std;
 
 using namespace ProtoMol::Report;
diff --git a/protomol/force/extended/ExtendedCompareForce.cpp b/protomol/force/extended/ExtendedCompareForce.cpp
index 274b7b2..c1a3fcd 100644
--- a/protomol/force/extended/ExtendedCompareForce.cpp
+++ b/protomol/force/extended/ExtendedCompareForce.cpp
@@ -1,7 +1,14 @@
 #include <protomol/force/extended/ExtendedCompareForce.h>
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
+
+#include "protomol/force/CompareForce.h"
+#include "protomol/force/Force.h"
+#include "protomol/force/extended/ExtendedForce.h"
+
+namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+}  // namespace ProtoMol
 
 using namespace ProtoMol;
 //____ ExtendedCompareForce
diff --git a/protomol/force/extended/ExtendedCompareForce.h b/protomol/force/extended/ExtendedCompareForce.h
index 37e5b93..4d5776d 100644
--- a/protomol/force/extended/ExtendedCompareForce.h
+++ b/protomol/force/extended/ExtendedCompareForce.h
@@ -8,6 +8,11 @@
 namespace ProtoMol {
   //________________________________________ ExtendedCompareForce
 
+class Force;
+class GenericTopology;
+class ScalarStructure;
+class Vector3DBlock;
+
   class ExtendedCompareForce : public CompareForce, public ExtendedForce {
     // This class contains the definition of one force
 
diff --git a/protomol/force/extended/ExtendedForce.cpp b/protomol/force/extended/ExtendedForce.cpp
index e6d7cfc..6fa4524 100644
--- a/protomol/force/extended/ExtendedForce.cpp
+++ b/protomol/force/extended/ExtendedForce.cpp
@@ -1,8 +1,12 @@
-#include <protomol/force/extended/ExtendedForce.h>
 #include <protomol/force/ForceGroup.h>
 #include <protomol/force/extended/ExtendedCompareForce.h>
+#include <protomol/force/extended/ExtendedForce.h>
 #include <protomol/force/extended/ExtendedTimeForce.h>
 
+namespace ProtoMol {
+class Force;
+}  // namespace ProtoMol
+
 using namespace ProtoMol;
 //____ ExtendedForce
 
diff --git a/protomol/force/extended/ExtendedForce.h b/protomol/force/extended/ExtendedForce.h
index d542b05..e3c24ca 100644
--- a/protomol/force/extended/ExtendedForce.h
+++ b/protomol/force/extended/ExtendedForce.h
@@ -6,12 +6,13 @@
 
 namespace ProtoMol {
   class CompareForce;
-  class TimeForce;
+  class CompareForce;
   class ForceGroup;
   class GenericTopology;
-  class Vector3DBlock;
-  class CompareForce;
   class TimeForce;
+  class TimeForce;
+  class Vector3DBlock;
+class ScalarStructure;
 
   //________________________________________ ExtendedForce
 
diff --git a/protomol/force/extended/ExtendedTimeForce.cpp b/protomol/force/extended/ExtendedTimeForce.cpp
index 82f3a91..9fa718f 100644
--- a/protomol/force/extended/ExtendedTimeForce.cpp
+++ b/protomol/force/extended/ExtendedTimeForce.cpp
@@ -1,7 +1,14 @@
 #include <protomol/force/extended/ExtendedTimeForce.h>
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
+
+#include "protomol/force/Force.h"
+#include "protomol/force/TimeForce.h"
+#include "protomol/force/extended/ExtendedForce.h"
+
+namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+}  // namespace ProtoMol
 
 using namespace ProtoMol;
 //____ ExtendedTimeForce
diff --git a/protomol/force/extended/ExtendedTimeForce.h b/protomol/force/extended/ExtendedTimeForce.h
index 64043a5..ab192d6 100644
--- a/protomol/force/extended/ExtendedTimeForce.h
+++ b/protomol/force/extended/ExtendedTimeForce.h
@@ -8,6 +8,11 @@
 namespace ProtoMol {
   //________________________________________ ExtendedTimeForce
 
+class Force;
+class GenericTopology;
+class ScalarStructure;
+class Vector3DBlock;
+
   class ExtendedTimeForce : public TimeForce, public ExtendedForce {
     // This class contains the definition of one force
 
diff --git a/protomol/force/hessian/HessDihedral.cpp b/protomol/force/hessian/HessDihedral.cpp
index 7f6cf04..528beb9 100644
--- a/protomol/force/hessian/HessDihedral.cpp
+++ b/protomol/force/hessian/HessDihedral.cpp
@@ -1,6 +1,11 @@
-#include <protomol/force/hessian/HessDihedral.h>
-#include <protomol/type/Vector3DBlock.h>
+#include <math.h>
 #include <protomol/base/Report.h>
+#include <protomol/force/hessian/HessDihedral.h>
+#include <vector>
+
+#include "protomol/topology/RBTorsion.h"
+#include "protomol/topology/Torsion.h"
+#include "protomol/type/Matrix3By3.h"
 
 using namespace ProtoMol::Report;
 
diff --git a/protomol/force/hessian/HessDihedral.h b/protomol/force/hessian/HessDihedral.h
index 84c8c59..92e7ced 100644
--- a/protomol/force/hessian/HessDihedral.h
+++ b/protomol/force/hessian/HessDihedral.h
@@ -5,6 +5,9 @@
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/type/Matrix3By3.h>
 
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+
 namespace ProtoMol {
   /**
    *
@@ -14,6 +17,9 @@ namespace ProtoMol {
    *  the results back again.
    *  Extended to Rykart-Bellman Dihedrals
    */
+class RBTorsion;
+class Torsion;
+
   class HessDihedral {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors, assignment
diff --git a/protomol/force/hessian/ReducedHessAngle.cpp b/protomol/force/hessian/ReducedHessAngle.cpp
index b7fc9d5..64c3d11 100644
--- a/protomol/force/hessian/ReducedHessAngle.cpp
+++ b/protomol/force/hessian/ReducedHessAngle.cpp
@@ -1,5 +1,8 @@
+#include <math.h>
 #include <protomol/force/hessian/ReducedHessAngle.h>
-#include <protomol/base/Report.h>
+#include <ostream>
+
+#include "protomol/type/Matrix3By3.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/force/hessian/ReducedHessAngle.h b/protomol/force/hessian/ReducedHessAngle.h
index a53301e..89ab67f 100644
--- a/protomol/force/hessian/ReducedHessAngle.h
+++ b/protomol/force/hessian/ReducedHessAngle.h
@@ -3,6 +3,10 @@
 #define REDUCEDHESSANGLE_H
 
 #include <protomol/type/Matrix3By3.h>
+#include <iosfwd>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 
 namespace ProtoMol {
diff --git a/protomol/force/hessian/ReducedHessBond.cpp b/protomol/force/hessian/ReducedHessBond.cpp
index edb9f63..f9b4a77 100644
--- a/protomol/force/hessian/ReducedHessBond.cpp
+++ b/protomol/force/hessian/ReducedHessBond.cpp
@@ -1,5 +1,9 @@
+#include <math.h>
 #include <protomol/force/hessian/ReducedHessBond.h>
 
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/Vector3D.h"
+
 using namespace ProtoMol;
 Matrix3By3 ProtoMol::reducedHessBond(const Vector3D &atom_i,
                                      const Vector3D &atom_j,
diff --git a/protomol/force/hessian/ReducedHessBond.h b/protomol/force/hessian/ReducedHessBond.h
index 17043bf..40e37db 100644
--- a/protomol/force/hessian/ReducedHessBond.h
+++ b/protomol/force/hessian/ReducedHessBond.h
@@ -2,8 +2,10 @@
 #ifndef REDUCEDHESSBOND_H
 #define REDUCEDHESSBOND_H
 
-#include <protomol/type/Vector3D.h>
 #include <protomol/type/Matrix3By3.h>
+#include <protomol/type/Vector3D.h>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   Matrix3By3 reducedHessBond(const Vector3D &atom_i, const Vector3D &atom_j,
diff --git a/protomol/force/hessian/ReducedHessBornSelf.cpp b/protomol/force/hessian/ReducedHessBornSelf.cpp
index badf81d..972153f 100644
--- a/protomol/force/hessian/ReducedHessBornSelf.cpp
+++ b/protomol/force/hessian/ReducedHessBornSelf.cpp
@@ -1,6 +1,14 @@
+#include <math.h>
+#include <protomol/force/born/BornSwitch.h>
 #include <protomol/force/hessian/ReducedHessBornSelf.h>
 #include <protomol/topology/GenericTopology.h>
-#include <protomol/force/born/BornSwitch.h>
+#include <string>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/type/Matrix3By3.h"
 
 using namespace ProtoMol;
 //____ ReducedHessBornSelf
diff --git a/protomol/force/hessian/ReducedHessBornSelf.h b/protomol/force/hessian/ReducedHessBornSelf.h
index 2b69558..4faadf7 100644
--- a/protomol/force/hessian/ReducedHessBornSelf.h
+++ b/protomol/force/hessian/ReducedHessBornSelf.h
@@ -2,8 +2,11 @@
 #ifndef REDUCEDHESSBORNSELF_H
 #define REDUCEDHESSBORNSELF_H
 
-#include <protomol/type/Matrix3By3.h>
 #include <protomol/topology/ExclusionTable.h>
+#include <protomol/type/Matrix3By3.h>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   class GenericTopology;
diff --git a/protomol/force/hessian/ReducedHessCoulomb.cpp b/protomol/force/hessian/ReducedHessCoulomb.cpp
index 5fd6cb2..44e6828 100644
--- a/protomol/force/hessian/ReducedHessCoulomb.cpp
+++ b/protomol/force/hessian/ReducedHessCoulomb.cpp
@@ -1,5 +1,11 @@
+#include <math.h>
 #include <protomol/force/hessian/ReducedHessCoulomb.h>
 #include <protomol/topology/GenericTopology.h>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/type/Matrix3By3.h"
 
 using namespace ProtoMol;
 //____ ReducedHessCoulomb
diff --git a/protomol/force/hessian/ReducedHessCoulomb.h b/protomol/force/hessian/ReducedHessCoulomb.h
index 306bce0..98871df 100644
--- a/protomol/force/hessian/ReducedHessCoulomb.h
+++ b/protomol/force/hessian/ReducedHessCoulomb.h
@@ -2,8 +2,11 @@
 #ifndef REDUCEDHESSCOULOMB_H
 #define REDUCEDHESSCOULOMB_H
 
-#include <protomol/type/Matrix3By3.h>
 #include <protomol/topology/ExclusionTable.h>
+#include <protomol/type/Matrix3By3.h>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   class GenericTopology;
diff --git a/protomol/force/hessian/ReducedHessCoulombDiElec.cpp b/protomol/force/hessian/ReducedHessCoulombDiElec.cpp
index 908d62a..9678cba 100644
--- a/protomol/force/hessian/ReducedHessCoulombDiElec.cpp
+++ b/protomol/force/hessian/ReducedHessCoulombDiElec.cpp
@@ -1,5 +1,11 @@
+#include <math.h>
 #include <protomol/force/hessian/ReducedHessCoulombDiElec.h>
 #include <protomol/topology/GenericTopology.h>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/type/Matrix3By3.h"
 
 using namespace ProtoMol;
 //____ ReducedHessCoulombDielec
diff --git a/protomol/force/hessian/ReducedHessCoulombDiElec.h b/protomol/force/hessian/ReducedHessCoulombDiElec.h
index a119664..cd75b4c 100644
--- a/protomol/force/hessian/ReducedHessCoulombDiElec.h
+++ b/protomol/force/hessian/ReducedHessCoulombDiElec.h
@@ -2,8 +2,11 @@
 #ifndef REDUCEDHESSCOULOMBDIELEC_H
 #define REDUCEDHESSCOULOMBDIELEC_H
 
-#include <protomol/type/Matrix3By3.h>
 #include <protomol/topology/ExclusionTable.h>
+#include <protomol/type/Matrix3By3.h>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   class GenericTopology;
diff --git a/protomol/force/hessian/ReducedHessCoulombSCPISM.cpp b/protomol/force/hessian/ReducedHessCoulombSCPISM.cpp
index 60245f3..ffbf469 100644
--- a/protomol/force/hessian/ReducedHessCoulombSCPISM.cpp
+++ b/protomol/force/hessian/ReducedHessCoulombSCPISM.cpp
@@ -1,5 +1,11 @@
+#include <math.h>
 #include <protomol/force/hessian/ReducedHessCoulombSCPISM.h>
 #include <protomol/topology/GenericTopology.h>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/type/Matrix3By3.h"
 
 using namespace ProtoMol;
 //____ ReducedHessCoulombSCPISM
diff --git a/protomol/force/hessian/ReducedHessCoulombSCPISM.h b/protomol/force/hessian/ReducedHessCoulombSCPISM.h
index 64024d9..9d6ddc7 100644
--- a/protomol/force/hessian/ReducedHessCoulombSCPISM.h
+++ b/protomol/force/hessian/ReducedHessCoulombSCPISM.h
@@ -2,8 +2,11 @@
 #ifndef REDUCEDHESSCOULOMBSCPISM_H
 #define REDUCEDHESSCOULOMBSCPISM_H
 
-#include <protomol/type/Matrix3By3.h>
 #include <protomol/topology/ExclusionTable.h>
+#include <protomol/type/Matrix3By3.h>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   class GenericTopology;
diff --git a/protomol/force/hessian/ReducedHessGB.cpp b/protomol/force/hessian/ReducedHessGB.cpp
index 46a4c06..02b6459 100644
--- a/protomol/force/hessian/ReducedHessGB.cpp
+++ b/protomol/force/hessian/ReducedHessGB.cpp
@@ -1,10 +1,12 @@
+#include <math.h>
 #include <protomol/force/hessian/ReducedHessGB.h>
 #include <protomol/topology/GenericTopology.h>
+#include <vector>
 
-#include <protomol/base/Report.h>
-
-#include <iomanip>
-#include <iostream>
+#include "protomol/base/MathUtilities.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/type/Matrix3By3.h"
 
 using namespace ProtoMol;
 using namespace ProtoMol::Report;
diff --git a/protomol/force/hessian/ReducedHessGB.h b/protomol/force/hessian/ReducedHessGB.h
index add2c11..b08b462 100644
--- a/protomol/force/hessian/ReducedHessGB.h
+++ b/protomol/force/hessian/ReducedHessGB.h
@@ -2,8 +2,11 @@
 #ifndef REDUCEDHESSGB_H
 #define REDUCEDHESSGB_H
 
-#include <protomol/type/Matrix3By3.h>
 #include <protomol/topology/ExclusionTable.h>
+#include <protomol/type/Matrix3By3.h>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   class GenericTopology;
diff --git a/protomol/force/hessian/ReducedHessGBACE.cpp b/protomol/force/hessian/ReducedHessGBACE.cpp
index 4adc3b1..dc4a7e9 100644
--- a/protomol/force/hessian/ReducedHessGBACE.cpp
+++ b/protomol/force/hessian/ReducedHessGBACE.cpp
@@ -1,10 +1,12 @@
+#include <math.h>
 #include <protomol/force/hessian/ReducedHessGBACE.h>
 #include <protomol/topology/GenericTopology.h>
+#include <vector>
 
-#include <protomol/base/Report.h>
-
-#include <iomanip>
-#include <iostream>
+#include "protomol/base/MathUtilities.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/type/Matrix3By3.h"
 
 #define PI 3.14169
 
diff --git a/protomol/force/hessian/ReducedHessGBACE.h b/protomol/force/hessian/ReducedHessGBACE.h
index bb2a88a..a92e240 100644
--- a/protomol/force/hessian/ReducedHessGBACE.h
+++ b/protomol/force/hessian/ReducedHessGBACE.h
@@ -1,8 +1,11 @@
 /*  -*- c++ -*-  */
 #ifndef REDUCEDHESSGBACE_H
 #define REDUCEDHESSGBACE_H
-#include <protomol/type/Matrix3By3.h>
 #include <protomol/topology/ExclusionTable.h>
+#include <protomol/type/Matrix3By3.h>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   class GenericTopology;
diff --git a/protomol/force/hessian/ReducedHessLennardJones.cpp b/protomol/force/hessian/ReducedHessLennardJones.cpp
index 2d4a7f3..c27286b 100644
--- a/protomol/force/hessian/ReducedHessLennardJones.cpp
+++ b/protomol/force/hessian/ReducedHessLennardJones.cpp
@@ -1,5 +1,12 @@
 #include <protomol/force/hessian/ReducedHessLennardJones.h>
 #include <protomol/topology/GenericTopology.h>
+#include <vector>
+
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/LennardJonesParameterTable.h"
+#include "protomol/topology/LennardJonesParameters.h"
+#include "protomol/type/Matrix3By3.h"
 
 using namespace ProtoMol;
 
diff --git a/protomol/force/hessian/ReducedHessLennardJones.h b/protomol/force/hessian/ReducedHessLennardJones.h
index ecf1818..fd9fc13 100644
--- a/protomol/force/hessian/ReducedHessLennardJones.h
+++ b/protomol/force/hessian/ReducedHessLennardJones.h
@@ -2,8 +2,11 @@
 #ifndef REDUCEDHESSLENNARDJONES_H
 #define REDUCEDHESSLENNARDJONES_H
 
-#include <protomol/type/Matrix3By3.h>
 #include <protomol/topology/ExclusionTable.h>
+#include <protomol/type/Matrix3By3.h>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 /*
  *  LennardJonesEnergy = LennardJonesEnergy * switchingHess.
diff --git a/protomol/force/system/SystemCompareForce.cpp b/protomol/force/system/SystemCompareForce.cpp
index 66c6f43..d7c3d1d 100644
--- a/protomol/force/system/SystemCompareForce.cpp
+++ b/protomol/force/system/SystemCompareForce.cpp
@@ -1,7 +1,14 @@
 #include <protomol/force/system/SystemCompareForce.h>
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
+
+#include "protomol/force/CompareForce.h"
+#include "protomol/force/Force.h"
+#include "protomol/force/system/SystemForce.h"
+
+namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/force/system/SystemCompareForce.h b/protomol/force/system/SystemCompareForce.h
index 076464b..c0a112f 100644
--- a/protomol/force/system/SystemCompareForce.h
+++ b/protomol/force/system/SystemCompareForce.h
@@ -3,12 +3,17 @@
 #define SYSTEMCOMPAREFORCE_H
 
 #include <protomol/force/CompareForce.h>
-#include <protomol/force/system/SystemForce.h>
 #include <protomol/force/hessian/ReducedHessAngle.h>
+#include <protomol/force/system/SystemForce.h>
 
 namespace ProtoMol {
   //________________________________________ SystemCompareForce
 
+class Force;
+class GenericTopology;
+class ScalarStructure;
+class Vector3DBlock;
+
   class SystemCompareForce : public CompareForce, public SystemForce {
     // This class contains the definition of one force
 
diff --git a/protomol/force/system/SystemForce.cpp b/protomol/force/system/SystemForce.cpp
index e3cfa03..3b1dfcb 100644
--- a/protomol/force/system/SystemForce.cpp
+++ b/protomol/force/system/SystemForce.cpp
@@ -1,8 +1,12 @@
-#include <protomol/force/system/SystemForce.h>
 #include <protomol/force/ForceGroup.h>
 #include <protomol/force/system/SystemCompareForce.h>
+#include <protomol/force/system/SystemForce.h>
 #include <protomol/force/system/SystemTimeForce.h>
 
+namespace ProtoMol {
+class Force;
+}  // namespace ProtoMol
+
 using namespace std;
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/force/system/SystemTimeForce.cpp b/protomol/force/system/SystemTimeForce.cpp
index 6c51224..ebac463 100644
--- a/protomol/force/system/SystemTimeForce.cpp
+++ b/protomol/force/system/SystemTimeForce.cpp
@@ -1,7 +1,14 @@
 #include <protomol/force/system/SystemTimeForce.h>
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
+
+#include "protomol/force/Force.h"
+#include "protomol/force/TimeForce.h"
+#include "protomol/force/system/SystemForce.h"
+
+namespace ProtoMol {
+class GenericTopology;
+class ScalarStructure;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/force/system/SystemTimeForce.h b/protomol/force/system/SystemTimeForce.h
index bebec13..113c14d 100644
--- a/protomol/force/system/SystemTimeForce.h
+++ b/protomol/force/system/SystemTimeForce.h
@@ -8,6 +8,11 @@
 namespace ProtoMol {
   //________________________________________ SystemTimeForce
 
+class Force;
+class GenericTopology;
+class ScalarStructure;
+class Vector3DBlock;
+
   class SystemTimeForce : public TimeForce, public SystemForce {
     // This class contains the definition of one force
 
diff --git a/protomol/integrator/Integrator.cpp b/protomol/integrator/Integrator.cpp
index 9bfe82c..c9c0212 100644
--- a/protomol/integrator/Integrator.cpp
+++ b/protomol/integrator/Integrator.cpp
@@ -1,13 +1,16 @@
-#include <protomol/integrator/Integrator.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
+#include <protomol/base/Zap.h>
 #include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/Integrator.h>
+#include <protomol/modifier/Modifier.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/modifier/Modifier.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/Zap.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/base/MakeableDefinition.h"
+#include "protomol/integrator/IntegratorDefinition.h"
+#include "protomol/type/Real.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/integrator/Integrator.h b/protomol/integrator/Integrator.h
index a0828b9..306bf26 100644
--- a/protomol/integrator/Integrator.h
+++ b/protomol/integrator/Integrator.h
@@ -5,16 +5,16 @@
 #include <protomol/base/Makeable.h>
 #include <protomol/integrator/IntegratorDefinition.h>
 #include <protomol/type/Real.h>
-
 #include <iostream>
-#include <string>
 #include <set>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
-  class ProtoMolApp;
   class ForceGroup;
   class MTSIntegrator;
   class Modifier;
+  class ProtoMolApp;
   class Vector3DBlock;
 
   //________________________________________ Integrator
diff --git a/protomol/integrator/IntegratorDefinition.cpp b/protomol/integrator/IntegratorDefinition.cpp
index b071ff4..8a54576 100644
--- a/protomol/integrator/IntegratorDefinition.cpp
+++ b/protomol/integrator/IntegratorDefinition.cpp
@@ -1,5 +1,9 @@
-#include <protomol/integrator/IntegratorDefinition.h>
 #include <protomol/force/Force.h>
+#include <protomol/integrator/IntegratorDefinition.h>
+
+#include "protomol/base/MakeableDefinition.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/integrator/IntegratorDefinition.h b/protomol/integrator/IntegratorDefinition.h
index 1039044..d49e7b4 100644
--- a/protomol/integrator/IntegratorDefinition.h
+++ b/protomol/integrator/IntegratorDefinition.h
@@ -3,6 +3,8 @@
 #define INTEGRATORDEFINITION_H
 
 #include <protomol/base/MakeableDefinition.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   //________________________________________ IntegratorDefinition
diff --git a/protomol/integrator/MTSIntegrator.cpp b/protomol/integrator/MTSIntegrator.cpp
index 43cfe25..cf2e95f 100644
--- a/protomol/integrator/MTSIntegrator.cpp
+++ b/protomol/integrator/MTSIntegrator.cpp
@@ -1,10 +1,14 @@
 #include <protomol/integrator/MTSIntegrator.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/base/Exception.h>
+#include <stddef.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/StandardIntegrator.h"
+
+namespace ProtoMol {
+class ProtoMolApp;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/integrator/MTSIntegrator.h b/protomol/integrator/MTSIntegrator.h
index 9ecfdc4..6468a7b 100644
--- a/protomol/integrator/MTSIntegrator.h
+++ b/protomol/integrator/MTSIntegrator.h
@@ -3,12 +3,20 @@
 #define MTSINTEGRATOR_H
 
 #include <protomol/integrator/StandardIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
+  class ForceGroup;
   class GenericTopology;
   class ScalarStructure;
   class Vector3DBlock;
-  class ForceGroup;
+class Integrator;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //________________________________________ MTSIntegrator
 
diff --git a/protomol/integrator/STSIntegrator.cpp b/protomol/integrator/STSIntegrator.cpp
index 46a8b4a..f4550e4 100644
--- a/protomol/integrator/STSIntegrator.cpp
+++ b/protomol/integrator/STSIntegrator.cpp
@@ -1,14 +1,15 @@
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/integrator/STSIntegrator.h>
-#include <protomol/base/Report.h>
+#include <protomol/modifier/ModifierIncrementTimestep.h>
+#include <protomol/topology/TopologyUtilities.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/modifier/ModifierIncrementTimestep.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/Exception.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/StandardIntegrator.h"
 
 using namespace ProtoMol::Report;
 using namespace std;
diff --git a/protomol/integrator/STSIntegrator.h b/protomol/integrator/STSIntegrator.h
index 859421d..4c9bdc9 100644
--- a/protomol/integrator/STSIntegrator.h
+++ b/protomol/integrator/STSIntegrator.h
@@ -4,10 +4,18 @@
 
 #include <protomol/integrator/StandardIntegrator.h>
 #include <protomol/topology/GenericTopology.h>
+#include <stddef.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class Integrator;
+class Value;
+struct Parameter;
 
   //________________________________________ STSIntegrator
 
diff --git a/protomol/integrator/StandardIntegrator.cpp b/protomol/integrator/StandardIntegrator.cpp
index d1f28d7..ae7c6e8 100644
--- a/protomol/integrator/StandardIntegrator.cpp
+++ b/protomol/integrator/StandardIntegrator.cpp
@@ -1,13 +1,19 @@
-#include <protomol/integrator/StandardIntegrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/StandardIntegrator.h>
+#include <protomol/parallel/Parallel.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/parallel/Parallel.h>
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+#include <vector>
+
+#include "protomol/integrator/Integrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 #ifdef HAVE_LIBFAH
 #include <fah/core/Core.h>
diff --git a/protomol/integrator/StandardIntegrator.h b/protomol/integrator/StandardIntegrator.h
index bda50ed..3250b98 100644
--- a/protomol/integrator/StandardIntegrator.h
+++ b/protomol/integrator/StandardIntegrator.h
@@ -5,11 +5,11 @@
 #include <protomol/integrator/Integrator.h>
 
 namespace ProtoMol {
+  class ForceGroup;
   //________________________________________ StandardIntegrator
   class GenericTopology;
   class ScalarStructure;
   class Vector3DBlock;
-  class ForceGroup;
 
   class StandardIntegrator : public Integrator {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/integrator/base/CGMinimizerIntegrator.cpp b/protomol/integrator/base/CGMinimizerIntegrator.cpp
index 9d98f54..4d73dbc 100644
--- a/protomol/integrator/base/CGMinimizerIntegrator.cpp
+++ b/protomol/integrator/base/CGMinimizerIntegrator.cpp
@@ -1,12 +1,15 @@
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/integrator/base/CGMinimizerIntegrator.h>
-#include <protomol/base/Report.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/base/CGMinimizerIntegrator.h b/protomol/integrator/base/CGMinimizerIntegrator.h
index 784cefa..16fc860 100644
--- a/protomol/integrator/base/CGMinimizerIntegrator.h
+++ b/protomol/integrator/base/CGMinimizerIntegrator.h
@@ -3,10 +3,18 @@
 #define CGMINIMIZER_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
+class Vector3DBlock;
+struct Parameter;
 
   /**
       Non-linear Conjugate Gradient Minimizer.
diff --git a/protomol/integrator/base/LangevinImpulseIntegrator.cpp b/protomol/integrator/base/LangevinImpulseIntegrator.cpp
index 9eb9900..fd67221 100644
--- a/protomol/integrator/base/LangevinImpulseIntegrator.cpp
+++ b/protomol/integrator/base/LangevinImpulseIntegrator.cpp
@@ -1,12 +1,18 @@
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/integrator/base/LangevinImpulseIntegrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/PMConstants.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std; 
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/base/LangevinImpulseIntegrator.h b/protomol/integrator/base/LangevinImpulseIntegrator.h
index 5e3ec01..b48fa82 100644
--- a/protomol/integrator/base/LangevinImpulseIntegrator.h
+++ b/protomol/integrator/base/LangevinImpulseIntegrator.h
@@ -3,11 +3,18 @@
 #define LANGEVINIMPULSEINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
   class Vector3DBlock;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //____ LangevinImpulseIntegrator
 
diff --git a/protomol/integrator/base/LangevinLeapfrogIntegrator.cpp b/protomol/integrator/base/LangevinLeapfrogIntegrator.cpp
index 1c3968f..c9a2ed6 100644
--- a/protomol/integrator/base/LangevinLeapfrogIntegrator.cpp
+++ b/protomol/integrator/base/LangevinLeapfrogIntegrator.cpp
@@ -1,12 +1,18 @@
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/integrator/base/LangevinLeapfrogIntegrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/PMConstants.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std; 
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/base/LangevinLeapfrogIntegrator.h b/protomol/integrator/base/LangevinLeapfrogIntegrator.h
index 2fd7eb6..a80aa56 100644
--- a/protomol/integrator/base/LangevinLeapfrogIntegrator.h
+++ b/protomol/integrator/base/LangevinLeapfrogIntegrator.h
@@ -3,11 +3,18 @@
 #define LANGEVINLEAPFROGINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
   class Vector3DBlock;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //____ LangevinLeapfrogIntegrator
 
diff --git a/protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.cpp b/protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.cpp
index 30afe6b..30b86cc 100644
--- a/protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.cpp
+++ b/protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.cpp
@@ -1,12 +1,17 @@
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/PMConstants.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
 
 using namespace std; 
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.h b/protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.h
index 47d8a6b..a4f5ad5 100644
--- a/protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.h
+++ b/protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.h
@@ -3,11 +3,19 @@
 #define LANGEVINLEAPFROGSWITCHINGINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
   class Vector3DBlock;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //____ LangevinLeapfrogSwitchingIntegrator
 
diff --git a/protomol/integrator/base/LangevinVVVRIntegrator.cpp b/protomol/integrator/base/LangevinVVVRIntegrator.cpp
index a8bc1f7..23df46a 100644
--- a/protomol/integrator/base/LangevinVVVRIntegrator.cpp
+++ b/protomol/integrator/base/LangevinVVVRIntegrator.cpp
@@ -1,12 +1,20 @@
-#include <protomol/integrator/base/LangevinVVVRIntegrator.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/base/LangevinVVVRIntegrator.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/PMConstants.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std; 
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/base/LangevinVVVRIntegrator.h b/protomol/integrator/base/LangevinVVVRIntegrator.h
index f227c65..facee59 100644
--- a/protomol/integrator/base/LangevinVVVRIntegrator.h
+++ b/protomol/integrator/base/LangevinVVVRIntegrator.h
@@ -3,11 +3,18 @@
 #define LANGEVINVVVRINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
   class Vector3DBlock;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //____ LangevinVVVRIntegrator
 
diff --git a/protomol/integrator/base/NumericalDifferentiation.cpp b/protomol/integrator/base/NumericalDifferentiation.cpp
index 485ae05..84d9256 100644
--- a/protomol/integrator/base/NumericalDifferentiation.cpp
+++ b/protomol/integrator/base/NumericalDifferentiation.cpp
@@ -1,12 +1,17 @@
-#include <protomol/integrator/base/NumericalDifferentiation.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/base/Report.h>
+#include <protomol/integrator/base/NumericalDifferentiation.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/hessian/Hessian.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/base/NumericalDifferentiation.h b/protomol/integrator/base/NumericalDifferentiation.h
index 6957c50..dbde38e 100644
--- a/protomol/integrator/base/NumericalDifferentiation.h
+++ b/protomol/integrator/base/NumericalDifferentiation.h
@@ -4,10 +4,17 @@
 
 #include <protomol/integrator/STSIntegrator.h>
 #include <protomol/integrator/hessian/Hessian.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //____ NumericalDifferentiation
   class NumericalDifferentiation : public STSIntegrator {
diff --git a/protomol/integrator/base/NumericallyDifferentiatedHessian.cpp b/protomol/integrator/base/NumericallyDifferentiatedHessian.cpp
index f544ac7..4439f95 100644
--- a/protomol/integrator/base/NumericallyDifferentiatedHessian.cpp
+++ b/protomol/integrator/base/NumericallyDifferentiatedHessian.cpp
@@ -1,12 +1,17 @@
-#include <protomol/integrator/base/NumericallyDifferentiatedHessian.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
+#include <protomol/integrator/base/NumericallyDifferentiatedHessian.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+#include <iostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/hessian/Hessian.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/base/NumericallyDifferentiatedHessian.h b/protomol/integrator/base/NumericallyDifferentiatedHessian.h
index 7acc50d..a4b6c14 100644
--- a/protomol/integrator/base/NumericallyDifferentiatedHessian.h
+++ b/protomol/integrator/base/NumericallyDifferentiatedHessian.h
@@ -4,10 +4,17 @@
 
 #include <protomol/integrator/STSIntegrator.h>
 #include <protomol/integrator/hessian/Hessian.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //____ NumericallyDifferentiatedHessian
   class NumericallyDifferentiatedHessian : public STSIntegrator {
diff --git a/protomol/integrator/base/RMTIntegrator.cpp b/protomol/integrator/base/RMTIntegrator.cpp
index 5af9804..7f8f9ce 100644
--- a/protomol/integrator/base/RMTIntegrator.cpp
+++ b/protomol/integrator/base/RMTIntegrator.cpp
@@ -1,12 +1,20 @@
-#include <protomol/integrator/base/RMTIntegrator.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/base/RMTIntegrator.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/PMConstants.h>
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/base/RMTIntegrator.h b/protomol/integrator/base/RMTIntegrator.h
index 033e7e5..3ea80d0 100644
--- a/protomol/integrator/base/RMTIntegrator.h
+++ b/protomol/integrator/base/RMTIntegrator.h
@@ -3,17 +3,24 @@
 #define RMTINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
-#include <iostream>
 #include <stdio.h>
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
 
 
   //_________________________________________________________________ RMTIntegrator
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
   class Vector3DBlock;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   class RMTIntegrator : public STSIntegrator {
 
diff --git a/protomol/integrator/hessian/BlockHessian.cpp b/protomol/integrator/hessian/BlockHessian.cpp
index 962bab9..590704e 100644
--- a/protomol/integrator/hessian/BlockHessian.cpp
+++ b/protomol/integrator/hessian/BlockHessian.cpp
@@ -1,45 +1,37 @@
-#include <protomol/integrator/hessian/BlockHessian.h>
-
 #include <protomol/base/Report.h>
-#include <protomol/force/hessian/HessDihedral.h>
-#include <protomol/force/hessian/ReducedHessBond.h>
-#include <protomol/force/hessian/ReducedHessAngle.h>
-
-#include <protomol/force/LennardJonesForce.h>
 #include <protomol/force/CoulombForce.h>
-#include <protomol/switch/CnSwitchingFunction.h>
-#include <protomol/switch/C2SwitchingFunction.h>
-#include <protomol/switch/C1SwitchingFunction.h>
-
+#include <protomol/force/LennardJonesForce.h>
+#include <protomol/force/bonded/AngleSystemForce.h>
+#include <protomol/force/bonded/BondSystemForce.h>
+#include <protomol/force/bonded/DihedralSystemForce.h>
+#include <protomol/force/bonded/ImproperSystemForce.h>
+#include <protomol/force/bonded/RBDihedralSystemForce.h>
 #include <protomol/force/hessian/HessDihedral.h>
+#include <protomol/force/hessian/ReducedHessAngle.h>
 #include <protomol/force/hessian/ReducedHessBond.h>
-#include <protomol/force/hessian/ReducedHessCoulomb.h>
-#include <protomol/force/hessian/ReducedHessCoulombDiElec.h>
-#include <protomol/force/hessian/ReducedHessCoulombSCPISM.h>
-#include <protomol/force/hessian/ReducedHessLennardJones.h>
-#include <protomol/force/coulomb/CoulombForceDiElec.h>
-#include <protomol/force/coulomb/CoulombSCPISMForce.h>
-
-//GB
-#include <protomol/force/GB/GBBornRadii.h>
-#include <protomol/force/GB/GBACEForce.h>
-#include <protomol/force/hessian/ReducedHessGBACE.h>
-#include <protomol/force/GB/GBForce.h>
-#include <protomol/force/hessian/ReducedHessGB.h>
-
+#include <protomol/integrator/hessian/BlockHessian.h>
 #include <protomol/topology/SemiGenericTopology.h>
 #include <protomol/topology/VacuumBoundaryConditions.h>
 #include <protomol/type/BlockMatrix.h>
-
-#include <protomol/force/bonded/BondSystemForce.h>
-#include <protomol/force/bonded/AngleSystemForce.h>
-#include <protomol/force/bonded/ImproperSystemForce.h>
-#include <protomol/force/bonded/DihedralSystemForce.h>
-#include <protomol/force/bonded/RBDihedralSystemForce.h>
-
-#include <iostream>
-#include <stdio.h>
+#include <stdlib.h>
+#include <algorithm>
+#include <cmath>
 #include <fstream>
+#include <new>
+#include <string>
+
+#include "protomol/force/Force.h"
+#include "protomol/integrator/hessian/Hessian.h"
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/topology/RBTorsion.h"
+#include "protomol/topology/Torsion.h"
+#include "protomol/type/ScalarStructure.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 //defines for including SCPISM and GB and
 //adding paiwise forces to evaluateResidues()
diff --git a/protomol/integrator/hessian/BlockHessian.h b/protomol/integrator/hessian/BlockHessian.h
index 8b4c42d..1170f13 100644
--- a/protomol/integrator/hessian/BlockHessian.h
+++ b/protomol/integrator/hessian/BlockHessian.h
@@ -5,6 +5,10 @@
 #include <protomol/integrator/hessian/Hessian.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/type/BlockMatrix.h>
+#include <vector>
+
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   /**
@@ -13,6 +17,10 @@ namespace ProtoMol {
    * for the current force field.
    *
    */
+class GenericTopology;
+class Torsion;
+class Vector3DBlock;
+
   class BlockHessian : public Hessian {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Types and Enums
diff --git a/protomol/integrator/hessian/BlockHessianDiagonalize.cpp b/protomol/integrator/hessian/BlockHessianDiagonalize.cpp
index ee63b22..c50b09c 100644
--- a/protomol/integrator/hessian/BlockHessianDiagonalize.cpp
+++ b/protomol/integrator/hessian/BlockHessianDiagonalize.cpp
@@ -1,15 +1,21 @@
-#include <protomol/integrator/hessian/BlockHessianDiagonalize.h>
-#include <protomol/integrator/hessian/BlockHessian.h>
-
+#include <math.h>
+#include <protomol/base/Lapack.h>
 #include <protomol/base/Report.h>
-
+#include <protomol/integrator/hessian/BlockHessian.h>
+#include <protomol/integrator/hessian/BlockHessianDiagonalize.h>
 #include <protomol/type/BlockMatrix.h>
-
-#include <protomol/base/Lapack.h>
-
-#include <iostream>
-#include <stdio.h>
+#include <algorithm>
 #include <fstream>
+#include <new>
+#include <string>
+
+#include "protomol/base/Exception.h"
+#include "protomol/base/Timer.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/hessian/BlockHessianDiagonalize.h b/protomol/integrator/hessian/BlockHessianDiagonalize.h
index 3c81e37..24b9b44 100644
--- a/protomol/integrator/hessian/BlockHessianDiagonalize.h
+++ b/protomol/integrator/hessian/BlockHessianDiagonalize.h
@@ -2,12 +2,15 @@
 #ifndef BLOCKHESSIANDIAGONALIZE_H
 #define BLOCKHESSIANDIAGONALIZE_H
 
-#include <protomol/integrator/normal/NormalModeUtilities.h>
-#include <protomol/integrator/hessian/BlockHessian.h>
-#include <protomol/type/BlockMatrix.h>
-#include <protomol/base/Timer.h>
 #include <protomol/ProtoMolApp.h>
+#include <protomol/base/Timer.h>
 #include <protomol/integrator/StandardIntegrator.h>
+#include <protomol/integrator/hessian/BlockHessian.h>
+#include <protomol/integrator/normal/NormalModeUtilities.h>
+#include <protomol/type/BlockMatrix.h>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   /**
@@ -16,6 +19,11 @@ namespace ProtoMol {
    * for the current force field.
    *
    */
+class BlockHessian;
+class GenericTopology;
+class StandardIntegrator;
+class Vector3DBlock;
+
   class BlockHessianDiagonalize {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Types and Enums
diff --git a/protomol/integrator/hessian/Hessian.cpp b/protomol/integrator/hessian/Hessian.cpp
index a770df5..9add32f 100644
--- a/protomol/integrator/hessian/Hessian.cpp
+++ b/protomol/integrator/hessian/Hessian.cpp
@@ -1,38 +1,51 @@
-#include <protomol/integrator/hessian/Hessian.h>
-
+#include <math.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
+#include <protomol/force/CoulombForce.h>
 #include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/force/hessian/ReducedHessAngle.h>
+#include <protomol/force/GB/GBBornRadii.h>
+#include <protomol/force/GB/GBPartialSum.h>
 #include <protomol/force/LennardJonesForce.h>
-#include <protomol/force/CoulombForce.h>
-#include <protomol/switch/CnSwitchingFunction.h>
-#include <protomol/switch/C2SwitchingFunction.h>
-#include <protomol/switch/C1SwitchingFunction.h>
-
+#include <protomol/force/born/BornRadii.h>
+#include <protomol/force/coulomb/CoulombForceDiElec.h>
+#include <protomol/force/coulomb/CoulombSCPISMForce.h>
 #include <protomol/force/hessian/HessDihedral.h>
+#include <protomol/force/hessian/ReducedHessAngle.h>
 #include <protomol/force/hessian/ReducedHessBond.h>
+#include <protomol/force/hessian/ReducedHessBornSelf.h>
 #include <protomol/force/hessian/ReducedHessCoulomb.h>
 #include <protomol/force/hessian/ReducedHessCoulombDiElec.h>
 #include <protomol/force/hessian/ReducedHessCoulombSCPISM.h>
-#include <protomol/force/hessian/ReducedHessLennardJones.h>
-#include <protomol/force/hessian/ReducedHessBornSelf.h>
-#include <protomol/force/coulomb/CoulombForceDiElec.h>
-#include <protomol/force/coulomb/CoulombSCPISMForce.h>
-#include <protomol/force/born/BornRadii.h>
-
-#include <protomol/force/GB/GBBornRadii.h>
-#include <protomol/force/GB/GBPartialSum.h>
-#include <protomol/force/GB/GBACEForce.h>
 #include <protomol/force/hessian/ReducedHessGBACE.h>
+#include <protomol/force/hessian/ReducedHessLennardJones.h>
+#include <protomol/integrator/hessian/Hessian.h>
+#include <protomol/switch/C1SwitchingFunction.h>
+#include <protomol/switch/C2SwitchingFunction.h>
+#include <protomol/switch/CnSwitchingFunction.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
 //#include <protomol/force/hessian/GB/ReducedHessGBForce.h>
 
-#include <protomol/force/GB/GBForce.h>
 #include <protomol/force/hessian/ReducedHessGB.h>
+#include <algorithm>
+#include <iostream>
+#include <new>
+#include <string>
+#include <vector>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/force/Force.h"
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/RBTorsion.h"
+#include "protomol/topology/Torsion.h"
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/hessian/Hessian.h b/protomol/integrator/hessian/Hessian.h
index d713de5..d128265 100644
--- a/protomol/integrator/hessian/Hessian.h
+++ b/protomol/integrator/hessian/Hessian.h
@@ -3,8 +3,10 @@
 #define HESSIAN_H
 
 #include <protomol/force/Force.h>
-#include <protomol/type/Vector3DBlock.h>
 #include <protomol/type/Matrix3By3.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   /**
@@ -13,6 +15,10 @@ namespace ProtoMol {
    * for the current force field.
    *
    */
+class ForceGroup;
+class GenericTopology;
+class Vector3DBlock;
+
   class Hessian {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Types and Enums
diff --git a/protomol/integrator/hessian/HessianInt.cpp b/protomol/integrator/hessian/HessianInt.cpp
index a6c7987..1e06ac8 100644
--- a/protomol/integrator/hessian/HessianInt.cpp
+++ b/protomol/integrator/hessian/HessianInt.cpp
@@ -1,21 +1,37 @@
-#include <protomol/integrator/hessian/HessianInt.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/SystemUtilities.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/Exception.h>
 #include <protomol/base/PMConstants.h>
+#include <protomol/base/Report.h>
+#include <protomol/base/SystemUtilities.h>
+#include <protomol/integrator/hessian/HessianInt.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/topology/TopologyUtilities.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <algorithm>
+#include <cmath>
 #include <iostream>
-#include <stdio.h>
+#include <new>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/base/Timer.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/hessian/BlockHessian.h"
+#include "protomol/integrator/hessian/BlockHessianDiagonalize.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/BlockMatrix.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
+
+namespace ProtoMol {
+class StandardIntegrator;
+}  // namespace ProtoMol
 
 #ifdef HAVE_LIBFAH
     #include <cbang/os/File.h>
 #else
-    #include <fstream>
 #endif
 
 #include <protomol/base/Lapack.h>
diff --git a/protomol/integrator/hessian/HessianInt.h b/protomol/integrator/hessian/HessianInt.h
index fe54246..de5d721 100644
--- a/protomol/integrator/hessian/HessianInt.h
+++ b/protomol/integrator/hessian/HessianInt.h
@@ -2,19 +2,29 @@
 #ifndef HESSIANINT_H
 #define HESSIANINT_H
 
-#include <protomol/integrator/STSIntegrator.h>
 #include <protomol/force/Force.h>
-#include <protomol/type/Vector3DBlock.h>
+#include <protomol/integrator/STSIntegrator.h>
 #include <protomol/integrator/hessian/BlockHessian.h>
 #include <protomol/integrator/hessian/BlockHessianDiagonalize.h>
 #include <protomol/type/TypeSelection.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+
+namespace ProtoMol {
+class ProtoMolApp;
+class Value;
+struct Parameter;
+}  // namespace ProtoMol
 
 using namespace std;
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
   class ReducedHessAngle;
+  class ScalarStructure;
 
   //____ HessianInt
   class HessianInt : public STSIntegrator {
diff --git a/protomol/integrator/leapfrog/DMDLeapfrogIntegrator.cpp b/protomol/integrator/leapfrog/DMDLeapfrogIntegrator.cpp
index f33b05b..ef21eef 100644
--- a/protomol/integrator/leapfrog/DMDLeapfrogIntegrator.cpp
+++ b/protomol/integrator/leapfrog/DMDLeapfrogIntegrator.cpp
@@ -1,12 +1,19 @@
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/integrator/leapfrog/DMDLeapfrogIntegrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/leapfrog/DMDLeapfrogIntegrator.h b/protomol/integrator/leapfrog/DMDLeapfrogIntegrator.h
index 71bf9b1..b93a1d4 100644
--- a/protomol/integrator/leapfrog/DMDLeapfrogIntegrator.h
+++ b/protomol/integrator/leapfrog/DMDLeapfrogIntegrator.h
@@ -3,11 +3,18 @@
 #define DMDLEAPFROGINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
   class Vector3DBlock;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   /**
       For Dissipative MD, and it is self-consistent
diff --git a/protomol/integrator/leapfrog/GPU.cpp b/protomol/integrator/leapfrog/GPU.cpp
index 8ca35d4..b0ba360 100644
--- a/protomol/integrator/leapfrog/GPU.cpp
+++ b/protomol/integrator/leapfrog/GPU.cpp
@@ -1,17 +1,33 @@
-#include <protomol/integrator/leapfrog/GPU.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
 #include <protomol/force/ForceGroup.h>
+#include <protomol/force/LennardJonesForce.h>
+#include <protomol/integrator/leapfrog/GPU.h>
+#include <protomol/switch/CnSwitchingFunction.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/PeriodicBoundaryConditions.h>
 #include <protomol/topology/SemiGenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
-
-#include <protomol/force/LennardJonesForce.h>
-#include <protomol/switch/CnSwitchingFunction.h>
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+#include <ostream>
+
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/force/Force.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/LennardJonesParameterTable.h"
+#include "protomol/topology/LennardJonesParameters.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 //#include <protomol/switch/C2SwitchingFunction.h>
 
 using namespace std;
diff --git a/protomol/integrator/leapfrog/GPU.h b/protomol/integrator/leapfrog/GPU.h
index 21fdb2b..c10ef60 100644
--- a/protomol/integrator/leapfrog/GPU.h
+++ b/protomol/integrator/leapfrog/GPU.h
@@ -2,13 +2,20 @@
 #ifndef GPU_H
 #define GPU_H
 
+#include <protomol/base/TimerStatistic.h>
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
 
-#include <protomol/base/TimerStatistic.h>
+#include "protomol/base/Timer.h"
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //____ GPU
   class GPU : public STSIntegrator {
diff --git a/protomol/integrator/leapfrog/LeapfrogDataAcquisition.cpp b/protomol/integrator/leapfrog/LeapfrogDataAcquisition.cpp
index d8e007d..7a51c22 100644
--- a/protomol/integrator/leapfrog/LeapfrogDataAcquisition.cpp
+++ b/protomol/integrator/leapfrog/LeapfrogDataAcquisition.cpp
@@ -1,7 +1,21 @@
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/SystemUtilities.h>
 #include <protomol/integrator/leapfrog/LeapfrogDataAcquisition.h>
 #include <protomol/io/DCDTrajectoryWriter.h>
-#include <protomol/base/SystemUtilities.h>
-#include <protomol/ProtoMolApp.h>
+#include <stddef.h>
+
+#include "protomol/base/Zap.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/leapfrog/LeapfrogIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/topology/Molecule.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+
 using namespace ProtoMol;
 
 const string LeapfrogDataAcquisition::keyword("LeapfrogDataAcquisition");
diff --git a/protomol/integrator/leapfrog/LeapfrogDataAcquisition.h b/protomol/integrator/leapfrog/LeapfrogDataAcquisition.h
index a42fe8d..202564b 100644
--- a/protomol/integrator/leapfrog/LeapfrogDataAcquisition.h
+++ b/protomol/integrator/leapfrog/LeapfrogDataAcquisition.h
@@ -3,14 +3,22 @@
 #define LEAPFROGDATAACQUISITION_H
 
 
-#include <string>
 #include <protomol/integrator/leapfrog/LeapfrogIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 
 namespace ProtoMol {
-  class ScalarStructure;
-  class ForceGroup;
   class DCDTrajectoryWriter;
+  class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class STSIntegrator;
+class Value;
+class Vector3DBlock;
+struct Parameter;
 
   class LeapfrogDataAcquisition : public LeapfrogIntegrator {
 
diff --git a/protomol/integrator/leapfrog/LeapfrogIntegrator.cpp b/protomol/integrator/leapfrog/LeapfrogIntegrator.cpp
index a39172f..f5a72a8 100644
--- a/protomol/integrator/leapfrog/LeapfrogIntegrator.cpp
+++ b/protomol/integrator/leapfrog/LeapfrogIntegrator.cpp
@@ -1,12 +1,15 @@
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/integrator/leapfrog/LeapfrogIntegrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/config/Value.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/leapfrog/LeapfrogIntegrator.h b/protomol/integrator/leapfrog/LeapfrogIntegrator.h
index 44ba8bf..745d832 100644
--- a/protomol/integrator/leapfrog/LeapfrogIntegrator.h
+++ b/protomol/integrator/leapfrog/LeapfrogIntegrator.h
@@ -3,10 +3,16 @@
 #define LEAPFROGINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
 
   //____ LeapfrogIntegrator
   class LeapfrogIntegrator : public STSIntegrator {
diff --git a/protomol/integrator/leapfrog/LeapfrogTruncatedShadow.cpp b/protomol/integrator/leapfrog/LeapfrogTruncatedShadow.cpp
index 27996c7..df1ba40 100644
--- a/protomol/integrator/leapfrog/LeapfrogTruncatedShadow.cpp
+++ b/protomol/integrator/leapfrog/LeapfrogTruncatedShadow.cpp
@@ -1,25 +1,39 @@
-#include <protomol/integrator/leapfrog/LeapfrogTruncatedShadow.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
+#include <protomol/force/CoulombForce.h>
 #include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
+#include <protomol/force/LennardJonesForce.h>
+#include <protomol/force/coulomb/CoulombForceDiElec.h>
+#include <protomol/force/coulomb/CoulombSCPISMForce.h>
 #include <protomol/force/hessian/ReducedHessAngle.h>
 #include <protomol/force/hessian/ReducedHessBond.h>
-#include <protomol/force/hessian/ReducedHessLennardJones.h>
-#include <protomol/force/LennardJonesForce.h>
 #include <protomol/force/hessian/ReducedHessCoulomb.h>
 #include <protomol/force/hessian/ReducedHessCoulombDiElec.h>
 #include <protomol/force/hessian/ReducedHessCoulombSCPISM.h>
-#include <protomol/force/CoulombForce.h>
-#include <protomol/force/coulomb/CoulombForceDiElec.h>
-#include <protomol/force/coulomb/CoulombSCPISMForce.h>
-#include <protomol/switch/CnSwitchingFunction.h>
-#include <protomol/switch/C2SwitchingFunction.h>
+#include <protomol/force/hessian/ReducedHessLennardJones.h>
+#include <protomol/integrator/leapfrog/LeapfrogTruncatedShadow.h>
 #include <protomol/switch/C1SwitchingFunction.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/switch/C2SwitchingFunction.h>
+#include <protomol/switch/CnSwitchingFunction.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/topology/TopologyUtilities.h>
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/force/Force.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/Torsion.h"
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/leapfrog/LeapfrogTruncatedShadow.h b/protomol/integrator/leapfrog/LeapfrogTruncatedShadow.h
index 321d55f..da47d9e 100644
--- a/protomol/integrator/leapfrog/LeapfrogTruncatedShadow.h
+++ b/protomol/integrator/leapfrog/LeapfrogTruncatedShadow.h
@@ -2,15 +2,27 @@
 #ifndef LEAPFROGTRUNCATEDSHADOW_H
 #define LEAPFROGTRUNCATEDSHADOW_H
 
-#include <protomol/integrator/STSIntegrator.h>
 #include <protomol/force/Force.h>
+#include <protomol/integrator/STSIntegrator.h>
 #include <protomol/type/Vector3DBlock.h>
+#include <algorithm>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+
+namespace ProtoMol {
+class ProtoMolApp;
+class Torsion;
+class Value;
+}  // namespace ProtoMol
+
 using namespace std;
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
   class ReducedHessAngle;
+  class ScalarStructure;
 
   //____ LeapfrogTruncatedShadow
   class LeapfrogTruncatedShadow : public STSIntegrator {
diff --git a/protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.cpp b/protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.cpp
index 5dcb5ad..91e0438 100644
--- a/protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.cpp
+++ b/protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.cpp
@@ -1,12 +1,17 @@
-#include <protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/PMConstants.h>
-#include <protomol/topology/TopologyUtilities.h>
 #include <protomol/integrator/leapfrog/ModifierFriction.h>
+#include <protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.h b/protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.h
index 5f09734..e98b196 100644
--- a/protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.h
+++ b/protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.h
@@ -3,13 +3,20 @@
 #define NOSENVTLEAPFROGINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   //____ NoseNVTLeapfrogIntegrator
 
-  class ScalarStructure;
   class ForceGroup;
   class ModifierFriction;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   class NoseNVTLeapfrogIntegrator : public STSIntegrator {
     friend class ModifierFriction;
diff --git a/protomol/integrator/leapfrog/PLeapfrogIntegrator.cpp b/protomol/integrator/leapfrog/PLeapfrogIntegrator.cpp
index 45780b7..1ce1770 100644
--- a/protomol/integrator/leapfrog/PLeapfrogIntegrator.cpp
+++ b/protomol/integrator/leapfrog/PLeapfrogIntegrator.cpp
@@ -1,12 +1,14 @@
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/integrator/leapfrog/PLeapfrogIntegrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/leapfrog/PLeapfrogIntegrator.h b/protomol/integrator/leapfrog/PLeapfrogIntegrator.h
index ffedf4d..bd90af5 100644
--- a/protomol/integrator/leapfrog/PLeapfrogIntegrator.h
+++ b/protomol/integrator/leapfrog/PLeapfrogIntegrator.h
@@ -3,10 +3,17 @@
 #define PLEAPFROGINTEGRATOR_H
 
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
+class Vector3DBlock;
 
   //____ PLeapfrogIntegrator
   class PLeapfrogIntegrator : public STSIntegrator {
diff --git a/protomol/integrator/normal/NormalModeBrownian.cpp b/protomol/integrator/normal/NormalModeBrownian.cpp
index ecc9e24..4cc614d 100644
--- a/protomol/integrator/normal/NormalModeBrownian.cpp
+++ b/protomol/integrator/normal/NormalModeBrownian.cpp
@@ -1,14 +1,22 @@
-#include <protomol/integrator/normal/NormalModeBrownian.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
-
+#include <protomol/base/PMConstants.h>
+#include <protomol/base/Report.h>
 #include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/integrator/normal/NormalModeBrownian.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/io/XYZTrajectoryWriter.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 
 using namespace std;
diff --git a/protomol/integrator/normal/NormalModeBrownian.h b/protomol/integrator/normal/NormalModeBrownian.h
index 30042c3..a041a05 100644
--- a/protomol/integrator/normal/NormalModeBrownian.h
+++ b/protomol/integrator/normal/NormalModeBrownian.h
@@ -4,15 +4,22 @@
 
 #include <protomol/integrator/STSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 //####diagnostics
 #include <protomol/io/XYZTrajectoryWriter.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 
 namespace ProtoMol {
 
-	class ScalarStructure;
 	class ForceGroup;
+	class ScalarStructure;
+class ProtoMolApp;
+class Value;
+class XYZTrajectoryWriter;
+struct Parameter;
 
 	//__________________________________________________ NormalModeBrownian
 	class NormalModeBrownian : public STSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeCompLang.cpp b/protomol/integrator/normal/NormalModeCompLang.cpp
index 8314ab1..d66d08d 100644
--- a/protomol/integrator/normal/NormalModeCompLang.cpp
+++ b/protomol/integrator/normal/NormalModeCompLang.cpp
@@ -1,14 +1,24 @@
-#include <protomol/integrator/normal/NormalModeCompLang.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/integrator/normal/NormalModeCompLang.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
-
-#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+#include <iostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 
 using namespace std;
diff --git a/protomol/integrator/normal/NormalModeCompLang.h b/protomol/integrator/normal/NormalModeCompLang.h
index 9f5f298..b605e59 100644
--- a/protomol/integrator/normal/NormalModeCompLang.h
+++ b/protomol/integrator/normal/NormalModeCompLang.h
@@ -4,13 +4,19 @@
 
 #include <protomol/integrator/STSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //__________________________________________________ NormalModeCompLang
   class NormalModeCompLang : public STSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeDamping.cpp b/protomol/integrator/normal/NormalModeDamping.cpp
index 15882df..283bd57 100644
--- a/protomol/integrator/normal/NormalModeDamping.cpp
+++ b/protomol/integrator/normal/NormalModeDamping.cpp
@@ -1,14 +1,21 @@
-#include <protomol/integrator/normal/NormalModeDamping.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
-
 #include <protomol/base/Lapack.h>
+#include <protomol/base/PMConstants.h>
+#include <protomol/base/Report.h>
+#include <protomol/integrator/normal/NormalModeDamping.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/io/DCDTrajectoryReader.h"
+#include "protomol/io/XYZTrajectoryWriter.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 
diff --git a/protomol/integrator/normal/NormalModeDamping.h b/protomol/integrator/normal/NormalModeDamping.h
index c32aa4c..b4179a8 100644
--- a/protomol/integrator/normal/NormalModeDamping.h
+++ b/protomol/integrator/normal/NormalModeDamping.h
@@ -4,15 +4,24 @@
 
 #include <protomol/integrator/STSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 #include <protomol/io/DCDTrajectoryReader.h>
 #include <protomol/io/XYZTrajectoryWriter.h>
+#include <iosfwd>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3DBlock.h"
 
 
 namespace ProtoMol {
 
-    class ScalarStructure;
     class ForceGroup;
+    class ScalarStructure;
+class ProtoMolApp;
+class Value;
+class XYZTrajectoryWriter;
+struct Parameter;
 
     //__________________________________________________ NormalModeDamping
     class NormalModeDamping : public STSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeDiagonalize.cpp b/protomol/integrator/normal/NormalModeDiagonalize.cpp
index 61e201e..f8aaf1e 100644
--- a/protomol/integrator/normal/NormalModeDiagonalize.cpp
+++ b/protomol/integrator/normal/NormalModeDiagonalize.cpp
@@ -1,22 +1,25 @@
-#include <protomol/integrator/normal/NormalModeDiagonalize.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/base/Report.h>
+#include <protomol/integrator/STSIntegrator.h>
+#include <protomol/integrator/normal/NormalModeDiagonalize.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/type/BlockMatrix.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/integrator/STSIntegrator.h>
-
+#include <algorithm>
 #include <cmath>
 #include <fstream>
-#include <iostream>
-#include <algorithm>
 
-#include <protomol/base/Lapack.h>
-#include <protomol/parallel/Parallel.h>
+#include "protomol/base/Timer.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/integrator/MTSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/hessian/BlockHessian.h"
+#include "protomol/integrator/hessian/BlockHessianDiagonalize.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/normal/NormalModeDiagonalize.h b/protomol/integrator/normal/NormalModeDiagonalize.h
index 02aaaed..75e773a 100644
--- a/protomol/integrator/normal/NormalModeDiagonalize.h
+++ b/protomol/integrator/normal/NormalModeDiagonalize.h
@@ -2,21 +2,31 @@
 #ifndef NORMALMODEDIAGONALIZE_H
 #define NORMALMODEDIAGONALIZE_H
 
+#include <protomol/base/Timer.h>
 #include <protomol/integrator/MTSIntegrator.h>
-#include <protomol/integrator/normal/NormalModeUtilities.h>
 #include <protomol/integrator/hessian/BlockHessian.h>
 #include <protomol/integrator/hessian/BlockHessianDiagonalize.h>
-
-#include <protomol/type/Vector3DBlock.h>
+#include <protomol/integrator/normal/NormalModeUtilities.h>
 #include <protomol/type/BlockMatrix.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <iosfwd>
+#include <string>
+#include <vector>
 
-#include <protomol/base/Timer.h>
+#include "protomol/type/Real.h"
+
+namespace ProtoMol {
+class ProtoMolApp;
+class StandardIntegrator;
+class Value;
+struct Parameter;
+}  // namespace ProtoMol
 
 namespace ProtoMol
 {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
 
   //__________________________________________________ NormalModeDiagonalize
   class NormalModeDiagonalize :
diff --git a/protomol/integrator/normal/NormalModeLangLf.cpp b/protomol/integrator/normal/NormalModeLangLf.cpp
index 3c7b62e..1da13c3 100644
--- a/protomol/integrator/normal/NormalModeLangLf.cpp
+++ b/protomol/integrator/normal/NormalModeLangLf.cpp
@@ -1,14 +1,25 @@
-#include <protomol/integrator/normal/NormalModeLangLf.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/integrator/normal/NormalModeLangLf.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
-
-#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/MTSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 
 using namespace std;
diff --git a/protomol/integrator/normal/NormalModeLangLf.h b/protomol/integrator/normal/NormalModeLangLf.h
index 4bdfdcf..4cfafa0 100644
--- a/protomol/integrator/normal/NormalModeLangLf.h
+++ b/protomol/integrator/normal/NormalModeLangLf.h
@@ -4,13 +4,20 @@
 
 #include <protomol/integrator/MTSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class StandardIntegrator;
+class Value;
+struct Parameter;
 
   //__________________________________________________ NormalModeLangLf
   class NormalModeLangLf : public MTSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeLangevin.cpp b/protomol/integrator/normal/NormalModeLangevin.cpp
index 6e1dd6d..36a4c05 100644
--- a/protomol/integrator/normal/NormalModeLangevin.cpp
+++ b/protomol/integrator/normal/NormalModeLangevin.cpp
@@ -1,14 +1,20 @@
-#include <protomol/integrator/normal/NormalModeLangevin.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
+#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/integrator/normal/NormalModeLangevin.h>
+#include <protomol/topology/GenericTopology.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
 
-#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/MTSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/normal/NormalModeLangevin.h b/protomol/integrator/normal/NormalModeLangevin.h
index 18b2e34..7683eb2 100644
--- a/protomol/integrator/normal/NormalModeLangevin.h
+++ b/protomol/integrator/normal/NormalModeLangevin.h
@@ -4,12 +4,19 @@
 
 #include <protomol/integrator/MTSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class StandardIntegrator;
+class Value;
+struct Parameter;
 
   //____ NormalModeLangevin
   class NormalModeLangevin : public MTSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.cpp b/protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.cpp
index 153b46b..1f3bafd 100644
--- a/protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.cpp
+++ b/protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.cpp
@@ -1,16 +1,25 @@
-#include <protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
-
-#include <protomol/integrator/normal/ModifierForceProjection.h>
-
-#include <iostream>
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/MTSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 
diff --git a/protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.h b/protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.h
index 08165e9..2ca58e1 100644
--- a/protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.h
+++ b/protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.h
@@ -4,13 +4,21 @@
 
 #include <protomol/integrator/MTSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class StandardIntegrator;
+class Value;
+struct Parameter;
 
   //__________________________________________________ NormalModeLangevinLeapfrogSwitchingSwitching
   class NormalModeLangevinLeapfrogSwitching : public MTSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeMinimizer.cpp b/protomol/integrator/normal/NormalModeMinimizer.cpp
index 958637a..8ecd6a3 100644
--- a/protomol/integrator/normal/NormalModeMinimizer.cpp
+++ b/protomol/integrator/normal/NormalModeMinimizer.cpp
@@ -1,12 +1,24 @@
-#include <protomol/integrator/normal/NormalModeMinimizer.h>
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
+#include <protomol/integrator/normal/NormalModeMinimizer.h>
+#include <protomol/topology/GenericTopology.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+#include <stddef.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 //#include "ModifierForceProjection.h"
 
diff --git a/protomol/integrator/normal/NormalModeMinimizer.h b/protomol/integrator/normal/NormalModeMinimizer.h
index a52c4ac..aae0c12 100644
--- a/protomol/integrator/normal/NormalModeMinimizer.h
+++ b/protomol/integrator/normal/NormalModeMinimizer.h
@@ -4,11 +4,18 @@
 
 #include <protomol/integrator/STSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class Value;
+struct Parameter;
 
   //__________________________________________________ NormalModeMinimizer
   class NormalModeMinimizer : public STSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeMori.cpp b/protomol/integrator/normal/NormalModeMori.cpp
index 46434a5..64fd36e 100644
--- a/protomol/integrator/normal/NormalModeMori.cpp
+++ b/protomol/integrator/normal/NormalModeMori.cpp
@@ -1,16 +1,24 @@
-#include <protomol/integrator/normal/NormalModeMori.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
+#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/integrator/normal/NormalModeMori.h>
+#include <protomol/topology/GenericTopology.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+#include <stddef.h>
+#include <fstream>
 
-#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/integrator/MTSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
-#include <fstream>
 using namespace std;
 
 
diff --git a/protomol/integrator/normal/NormalModeMori.h b/protomol/integrator/normal/NormalModeMori.h
index 048850b..51000d1 100644
--- a/protomol/integrator/normal/NormalModeMori.h
+++ b/protomol/integrator/normal/NormalModeMori.h
@@ -4,14 +4,22 @@
 
 #include <protomol/integrator/MTSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 
 namespace ProtoMol {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class StandardIntegrator;
+class Value;
+class Vector3DBlock;
+struct Parameter;
 
   //__________________________________________________ NormalModeMori
   class NormalModeMori : public MTSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeQuadratic.cpp b/protomol/integrator/normal/NormalModeQuadratic.cpp
index af49caf..be00104 100644
--- a/protomol/integrator/normal/NormalModeQuadratic.cpp
+++ b/protomol/integrator/normal/NormalModeQuadratic.cpp
@@ -1,14 +1,24 @@
-#include <protomol/integrator/normal/NormalModeQuadratic.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
-
 #include <protomol/base/Lapack.h>
+#include <protomol/base/PMConstants.h>
+#include <protomol/base/Report.h>
+#include <protomol/integrator/normal/NormalModeQuadratic.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+#include <algorithm>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 
diff --git a/protomol/integrator/normal/NormalModeQuadratic.h b/protomol/integrator/normal/NormalModeQuadratic.h
index e87ac06..d39c764 100644
--- a/protomol/integrator/normal/NormalModeQuadratic.h
+++ b/protomol/integrator/normal/NormalModeQuadratic.h
@@ -4,12 +4,23 @@
 
 #include <protomol/integrator/STSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+
+namespace ProtoMol {
+class ProtoMolApp;
+class Value;
+class Vector3DBlock;
+struct Parameter;
+}  // namespace ProtoMol
 
 namespace ProtoMol
 {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
 
   //__________________________________________________ NormalModeQuadratic
   class NormalModeQuadratic : public STSIntegrator, public NormalModeUtilities
diff --git a/protomol/integrator/normal/NormalModeRelax.cpp b/protomol/integrator/normal/NormalModeRelax.cpp
index 52f3372..56bc257 100644
--- a/protomol/integrator/normal/NormalModeRelax.cpp
+++ b/protomol/integrator/normal/NormalModeRelax.cpp
@@ -1,12 +1,17 @@
-#include <protomol/integrator/normal/NormalModeRelax.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/base/Report.h>
+#include <protomol/integrator/normal/NormalModeRelax.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+#include <stddef.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/MTSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/type/SimpleTypes.h"
 
 
 using namespace std;
diff --git a/protomol/integrator/normal/NormalModeRelax.h b/protomol/integrator/normal/NormalModeRelax.h
index 8496d20..a8bd67f 100644
--- a/protomol/integrator/normal/NormalModeRelax.h
+++ b/protomol/integrator/normal/NormalModeRelax.h
@@ -4,13 +4,20 @@
 
 #include <protomol/integrator/MTSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class StandardIntegrator;
+class Value;
+struct Parameter;
 
   //__________________________________________________ NormalModeRelax
   class NormalModeRelax : public MTSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeSubspaceSampling.cpp b/protomol/integrator/normal/NormalModeSubspaceSampling.cpp
index b3cfdae..555a302 100644
--- a/protomol/integrator/normal/NormalModeSubspaceSampling.cpp
+++ b/protomol/integrator/normal/NormalModeSubspaceSampling.cpp
@@ -1,16 +1,25 @@
-#include <protomol/integrator/normal/NormalModeSubspaceSampling.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
+#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <protomol/integrator/normal/NormalModeSubspaceSampling.h>
+#include <protomol/topology/GenericTopology.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
-
-#include <protomol/integrator/normal/ModifierForceProjection.h>
+#include <stddef.h>
+#include <iostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/integrator/MTSIntegrator.h"
+#include "protomol/integrator/StandardIntegrator.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
-#include <fstream>
 using namespace std;
 
 
diff --git a/protomol/integrator/normal/NormalModeSubspaceSampling.h b/protomol/integrator/normal/NormalModeSubspaceSampling.h
index 5cff102..93c09fa 100644
--- a/protomol/integrator/normal/NormalModeSubspaceSampling.h
+++ b/protomol/integrator/normal/NormalModeSubspaceSampling.h
@@ -4,14 +4,21 @@
 
 #include <protomol/integrator/MTSIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
-
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 
 namespace ProtoMol {
 
-  class ScalarStructure;
   class ForceGroup;
+  class ScalarStructure;
+class ProtoMolApp;
+class StandardIntegrator;
+class Value;
+struct Parameter;
 
   //__________________________________________________ NormalModeSubspaceSampling
   class NormalModeSubspaceSampling : public MTSIntegrator, public NormalModeUtilities {
diff --git a/protomol/integrator/normal/NormalModeUtilities.cpp b/protomol/integrator/normal/NormalModeUtilities.cpp
index 39aad3c..9435815 100644
--- a/protomol/integrator/normal/NormalModeUtilities.cpp
+++ b/protomol/integrator/normal/NormalModeUtilities.cpp
@@ -1,8 +1,24 @@
+#include <math.h>
+#include <protomol/base/Lapack.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
 #include <protomol/topology/TopologyUtilities.h>
 #include <protomol/type/ScalarStructure.h>
-
-#include <protomol/base/Lapack.h>
+#include <stddef.h>
+#include <ostream>
+#include <string>
+#include <vector>
+
+#include "protomol/ProtoMolApp.h"
+#include "protomol/base/Exception.h"
+#include "protomol/base/MathUtilities.h"
+#include "protomol/base/PMConstants.h"
+#include "protomol/base/Report.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace ProtoMol::Report;
 
diff --git a/protomol/integrator/normal/NormalModeUtilities.h b/protomol/integrator/normal/NormalModeUtilities.h
index 9ec6fb8..3cb6506 100644
--- a/protomol/integrator/normal/NormalModeUtilities.h
+++ b/protomol/integrator/normal/NormalModeUtilities.h
@@ -2,15 +2,21 @@
 #ifndef NORMALMODEUTILITIES_H
 #define NORMALMODEUTILITIES_H
 
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
 #include <protomol/ProtoMolApp.h>
-
-#include <protomol/type/EigenvectorInfo.h>
 #include <protomol/integrator/Integrator.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/type/EigenvectorInfo.h>
+#include <protomol/type/Vector3DBlock.h>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   class ScalarStructure;
+class GenericTopology;
+class Integrator;
+class ProtoMolApp;
+struct EigenvectorInfo;
+
     /**
     *
     * Specific NormalModeUtilities routines
diff --git a/protomol/integrator/openMM/NormalModeOpenMM.cpp b/protomol/integrator/openMM/NormalModeOpenMM.cpp
index b6d91db..32f9aff 100644
--- a/protomol/integrator/openMM/NormalModeOpenMM.cpp
+++ b/protomol/integrator/openMM/NormalModeOpenMM.cpp
@@ -1,12 +1,25 @@
-#include <protomol/integrator/openMM/NormalModeOpenMM.h>
+#include <LTMD/Parameters.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Report.h>
-#include <protomol/force/ForceGroup.h>
+#include <protomol/integrator/openMM/NormalModeOpenMM.h>
 #include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+#include <iostream>
+
+#include "openmm/Vec3.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/normal/NormalModeUtilities.h"
+#include "protomol/integrator/openMM/OpenMMIntegrator.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3DBlock.h"
 
-#include <LTMD/Parameters.h>
+namespace ProtoMol {
+class STSIntegrator;
+}  // namespace ProtoMol
 
 using namespace ProtoMol::Report;
 
diff --git a/protomol/integrator/openMM/NormalModeOpenMM.h b/protomol/integrator/openMM/NormalModeOpenMM.h
index 2e61c28..6787fd1 100644
--- a/protomol/integrator/openMM/NormalModeOpenMM.h
+++ b/protomol/integrator/openMM/NormalModeOpenMM.h
@@ -1,12 +1,20 @@
 #ifndef NORMALMODEOPENMM_H
 #define NORMALMODEOPENMM_H
 
-#include <protomol/integrator/openMM/OpenMMIntegrator.h>
 #include <protomol/integrator/normal/NormalModeUtilities.h>
+#include <protomol/integrator/openMM/OpenMMIntegrator.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
-	class ScalarStructure;
 	class ForceGroup;
+	class ScalarStructure;
+class ProtoMolApp;
+class STSIntegrator;
+class Value;
+struct Parameter;
 
 	class NormalModeOpenMM : public OpenMMIntegrator, public NormalModeUtilities {
 		public:
diff --git a/protomol/integrator/openMM/OpenMMIntegrator.cpp b/protomol/integrator/openMM/OpenMMIntegrator.cpp
index d62d7e2..496a902 100644
--- a/protomol/integrator/openMM/OpenMMIntegrator.cpp
+++ b/protomol/integrator/openMM/OpenMMIntegrator.cpp
@@ -1,21 +1,50 @@
-#include <protomol/integrator/openMM/OpenMMIntegrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/force/ForceGroup.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/TopologyUtilities.h>
+#include <math.h>
+#include <openmm/LocalEnergyMinimizer.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/PMConstants.h>
+#include <protomol/base/Report.h>
 #include <protomol/base/Zap.h>
+#include <protomol/integrator/openMM/OpenMMIntegrator.h>
+#include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/LennardJonesParameters.h>
-
-#include <openmm/LocalEnergyMinimizer.h>
-
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <iostream>
 #include <vector>
-#include <algorithm>
 
-#include <iostream>
+#include "LTMD/Integrator.h"
+#include "LTMD/Parameters.h"
+#include "openmm/CMMotionRemover.h"
+#include "openmm/Context.h"
+#include "openmm/CustomBondForce.h"
+#include "openmm/CustomGBForce.h"
+#include "openmm/CustomNonbondedForce.h"
+#include "openmm/CustomTorsionForce.h"
+#include "openmm/GBSAOBCForce.h"
+#include "openmm/HarmonicAngleForce.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/Integrator.h"
+#include "openmm/LangevinIntegrator.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/PeriodicTorsionForce.h"
+#include "openmm/Platform.h"
+#include "openmm/RBTorsionForce.h"
+#include "openmm/State.h"
+#include "openmm/System.h"
+#include "openmm/Vec3.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/STSIntegrator.h"
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/LennardJonesParameterTable.h"
+#include "protomol/topology/RBTorsion.h"
+#include "protomol/topology/Torsion.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/integrator/openMM/OpenMMIntegrator.h b/protomol/integrator/openMM/OpenMMIntegrator.h
index 5e3cdf7..0142ccb 100644
--- a/protomol/integrator/openMM/OpenMMIntegrator.h
+++ b/protomol/integrator/openMM/OpenMMIntegrator.h
@@ -1,9 +1,23 @@
 #ifndef OPENMMINTEGRATOR_H
 #define OPENMMINTEGRATOR_H
 
+#include <OpenMM.h>
 #include <protomol/integrator/STSIntegrator.h>
+#include <string>
+#include <vector>
 
-#include <OpenMM.h>
+#include "protomol/type/Real.h"
+
+namespace OpenMM {
+class Context;
+class Integrator;
+class System;
+}  // namespace OpenMM
+namespace ProtoMol {
+class ProtoMolApp;
+class Value;
+struct Parameter;
+}  // namespace ProtoMol
 
 #ifdef HAVE_OPENMM_LTMD
 #include <LTMD/Integrator.h>
@@ -15,8 +29,8 @@
 #endif
 
 namespace ProtoMol {
-	class ScalarStructure;
 	class ForceGroup;
+	class ScalarStructure;
 	class Vector3DBlock;
 
 	class OpenMMIntegrator : public STSIntegrator {
diff --git a/protomol/io/CheckpointConfigReader.cpp b/protomol/io/CheckpointConfigReader.cpp
index 08403cb..8bb4828 100644
--- a/protomol/io/CheckpointConfigReader.cpp
+++ b/protomol/io/CheckpointConfigReader.cpp
@@ -1,13 +1,17 @@
-#include <protomol/io/CheckpointConfigReader.h>
-
 #include <protomol/base/Report.h>
 #include <protomol/base/StringUtilities.h>
-
+#include <protomol/io/CheckpointConfigReader.h>
+#include <protomol/io/DCDTrajectoryReader.h>
 #include <protomol/module/IOModule.h>
 #include <protomol/module/MainModule.h>
 #include <protomol/module/ModifierModule.h>
+#include <iostream>
 
-#include <protomol/io/DCDTrajectoryReader.h>
+#include "protomol/base/Random.h"
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/io/Reader.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/CheckpointConfigReader.h b/protomol/io/CheckpointConfigReader.h
index 77edda2..cb269cf 100644
--- a/protomol/io/CheckpointConfigReader.h
+++ b/protomol/io/CheckpointConfigReader.h
@@ -2,15 +2,21 @@
 #ifndef CHECKPOINTCONFIGREADER_H
 #define CHECKPOINTREADERREADER_H
 
-#include <protomol/io/Reader.h>
 #include <protomol/base/Random.h>
 #include <protomol/config/Configuration.h>
 #include <protomol/integrator/Integrator.h>
+#include <protomol/io/Reader.h>
+#include <iosfwd>
+#include <string>
 
 namespace ProtoMol {
   //_________________________________________________________CheckpointConfigReader
   /*
    */
+class Configuration;
+class Integrator;
+class Random;
+
   class CheckpointConfigReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/CheckpointConfigWriter.cpp b/protomol/io/CheckpointConfigWriter.cpp
index 2a69c10..fe0d3c9 100644
--- a/protomol/io/CheckpointConfigWriter.cpp
+++ b/protomol/io/CheckpointConfigWriter.cpp
@@ -1,4 +1,9 @@
 #include <protomol/io/CheckpointConfigWriter.h>
+#include <ostream>
+
+#include "protomol/base/Random.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/io/Writer.h"
 
 using namespace ProtoMol;
 
diff --git a/protomol/io/CheckpointConfigWriter.h b/protomol/io/CheckpointConfigWriter.h
index f3695c0..fe741e0 100644
--- a/protomol/io/CheckpointConfigWriter.h
+++ b/protomol/io/CheckpointConfigWriter.h
@@ -2,13 +2,17 @@
 #ifndef CHECKPOINTCONFIGWRITER_H
 #define CHECKPOINTCONFIGWRITER_H
 
-#include <protomol/io/Writer.h>
 #include <protomol/base/Random.h>
 #include <protomol/integrator/Integrator.h>
+#include <protomol/io/Writer.h>
+#include <string>
 
 namespace ProtoMol {
   //____CheckpointConfigWriter
 
+class Integrator;
+class Random;
+
   class CheckpointConfigWriter : public Writer {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/ConfigurationReader.cpp b/protomol/io/ConfigurationReader.cpp
index bebdc77..1ea98d8 100644
--- a/protomol/io/ConfigurationReader.cpp
+++ b/protomol/io/ConfigurationReader.cpp
@@ -1,7 +1,12 @@
-#include <protomol/io/ConfigurationReader.h>
-
 #include <protomol/base/Report.h>
 #include <protomol/base/StringUtilities.h>
+#include <protomol/io/ConfigurationReader.h>
+#include <algorithm>
+#include <istream>
+
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/io/Reader.h"
 
 using namespace std; 
 using namespace ProtoMol::Report;
diff --git a/protomol/io/ConfigurationReader.h b/protomol/io/ConfigurationReader.h
index 1153c9f..693bd7a 100644
--- a/protomol/io/ConfigurationReader.h
+++ b/protomol/io/ConfigurationReader.h
@@ -2,8 +2,11 @@
 #ifndef CONFIGURATIONREADER_H
 #define CONFIGURATIONREADER_H
 
-#include <protomol/io/Reader.h>
 #include <protomol/config/Configuration.h>
+#include <protomol/io/Reader.h>
+#include <string>
+
+#include "protomol/io/File.h"
 
 namespace ProtoMol {
   //_________________________________________________________ConfigurationReader
@@ -13,6 +16,8 @@ namespace ProtoMol {
    * a keyowrd (identifier) and a value with associated type and constraint.
    * The parsing is implemented in the traits of the types.
    */
+class Configuration;
+
   class ConfigurationReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/DCDTrajectoryReader.cpp b/protomol/io/DCDTrajectoryReader.cpp
index 6f73507..f8bded4 100644
--- a/protomol/io/DCDTrajectoryReader.cpp
+++ b/protomol/io/DCDTrajectoryReader.cpp
@@ -1,8 +1,15 @@
-#include <protomol/io/DCDTrajectoryReader.h>
-
+#include <protomol/base/Exception.h>
 #include <protomol/base/Report.h>
 #include <protomol/base/SystemUtilities.h>
-#include <protomol/base/Exception.h>
+#include <protomol/io/DCDTrajectoryReader.h>
+#include <cstring>
+#include <istream>
+#include <vector>
+
+#include "protomol/io/File.h"
+#include "protomol/io/Reader.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/DCDTrajectoryReader.h b/protomol/io/DCDTrajectoryReader.h
index fadface..bc0a32f 100644
--- a/protomol/io/DCDTrajectoryReader.h
+++ b/protomol/io/DCDTrajectoryReader.h
@@ -3,11 +3,11 @@
 #define DCDTRAJECTORYREADER_H
 
 #include <protomol/io/Reader.h>
-#include <protomol/type/XYZ.h>
 #include <protomol/type/TypeSelection.h>
-
-#include <vector>
+#include <protomol/type/XYZ.h>
 #include <cstring>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   //____DCDTrajectoryReader
@@ -16,6 +16,8 @@ namespace ProtoMol {
    * Reads a DCD trajectory file, frame by frame. Automatic endianess
    * detection.
    */
+class Vector3DBlock;
+
   class DCDTrajectoryReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Typedef
diff --git a/protomol/io/DCDTrajectoryWriter.cpp b/protomol/io/DCDTrajectoryWriter.cpp
index 4380dd6..af01bfe 100644
--- a/protomol/io/DCDTrajectoryWriter.cpp
+++ b/protomol/io/DCDTrajectoryWriter.cpp
@@ -1,8 +1,15 @@
-#include <protomol/io/DCDTrajectoryWriter.h>
-
+#include <protomol/base/Exception.h>
 #include <protomol/base/Report.h>
 #include <protomol/base/StringUtilities.h>
-#include <protomol/base/Exception.h>
+#include <protomol/io/DCDTrajectoryWriter.h>
+#include <iostream>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/base/SystemUtilities.h"
+#include "protomol/io/Writer.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+#include "protomol/type/XYZ.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/DCDTrajectoryWriter.h b/protomol/io/DCDTrajectoryWriter.h
index ff9d6b5..f6f45f6 100644
--- a/protomol/io/DCDTrajectoryWriter.h
+++ b/protomol/io/DCDTrajectoryWriter.h
@@ -2,10 +2,15 @@
 #ifndef DCDTRAJECTORYWRITER_H
 #define DCDTRAJECTORYWRITER_H
 
-#include <protomol/io/Writer.h>
-#include <protomol/type/XYZ.h>
 #include <protomol/base/SystemUtilities.h>
+#include <protomol/io/Writer.h>
 #include <protomol/type/TypeSelection.h>
+#include <protomol/type/XYZ.h>
+#include <iosfwd>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   //____DCDTrajectoryWriter
@@ -14,6 +19,9 @@ namespace ProtoMol {
    * Writes DCD trajectories and updates the number of coordinate sets
    * after each write, no need to know the final number of sets.
    */
+class Vector3DBlock;
+struct XYZ;
+
   class DCDTrajectoryWriter : public Writer {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Typedef
diff --git a/protomol/io/EigenvectorReader.cpp b/protomol/io/EigenvectorReader.cpp
index 90e277c..4e5c80d 100644
--- a/protomol/io/EigenvectorReader.cpp
+++ b/protomol/io/EigenvectorReader.cpp
@@ -1,9 +1,11 @@
+#include <protomol/base/SystemUtilities.h>
 #include <protomol/io/EigenvectorReader.h>
+#include <stddef.h>
+#include <iostream>
 
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
-#include <protomol/base/SystemUtilities.h>
+#include "protomol/io/File.h"
+#include "protomol/io/Reader.h"
+#include "protomol/type/EigenvectorInfo.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/EigenvectorReader.h b/protomol/io/EigenvectorReader.h
index 80fd1da..c878e8a 100644
--- a/protomol/io/EigenvectorReader.h
+++ b/protomol/io/EigenvectorReader.h
@@ -5,12 +5,15 @@
 #include <protomol/io/Reader.h>
 #include <protomol/type/EigenvectorInfo.h>
 #include <protomol/type/TypeSelection.h>
+#include <string>
 
 namespace ProtoMol {
   //_________________________________________________________________PDBReader
   /**
    * Reads an EigenvectorInfo binary file.
    */
+struct EigenvectorInfo;
+
   class EigenvectorReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/EigenvectorTextReader.cpp b/protomol/io/EigenvectorTextReader.cpp
index 6bd6566..2cf6e38 100644
--- a/protomol/io/EigenvectorTextReader.cpp
+++ b/protomol/io/EigenvectorTextReader.cpp
@@ -1,9 +1,9 @@
+#include <protomol/base/Report.h>
 #include <protomol/io/EigenvectorTextReader.h>
+#include <istream>
 
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
-#include <protomol/base/SystemUtilities.h>
+#include "protomol/io/Reader.h"
+#include "protomol/type/EigenvectorInfo.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/EigenvectorTextReader.h b/protomol/io/EigenvectorTextReader.h
index 187714f..540cbe5 100644
--- a/protomol/io/EigenvectorTextReader.h
+++ b/protomol/io/EigenvectorTextReader.h
@@ -5,6 +5,9 @@
 #include <protomol/io/Reader.h>
 #include <protomol/type/EigenvectorInfo.h>
 #include <protomol/type/TypeSelection.h>
+#include <string>
+
+#include "protomol/io/File.h"
 
 namespace ProtoMol {
   //____PDBReader
@@ -12,6 +15,8 @@ namespace ProtoMol {
   /**
    * Reads an EigenvectorInfo ASCII file.
    */
+struct EigenvectorInfo;
+
   class EigenvectorTextReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/File.cpp b/protomol/io/File.cpp
index 2fd8acb..5c596a2 100644
--- a/protomol/io/File.cpp
+++ b/protomol/io/File.cpp
@@ -1,16 +1,9 @@
-#include <protomol/io/File.h>
-
 #include <protomol/base/SystemUtilities.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/Zap.h>
-#include <protomol/type/String.h>
+#include <protomol/io/File.h>
 
 using namespace std;
 using namespace ProtoMol;
 
-#include <sstream>
-#include <iostream>
-
 //____ File
 File::File() : mode(ios::in | ios::out) {}
 File::File(std::ios::openmode mode) : mode(mode) {}
diff --git a/protomol/io/File.h b/protomol/io/File.h
index 906278d..e3eccb9 100644
--- a/protomol/io/File.h
+++ b/protomol/io/File.h
@@ -2,9 +2,9 @@
 #ifndef FILE_H
 #define FILE_H
 
+#include <protomol/base/Exception.h>
 #include <string>
 #include <vector>
-#include <protomol/base/Exception.h>
 
 #ifdef HAVE_LIBFAH
 #include <cbang/os/File.h>
diff --git a/protomol/io/PARReader.cpp b/protomol/io/PARReader.cpp
index da80b8e..d1a7511 100644
--- a/protomol/io/PARReader.cpp
+++ b/protomol/io/PARReader.cpp
@@ -1,8 +1,14 @@
-#include <protomol/io/PARReader.h>
-
-#include <protomol/base/StringUtilities.h>
 #include <protomol/base/Report.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/io/PARReader.h>
+#include <stddef.h>
 #include <algorithm>
+#include <istream>
+#include <vector>
+
+#include "protomol/io/Reader.h"
+#include "protomol/type/PAR.h"
+#include "protomol/type/Real.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/PARReader.h b/protomol/io/PARReader.h
index 5710a9a..8031c52 100644
--- a/protomol/io/PARReader.h
+++ b/protomol/io/PARReader.h
@@ -4,6 +4,7 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/PAR.h>
+#include <string>
 
 namespace ProtoMol {
   //_________________________________________________________________PARReader
diff --git a/protomol/io/PDBReader.cpp b/protomol/io/PDBReader.cpp
index b67047a..ae0aeeb 100644
--- a/protomol/io/PDBReader.cpp
+++ b/protomol/io/PDBReader.cpp
@@ -1,8 +1,14 @@
-#include <protomol/io/PDBReader.h>
-
-#include <protomol/base/StringUtilities.h>
 #include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/io/PDBReader.h>
+#include <stddef.h>
+#include <istream>
+
+#include "protomol/io/Reader.h"
+#include "protomol/type/PDB.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+#include "protomol/type/XYZ.h"
 
 //____#define DEBUG_PDB
 
diff --git a/protomol/io/PDBReader.h b/protomol/io/PDBReader.h
index 9788488..6fc062a 100644
--- a/protomol/io/PDBReader.h
+++ b/protomol/io/PDBReader.h
@@ -5,6 +5,8 @@
 #include <protomol/io/Reader.h>
 #include <protomol/type/PDB.h>
 #include <protomol/type/XYZ.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
 
@@ -12,6 +14,9 @@ namespace ProtoMol {
   /**
    * Reads a PDB (ASCII) file, ATOM, HETATOM and TER record only.
    */
+class Vector3DBlock;
+struct XYZ;
+
   class PDBReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/PDBWriter.cpp b/protomol/io/PDBWriter.cpp
index fab8a6a..7067483 100644
--- a/protomol/io/PDBWriter.cpp
+++ b/protomol/io/PDBWriter.cpp
@@ -1,11 +1,13 @@
-#include <protomol/io/PDBWriter.h>
-
-#include <protomol/type/PDB.h>
 #include <protomol/base/Report.h>
 #include <protomol/base/StringUtilities.h>
-
-#include <iomanip>
+#include <protomol/io/PDBWriter.h>
+#include <protomol/type/PDB.h>
 #include <map>
+#include <ostream>
+
+#include "protomol/io/Writer.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/PDBWriter.h b/protomol/io/PDBWriter.h
index 545888f..d98746a 100644
--- a/protomol/io/PDBWriter.h
+++ b/protomol/io/PDBWriter.h
@@ -4,6 +4,8 @@
 
 #include <protomol/io/Writer.h>
 #include <protomol/type/PDB.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   //____PDBWriter
@@ -11,6 +13,8 @@ namespace ProtoMol {
   /**
    * Writes a PDB (ASCII) file, ATOM record only.
    */
+class Vector3DBlock;
+
   class PDBWriter : public Writer {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/PSFReader.cpp b/protomol/io/PSFReader.cpp
index 3473269..47cf2b0 100644
--- a/protomol/io/PSFReader.cpp
+++ b/protomol/io/PSFReader.cpp
@@ -1,8 +1,13 @@
+#include <protomol/base/Report.h>
+#include <protomol/base/StringUtilities.h>
 #include <protomol/io/PSFReader.h>
+#include <stddef.h>
+#include <algorithm>
+#include <istream>
+#include <vector>
 
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
+#include "protomol/io/Reader.h"
+#include "protomol/type/PSF.h"
 
 //____#define DEBUG_PSF
 
diff --git a/protomol/io/PSFReader.h b/protomol/io/PSFReader.h
index 23f8b17..0baf5ff 100644
--- a/protomol/io/PSFReader.h
+++ b/protomol/io/PSFReader.h
@@ -4,6 +4,7 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/PSF.h>
+#include <string>
 
 namespace ProtoMol {
   //_________________________________________________________________PSFReader
@@ -11,6 +12,8 @@ namespace ProtoMol {
    * Reads a PSD file (ASCII)
    */
 
+class PSF;
+
   class PSFReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/PosVelReader.cpp b/protomol/io/PosVelReader.cpp
index 0a0bdc0..669696b 100644
--- a/protomol/io/PosVelReader.cpp
+++ b/protomol/io/PosVelReader.cpp
@@ -1,11 +1,16 @@
-#include <protomol/io/PosVelReader.h>
-
-#include <protomol/type/Vector.h>
 #include <protomol/base/SystemUtilities.h>
-
+#include <protomol/io/PDBReader.h>
+#include <protomol/io/PosVelReader.h>
 #include <protomol/io/XYZBinReader.h>
 #include <protomol/io/XYZReader.h>
-#include <protomol/io/PDBReader.h>
+
+#include "protomol/io/PosVelReaderType.h"
+
+namespace ProtoMol {
+class Vector3DBlock;
+struct PDB;
+struct XYZ;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/io/PosVelReader.h b/protomol/io/PosVelReader.h
index 4b9231f..eca2f80 100644
--- a/protomol/io/PosVelReader.h
+++ b/protomol/io/PosVelReader.h
@@ -3,11 +3,15 @@
 #define POS_VEL_READER_H
 
 #include <protomol/io/PosVelReaderType.h>
-#include <protomol/type/XYZ.h>
 #include <protomol/type/PDB.h>
+#include <protomol/type/XYZ.h>
+#include <string>
 
 namespace ProtoMol {
   class Configuration;
+class Vector3DBlock;
+struct PDB;
+struct XYZ;
 
   //________________________________________________________ PosVelReader
   class PosVelReader {
diff --git a/protomol/io/PosVelReaderType.h b/protomol/io/PosVelReaderType.h
index 897e881..1cc8ade 100644
--- a/protomol/io/PosVelReaderType.h
+++ b/protomol/io/PosVelReaderType.h
@@ -3,6 +3,7 @@
 #define POS_VEL_READERTYPE_H
 
 #include <protomol/type/AbstractEnumType.h>
+#include <string>
 
 namespace ProtoMol {
   //_____________________________________________________ PosVelReaderEnum
diff --git a/protomol/io/Reader.cpp b/protomol/io/Reader.cpp
index ffe6503..398a0ad 100644
--- a/protomol/io/Reader.cpp
+++ b/protomol/io/Reader.cpp
@@ -1,4 +1,7 @@
 #include <protomol/io/Reader.h>
+#include <iostream>
+
+#include "protomol/io/File.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/io/Reader.h b/protomol/io/Reader.h
index 3ae8a48..49db6bb 100644
--- a/protomol/io/Reader.h
+++ b/protomol/io/Reader.h
@@ -3,6 +3,8 @@
 #define READER_H
 
 #include <protomol/io/File.h>
+#include <iosfwd>
+#include <string>
 
 namespace ProtoMol {
   //_________________________________________________________________ Reader
diff --git a/protomol/io/SCPISMReader.cpp b/protomol/io/SCPISMReader.cpp
index de019a3..70f9b33 100644
--- a/protomol/io/SCPISMReader.cpp
+++ b/protomol/io/SCPISMReader.cpp
@@ -1,8 +1,9 @@
 #include <protomol/io/SCPISMReader.h>
+#include <sstream>
 
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
+#include "protomol/io/Reader.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/topology/CoulombSCPISMParameters.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/SCPISMReader.h b/protomol/io/SCPISMReader.h
index 2bf8a53..1338bfd 100644
--- a/protomol/io/SCPISMReader.h
+++ b/protomol/io/SCPISMReader.h
@@ -1,12 +1,15 @@
 #ifndef SCPISMREADER_H
 #define SCPISMREADER_H
 
-#include <map>
-#include <sstream>
 #include <protomol/io/Reader.h>
 #include <protomol/topology/CoulombSCPISMParameters.h>
+#include <map>
+#include <sstream>
+#include <string>
 
 namespace ProtoMol {
+struct CoulombSCPISMParameters;
+
     class SCPISMReader : public Reader {
             //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
             // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/Writer.cpp b/protomol/io/Writer.cpp
index d010b42..dba7e56 100644
--- a/protomol/io/Writer.cpp
+++ b/protomol/io/Writer.cpp
@@ -1,4 +1,7 @@
 #include <protomol/io/Writer.h>
+#include <iostream>
+
+#include "protomol/io/File.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/io/Writer.h b/protomol/io/Writer.h
index 3b3a124..941cad2 100644
--- a/protomol/io/Writer.h
+++ b/protomol/io/Writer.h
@@ -3,6 +3,8 @@
 #define WRITER_H
 
 #include <protomol/io/File.h>
+#include <iosfwd>
+#include <string>
 
 namespace ProtoMol {
   //_________________________________________________________________ Writer
diff --git a/protomol/io/XYZBinReader.cpp b/protomol/io/XYZBinReader.cpp
index 5f37982..472f70b 100644
--- a/protomol/io/XYZBinReader.cpp
+++ b/protomol/io/XYZBinReader.cpp
@@ -1,8 +1,17 @@
-#include <protomol/io/XYZBinReader.h>
-
 #include <protomol/base/Report.h>
 #include <protomol/base/SystemUtilities.h>
+#include <protomol/io/XYZBinReader.h>
 #include <protomol/type/TypeSelection.h>
+#include <stddef.h>
+#include <iostream>
+#include <vector>
+
+#include "protomol/io/File.h"
+#include "protomol/io/Reader.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+#include "protomol/type/XYZ.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/XYZBinReader.h b/protomol/io/XYZBinReader.h
index 00f0d79..a69b4d4 100644
--- a/protomol/io/XYZBinReader.h
+++ b/protomol/io/XYZBinReader.h
@@ -4,12 +4,15 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/XYZ.h>
+#include <string>
 
 namespace ProtoMol {
   //________________________________________________________________XYZBinReader
   /**
    * Reads a XYZ binary file.
    */
+class Vector3DBlock;
+
   class XYZBinReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/XYZReader.cpp b/protomol/io/XYZReader.cpp
index a1d38e1..68c5d64 100644
--- a/protomol/io/XYZReader.cpp
+++ b/protomol/io/XYZReader.cpp
@@ -1,7 +1,13 @@
 #include <protomol/io/XYZReader.h>
-
 #include <protomol/type/String.h>
-#include <protomol/base/StringUtilities.h>
+#include <stddef.h>
+#include <istream>
+
+#include "protomol/base/Exception.h"
+#include "protomol/io/Reader.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+#include "protomol/type/XYZ.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/io/XYZReader.h b/protomol/io/XYZReader.h
index a6b0693..e3e7256 100644
--- a/protomol/io/XYZReader.h
+++ b/protomol/io/XYZReader.h
@@ -4,6 +4,12 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/XYZ.h>
+#include <string>
+#include <vector>
+
+namespace ProtoMol {
+class Vector3DBlock;
+}  // namespace ProtoMol
 
 #ifdef HAVE_LIBFAH
 namespace FAH {
diff --git a/protomol/io/XYZTrajectoryReader.cpp b/protomol/io/XYZTrajectoryReader.cpp
index 033d085..133f9a4 100644
--- a/protomol/io/XYZTrajectoryReader.cpp
+++ b/protomol/io/XYZTrajectoryReader.cpp
@@ -1,7 +1,10 @@
 #include <protomol/io/XYZTrajectoryReader.h>
+#include <istream>
+#include <vector>
 
-#include <protomol/type/String.h>
-#include <protomol/base/StringUtilities.h>
+#include "protomol/base/Exception.h"
+#include "protomol/io/XYZReader.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/io/XYZTrajectoryReader.h b/protomol/io/XYZTrajectoryReader.h
index c7cca44..a3cb45a 100644
--- a/protomol/io/XYZTrajectoryReader.h
+++ b/protomol/io/XYZTrajectoryReader.h
@@ -4,6 +4,7 @@
 
 #include <protomol/io/XYZReader.h>
 #include <protomol/type/XYZ.h>
+#include <string>
 
 namespace ProtoMol {
   //____XYZTrajectoryReader
@@ -11,6 +12,8 @@ namespace ProtoMol {
   /**
    * Reads a XYY trajectory files (ASCII).
    */
+class Vector3DBlock;
+
   class XYZTrajectoryReader : public XYZReader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/XYZTrajectoryWriter.cpp b/protomol/io/XYZTrajectoryWriter.cpp
index 7d354a0..c3c06ec 100644
--- a/protomol/io/XYZTrajectoryWriter.cpp
+++ b/protomol/io/XYZTrajectoryWriter.cpp
@@ -1,9 +1,16 @@
-#include <protomol/io/XYZTrajectoryWriter.h>
-
-#include <iomanip>
-
 #include <protomol/base/Report.h>
 #include <protomol/base/StringUtilities.h>
+#include <protomol/io/XYZTrajectoryWriter.h>
+#include <stddef.h>
+#include <iomanip>
+#include <istream>
+
+#include "protomol/io/Writer.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+#include "protomol/type/XYZ.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/XYZTrajectoryWriter.h b/protomol/io/XYZTrajectoryWriter.h
index 59a8074..2651dac 100644
--- a/protomol/io/XYZTrajectoryWriter.h
+++ b/protomol/io/XYZTrajectoryWriter.h
@@ -3,9 +3,11 @@
 #define XYZTRAJECTORYWRITER_H
 
 #include <protomol/io/Writer.h>
-#include <protomol/type/XYZ.h>
 #include <protomol/topology/Atom.h>
 #include <protomol/topology/AtomType.h>
+#include <protomol/type/XYZ.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   //____XYZTrajectoryWriter
@@ -14,6 +16,10 @@ namespace ProtoMol {
    * Writes XYZ trajectories (ASCII) and updates the number of coordinate sets
    * after each write, no need to know the final number of sets.
    */
+class Vector3DBlock;
+struct Atom;
+struct AtomType;
+
   class XYZTrajectoryWriter : public Writer {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/XYZWriter.cpp b/protomol/io/XYZWriter.cpp
index 97f486b..9fe823c 100644
--- a/protomol/io/XYZWriter.cpp
+++ b/protomol/io/XYZWriter.cpp
@@ -1,9 +1,13 @@
-#include <protomol/io/XYZWriter.h>
-
-#include <iomanip>
-
 #include <protomol/base/Report.h>
-#include <protomol/base/StringUtilities.h>
+#include <protomol/io/XYZWriter.h>
+#include <ostream>
+
+#include "protomol/io/Writer.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+#include "protomol/type/XYZ.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/XYZWriter.h b/protomol/io/XYZWriter.h
index 1dd3f22..08ecddd 100644
--- a/protomol/io/XYZWriter.h
+++ b/protomol/io/XYZWriter.h
@@ -3,9 +3,11 @@
 #define XYZWRITER_H
 
 #include <protomol/io/Writer.h>
-#include <protomol/type/XYZ.h>
 #include <protomol/topology/Atom.h>
 #include <protomol/topology/AtomType.h>
+#include <protomol/type/XYZ.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   //____XYZWriter
@@ -22,6 +24,10 @@ namespace ProtoMol {
    * C        2.16940       -4.22350        2.03080@n
    * ...
    */
+class Vector3DBlock;
+struct Atom;
+struct AtomType;
+
   class XYZWriter : public Writer {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/gromacs/GromacsBondedParameterFileReader.cpp b/protomol/io/gromacs/GromacsBondedParameterFileReader.cpp
index ec5b10e..c27fd4b 100644
--- a/protomol/io/gromacs/GromacsBondedParameterFileReader.cpp
+++ b/protomol/io/gromacs/GromacsBondedParameterFileReader.cpp
@@ -1,7 +1,14 @@
-#include <protomol/io/gromacs/GromacsBondedParameterFileReader.h>
-#include <protomol/base/StringUtilities.h>
 #include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/io/gromacs/GromacsBondedParameterFileReader.h>
+#include <stddef.h>
+#include <iostream>
+#include <map>
+#include <vector>
+
+#include "protomol/io/Reader.h"
+#include "protomol/type/GromacsParameters.h"
+#include "protomol/type/Real.h"
 
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/io/gromacs/GromacsBondedParameterFileReader.h b/protomol/io/gromacs/GromacsBondedParameterFileReader.h
index f94cdc4..f66be73 100644
--- a/protomol/io/gromacs/GromacsBondedParameterFileReader.h
+++ b/protomol/io/gromacs/GromacsBondedParameterFileReader.h
@@ -4,12 +4,14 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/GromacsParameters.h>
- 
 #include <iostream>
 #include <map>
+#include <string>
 
 namespace ProtoMol {
 
+class GromacsParameters;
+
   class GromacsBondedParameterFileReader : public Reader {
 
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/io/gromacs/GromacsGBParameterFileReader.cpp b/protomol/io/gromacs/GromacsGBParameterFileReader.cpp
index 8a18791..1b1b92a 100644
--- a/protomol/io/gromacs/GromacsGBParameterFileReader.cpp
+++ b/protomol/io/gromacs/GromacsGBParameterFileReader.cpp
@@ -1,7 +1,12 @@
-#include <protomol/io/gromacs/GromacsGBParameterFileReader.h>
-#include <protomol/base/StringUtilities.h>
 #include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/io/gromacs/GromacsGBParameterFileReader.h>
+#include <stddef.h>
+#include <iostream>
+#include <vector>
+
+#include "protomol/io/Reader.h"
+#include "protomol/type/GromacsParameters.h"
  
  
 using namespace ProtoMol::Report;
diff --git a/protomol/io/gromacs/GromacsGBParameterFileReader.h b/protomol/io/gromacs/GromacsGBParameterFileReader.h
index e8a2312..c3ff3e2 100644
--- a/protomol/io/gromacs/GromacsGBParameterFileReader.h
+++ b/protomol/io/gromacs/GromacsGBParameterFileReader.h
@@ -5,11 +5,13 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/GromacsParameters.h>
- 
 #include <iostream>
+#include <string>
 
 namespace ProtoMol {
 
+class GromacsParameters;
+
   class GromacsGBParameterFileReader : public Reader {
 
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/io/gromacs/GromacsNonbondedParameterFileReader.cpp b/protomol/io/gromacs/GromacsNonbondedParameterFileReader.cpp
index a73dc44..b59e3e2 100644
--- a/protomol/io/gromacs/GromacsNonbondedParameterFileReader.cpp
+++ b/protomol/io/gromacs/GromacsNonbondedParameterFileReader.cpp
@@ -1,7 +1,12 @@
-#include <protomol/io/gromacs/GromacsNonbondedParameterFileReader.h>
-#include <protomol/base/StringUtilities.h>
 #include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/io/gromacs/GromacsNonbondedParameterFileReader.h>
+#include <stddef.h>
+#include <iostream>
+#include <utility>
+
+#include "protomol/io/Reader.h"
+#include "protomol/type/GromacsParameters.h"
 
 
 using namespace ProtoMol::Report;
diff --git a/protomol/io/gromacs/GromacsNonbondedParameterFileReader.h b/protomol/io/gromacs/GromacsNonbondedParameterFileReader.h
index 9236f02..9fe33c2 100644
--- a/protomol/io/gromacs/GromacsNonbondedParameterFileReader.h
+++ b/protomol/io/gromacs/GromacsNonbondedParameterFileReader.h
@@ -4,12 +4,14 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/GromacsParameters.h>
-
 #include <iostream>
 #include <map>
+#include <string>
 
 namespace ProtoMol {
 
+class GromacsParameters;
+
   class GromacsNonbondedParameterFileReader : public Reader {
 
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/io/gromacs/GromacsParameterFileReader.cpp b/protomol/io/gromacs/GromacsParameterFileReader.cpp
index 8957c10..6c66ee8 100644
--- a/protomol/io/gromacs/GromacsParameterFileReader.cpp
+++ b/protomol/io/gromacs/GromacsParameterFileReader.cpp
@@ -1,7 +1,13 @@
-#include <protomol/io/gromacs/GromacsParameterFileReader.h>
-#include <protomol/base/StringUtilities.h>
 #include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/io/gromacs/GromacsParameterFileReader.h>
+#include <stddef.h>
+#include <iostream>
+#include <map>
+#include <vector>
+
+#include "protomol/io/Reader.h"
+#include "protomol/type/GromacsParameters.h"
 
 
 using namespace ProtoMol::Report;
diff --git a/protomol/io/gromacs/GromacsParameterFileReader.h b/protomol/io/gromacs/GromacsParameterFileReader.h
index 3f1f085..9c12dec 100644
--- a/protomol/io/gromacs/GromacsParameterFileReader.h
+++ b/protomol/io/gromacs/GromacsParameterFileReader.h
@@ -4,14 +4,16 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/GromacsParameters.h>
-
 #include <iostream>
 #include <map>
+#include <string>
 
 
 
 namespace ProtoMol {
 
+class GromacsParameters;
+
   class GromacsParameterFileReader : public Reader {
 
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/io/gromacs/GromacsTopologyReader.cpp b/protomol/io/gromacs/GromacsTopologyReader.cpp
index 582824b..f806693 100644
--- a/protomol/io/gromacs/GromacsTopologyReader.cpp
+++ b/protomol/io/gromacs/GromacsTopologyReader.cpp
@@ -1,8 +1,12 @@
+#include <protomol/base/Report.h>
+#include <protomol/base/StringUtilities.h>
 #include <protomol/io/gromacs/GromacsTopologyReader.h>
+#include <stddef.h>
+#include <iostream>
+#include <map>
 
-#include <protomol/base/StringUtilities.h>
-#include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
+#include "protomol/io/Reader.h"
+#include "protomol/type/GromacsTopology.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/io/gromacs/GromacsTopologyReader.h b/protomol/io/gromacs/GromacsTopologyReader.h
index de79971..e493a8d 100644
--- a/protomol/io/gromacs/GromacsTopologyReader.h
+++ b/protomol/io/gromacs/GromacsTopologyReader.h
@@ -5,14 +5,17 @@
 
 #include <protomol/io/Reader.h>
 #include <protomol/type/GromacsTopology.h>
-
 #include <iostream>
 #include <map>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
 
   //___________________________________________ GromacsTopologyReader
 
+class GromacsTopology;
+
   class GromacsTopologyReader : public Reader {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors (both default here), assignment
diff --git a/protomol/io/gromacs/PortGromacsParameters.cpp b/protomol/io/gromacs/PortGromacsParameters.cpp
index 3cc067d..27de499 100644
--- a/protomol/io/gromacs/PortGromacsParameters.cpp
+++ b/protomol/io/gromacs/PortGromacsParameters.cpp
@@ -1,19 +1,24 @@
-#include <protomol/io/gromacs/PortGromacsParameters.h>
-
-#include <protomol/type/PSF.h>
-#include <protomol/type/PAR.h>
-#include <protomol/type/GromacsTopology.h>
-#include <protomol/type/GromacsParameters.h>
-#include <protomol/io/gromacs/GromacsTopologyReader.h>
-#include <protomol/io/gromacs/GromacsParameterFileReader.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/io/gromacs/GromacsBondedParameterFileReader.h>
-#include <protomol/io/gromacs/GromacsNonbondedParameterFileReader.h>
 #include <protomol/io/gromacs/GromacsGBParameterFileReader.h>
-
-#include <protomol/base/PMConstants.h>
-
-#include <iterator>
+#include <protomol/io/gromacs/GromacsNonbondedParameterFileReader.h>
+#include <protomol/io/gromacs/GromacsParameterFileReader.h>
+#include <protomol/io/gromacs/GromacsTopologyReader.h>
+#include <protomol/io/gromacs/PortGromacsParameters.h>
+#include <protomol/type/GromacsParameters.h>
+#include <protomol/type/GromacsTopology.h>
+#include <protomol/type/PAR.h>
+#include <protomol/type/PSF.h>
+#include <stddef.h>
 #include <algorithm>
+#include <iostream>
+#include <iterator>
+#include <map>
+#include <utility>
+#include <vector>
+
+#include "protomol/base/Report.h"
+#include "protomol/type/Real.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/io/gromacs/PortGromacsParameters.h b/protomol/io/gromacs/PortGromacsParameters.h
index 1f8fcc5..3a2a6f1 100644
--- a/protomol/io/gromacs/PortGromacsParameters.h
+++ b/protomol/io/gromacs/PortGromacsParameters.h
@@ -1,8 +1,9 @@
 #ifndef PORTGROMACSPARAMETERS_H
 #define PORTGROMACSPARAMETERS_H
 
-#include <iostream>
 #include <protomol/type/Real.h>
+#include <iostream>
+#include <string>
 
 //#define PROPER_DIHEDRAL 1
 //#define RYCKERT_BELLEMAN_DIHEDRAL 3
@@ -15,10 +16,10 @@
 
 namespace ProtoMol {
 
-  class PSF;
-  class PAR;
-  class GromacsTopology;
   class GromacsParameters;
+  class GromacsTopology;
+  class PAR;
+  class PSF;
 
 
   class PortGromacsParameters {
diff --git a/protomol/main.cpp b/protomol/main.cpp
index 3878f8c..1d43db7 100644
--- a/protomol/main.cpp
+++ b/protomol/main.cpp
@@ -3,8 +3,12 @@
 #include <protomol/base/ModuleManager.h>    // for ModuleManager
 #include <protomol/module/MainModule.h>     // for InputDebug
 #include <iostream>                         // for cout, operator<<, ostream, basic_ostream, cerr, endl
+
+#include "protomol/base/Report.h"
 #include "protomol/base/Report.h"           // for cerr
+#include "protomol/config/Configuration.h"
 #include "protomol/config/Configuration.h"  // for Configuration
+#include "protomol/config/Value.h"
 #include "protomol/config/Value.h"          // for Value
 
 using namespace std;
diff --git a/protomol/modifier/Modifier.cpp b/protomol/modifier/Modifier.cpp
index a492d05..4795a1c 100644
--- a/protomol/modifier/Modifier.cpp
+++ b/protomol/modifier/Modifier.cpp
@@ -1,11 +1,8 @@
-#include <protomol/modifier/Modifier.h>
-
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/Report.h>
+#include <protomol/modifier/Modifier.h>
 #include <protomol/topology/GenericTopology.h>
 
-#include <sstream>
-
 using namespace std;
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/modifier/Modifier.h b/protomol/modifier/Modifier.h
index 2d6e0a1..9f2b1aa 100644
--- a/protomol/modifier/Modifier.h
+++ b/protomol/modifier/Modifier.h
@@ -1,16 +1,17 @@
 /*  -*- c++ -*-  */
 #ifndef MODIFIER_H
 #define MODIFIER_H
-#include <vector>
-
 #include <protomol/base/Makeable.h>
-
 #include <ostream>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
+  class Integrator;
   class ProtoMolApp;
   class Vector3DBlock;
-  class Integrator;
+class Value;
+struct Parameter;
 
   //________________________________________ Modifier
   /**
diff --git a/protomol/modifier/ModifierMetaRattle.cpp b/protomol/modifier/ModifierMetaRattle.cpp
index 12d6030..7b86853 100644
--- a/protomol/modifier/ModifierMetaRattle.cpp
+++ b/protomol/modifier/ModifierMetaRattle.cpp
@@ -1,6 +1,12 @@
-#include <protomol/modifier/ModifierMetaRattle.h>
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
-#include <protomol/topology/Topology.h>
+#include <protomol/modifier/ModifierMetaRattle.h>
+#include <vector>
+
+#include "protomol/modifier/ModifierMetaRattleShake.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/modifier/ModifierMetaRattle.h b/protomol/modifier/ModifierMetaRattle.h
index ba55530..56ec339 100644
--- a/protomol/modifier/ModifierMetaRattle.h
+++ b/protomol/modifier/ModifierMetaRattle.h
@@ -5,8 +5,11 @@
 #include <protomol/modifier/ModifierMetaRattleShake.h>
 #include <protomol/type/Vector3DBlock.h>
 
+#include "protomol/type/Real.h"
+
 namespace ProtoMol {
   class Integrator;
+
   //____ ModifierMetaRattle
   class ModifierMetaRattle : public ModifierMetaRattleShake {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/modifier/ModifierMetaRattleShake.cpp b/protomol/modifier/ModifierMetaRattleShake.cpp
index e8a9e27..6f4e888 100644
--- a/protomol/modifier/ModifierMetaRattleShake.cpp
+++ b/protomol/modifier/ModifierMetaRattleShake.cpp
@@ -1,7 +1,13 @@
+#include <protomol/ProtoMolApp.h>
 #include <protomol/modifier/ModifierMetaRattleShake.h>
-#include <protomol/topology/Topology.h>
 #include <protomol/topology/TopologyUtilities.h>
-#include <protomol/ProtoMolApp.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/modifier/Modifier.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/modifier/ModifierMetaRattleShake.h b/protomol/modifier/ModifierMetaRattleShake.h
index 5cf912c..7da3f15 100644
--- a/protomol/modifier/ModifierMetaRattleShake.h
+++ b/protomol/modifier/ModifierMetaRattleShake.h
@@ -5,6 +5,9 @@
 #include <protomol/modifier/Modifier.h>
 #include <protomol/topology/Bond.h>
 #include <protomol/type/Vector3DBlock.h>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   //____ ModifierMetaRattleShake
@@ -18,6 +21,8 @@ namespace ProtoMol {
       getEpsilonVel() and getEtaVel() must be accessible). myListOfConstraints
       is pointer to the actual list.
    */
+struct Parameter;
+
   class ModifierMetaRattleShake : public Modifier {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors, assignment
diff --git a/protomol/modifier/ModifierMetaShake.cpp b/protomol/modifier/ModifierMetaShake.cpp
index bfa3961..189276a 100644
--- a/protomol/modifier/ModifierMetaShake.cpp
+++ b/protomol/modifier/ModifierMetaShake.cpp
@@ -1,6 +1,13 @@
-#include <protomol/modifier/ModifierMetaShake.h>
-#include <protomol/topology/Topology.h>
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
+#include <protomol/modifier/ModifierMetaShake.h>
+#include <vector>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/modifier/ModifierMetaRattleShake.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace ProtoMol;
 
diff --git a/protomol/modifier/ModifierMetaShake.h b/protomol/modifier/ModifierMetaShake.h
index 7a7fe27..39c9531 100644
--- a/protomol/modifier/ModifierMetaShake.h
+++ b/protomol/modifier/ModifierMetaShake.h
@@ -5,8 +5,11 @@
 #include <protomol/modifier/ModifierMetaRattleShake.h>
 #include <protomol/type/Vector3DBlock.h>
 
+#include "protomol/type/Real.h"
+
 namespace ProtoMol {
   class Integrator;
+
   //____ ModifierMetaShake
   class ModifierMetaShake : public ModifierMetaRattleShake {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/modifier/ModifierRattle.cpp b/protomol/modifier/ModifierRattle.cpp
index d8fdf40..35ffc7e 100644
--- a/protomol/modifier/ModifierRattle.cpp
+++ b/protomol/modifier/ModifierRattle.cpp
@@ -1,9 +1,16 @@
-#include <protomol/modifier/ModifierRattle.h>
-#include <protomol/integrator/Integrator.h>
-#include <protomol/topology/Topology.h>
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/PMConstants.h>
+#include <protomol/integrator/Integrator.h>
+#include <protomol/modifier/ModifierRattle.h>
+#include <protomol/type/ScalarStructure.h>
+
+#include "protomol/base/Report.h"
+#include "protomol/modifier/ModifierMetaRattle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/modifier/ModifierRattle.h b/protomol/modifier/ModifierRattle.h
index 3cabf17..9774021 100644
--- a/protomol/modifier/ModifierRattle.h
+++ b/protomol/modifier/ModifierRattle.h
@@ -4,9 +4,16 @@
 
 #include <protomol/modifier/ModifierMetaRattle.h>
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   class Integrator;
+class Modifier;
 
   //____ ModifierRattle
   class ModifierRattle : public ModifierMetaRattle {
diff --git a/protomol/modifier/ModifierShadow.cpp b/protomol/modifier/ModifierShadow.cpp
index c0fe676..42021d5 100644
--- a/protomol/modifier/ModifierShadow.cpp
+++ b/protomol/modifier/ModifierShadow.cpp
@@ -1,9 +1,15 @@
-#include <protomol/modifier/ModifierShadow.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/PMConstants.h>
 #include <protomol/integrator/Integrator.h>
-#include <protomol/topology/Topology.h>
+#include <protomol/modifier/ModifierShadow.h>
 #include <protomol/type/ScalarStructure.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/ProtoMolApp.h>
+
+#include "protomol/base/Report.h"
+#include "protomol/modifier/Modifier.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace ProtoMol::Report;
 using std::deque;
diff --git a/protomol/modifier/ModifierShadow.h b/protomol/modifier/ModifierShadow.h
index 089eb64..2cc5e1d 100644
--- a/protomol/modifier/ModifierShadow.h
+++ b/protomol/modifier/ModifierShadow.h
@@ -3,6 +3,11 @@
 
 #include <protomol/modifier/Modifier.h>
 #include <protomol/type/Vector3DBlock.h>
+#include <deque>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
 
diff --git a/protomol/modifier/ModifierShake.cpp b/protomol/modifier/ModifierShake.cpp
index 437abd8..9947f74 100644
--- a/protomol/modifier/ModifierShake.cpp
+++ b/protomol/modifier/ModifierShake.cpp
@@ -1,9 +1,16 @@
-#include <protomol/modifier/ModifierShake.h>
-#include <protomol/integrator/Integrator.h>
-#include <protomol/topology/Topology.h>
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/PMConstants.h>
+#include <protomol/integrator/Integrator.h>
+#include <protomol/modifier/ModifierShake.h>
+#include <protomol/type/ScalarStructure.h>
+
+#include "protomol/base/Report.h"
+#include "protomol/modifier/ModifierMetaShake.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/modifier/ModifierShake.h b/protomol/modifier/ModifierShake.h
index 0356903..bd18439 100644
--- a/protomol/modifier/ModifierShake.h
+++ b/protomol/modifier/ModifierShake.h
@@ -4,9 +4,16 @@
 
 #include <protomol/modifier/ModifierMetaShake.h>
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   class Integrator;
+class Modifier;
 
   //____ ModifierShake
   class ModifierShake : public ModifierMetaShake {
diff --git a/protomol/module/AnalysisModule.cpp b/protomol/module/AnalysisModule.cpp
index c9a0468..e38626f 100644
--- a/protomol/module/AnalysisModule.cpp
+++ b/protomol/module/AnalysisModule.cpp
@@ -1,10 +1,7 @@
-#include <protomol/module/AnalysisModule.h>
-
 #include <protomol/ProtoMolApp.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/factory/AnalysisFactory.h>
-
 #include <protomol/analysis/AnalysisDihedral.h>
+#include <protomol/factory/AnalysisFactory.h>
+#include <protomol/module/AnalysisModule.h>
 
 using namespace ProtoMol;
 
diff --git a/protomol/module/AnalysisModule.h b/protomol/module/AnalysisModule.h
index 4d6e457..d250913 100644
--- a/protomol/module/AnalysisModule.h
+++ b/protomol/module/AnalysisModule.h
@@ -3,9 +3,10 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
-
 #include <string>
 
+#include "protomol/config/InputValueMacros.h"
+
 namespace ProtoMol {
 	class ProtoMolApp;
 
diff --git a/protomol/module/BondedForcesModule.cpp b/protomol/module/BondedForcesModule.cpp
index 8d9dac6..0a781e5 100644
--- a/protomol/module/BondedForcesModule.cpp
+++ b/protomol/module/BondedForcesModule.cpp
@@ -1,17 +1,22 @@
-#include <protomol/module/BondedForcesModule.h>
-
-#include <protomol/force/bonded/RBDihedralSystemForce.h>
-#include <protomol/force/bonded/DihedralSystemForce.h>
-#include <protomol/force/bonded/BondSystemForce.h>
-#include <protomol/force/bonded/AngleSystemForce.h>
-#include <protomol/force/bonded/ImproperSystemForce.h>
-#include <protomol/force/bonded/HarmDihedralSystemForce.h>
-
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/StringUtilities.h>
+#include <protomol/force/bonded/AngleSystemForce.h>
+#include <protomol/force/bonded/BondSystemForce.h>
+#include <protomol/force/bonded/DihedralSystemForce.h>
+#include <protomol/force/bonded/HarmDihedralSystemForce.h>
+#include <protomol/force/bonded/ImproperSystemForce.h>
+#include <protomol/force/bonded/RBDihedralSystemForce.h>
+#include <protomol/module/BondedForcesModule.h>
 #include <protomol/module/TopologyModule.h>
 #include <protomol/topology/PeriodicBoundaryConditions.h>
 #include <protomol/topology/VacuumBoundaryConditions.h>
+#include <algorithm>
+
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/ForceFactory.h"
+#include "protomol/force/Force.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/CheckpointModule.cpp b/protomol/module/CheckpointModule.cpp
index c8e5014..75ce13e 100644
--- a/protomol/module/CheckpointModule.cpp
+++ b/protomol/module/CheckpointModule.cpp
@@ -1,11 +1,14 @@
 #include "CheckpointModule.h"
 
-#include "IOModule.h"
-
 #include <protomol/ProtoMolApp.h>
+#include <protomol/factory/OutputFactory.h>
 #include <protomol/io/CheckpointConfigReader.h>
 #include <protomol/output/OutputCheckpoint.h>
-#include <protomol/factory/OutputFactory.h>
+#include <iostream>
+
+#include "protomol/base/Random.h"
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/CheckpointModule.h b/protomol/module/CheckpointModule.h
index 2883baa..88f4dfd 100644
--- a/protomol/module/CheckpointModule.h
+++ b/protomol/module/CheckpointModule.h
@@ -3,10 +3,11 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
-
 #include <string>
 
 namespace ProtoMol {
+class ProtoMolApp;
+
   class CheckpointModule : public Module {
     bool enabled;
 
diff --git a/protomol/module/CommandLineModule.cpp b/protomol/module/CommandLineModule.cpp
index 61ef858..657a60c 100644
--- a/protomol/module/CommandLineModule.cpp
+++ b/protomol/module/CommandLineModule.cpp
@@ -1,11 +1,27 @@
-#include <protomol/module/CommandLineModule.h>
-
+#include <protomol/ProtoMolApp.h>
 #include <protomol/base/ModuleManager.h>
 #include <protomol/config/CommandLine.h>
+#include <protomol/module/CommandLineModule.h>
+#include <protomol/module/TopologyModule.h>
 #include <protomol/topology/PeriodicBoundaryConditions.h>
 #include <protomol/topology/VacuumBoundaryConditions.h>
-#include <protomol/module/TopologyModule.h>
-#include <protomol/ProtoMolApp.h>
+#include <iostream>
+
+#include "protomol/analysis/Analysis.h"
+#include "protomol/base/Factory.h"
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/CommandLineOption.h"
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/AnalysisFactory.h"
+#include "protomol/factory/ForceFactory.h"
+#include "protomol/factory/IntegratorFactory.h"
+#include "protomol/factory/OutputFactory.h"
+#include "protomol/factory/TopologyFactory.h"
+#include "protomol/force/Force.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/output/Output.h"
+#include "protomol/topology/GenericTopology.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/ConfigurationModule.cpp b/protomol/module/ConfigurationModule.cpp
index 3e64993..0ba05b2 100644
--- a/protomol/module/ConfigurationModule.cpp
+++ b/protomol/module/ConfigurationModule.cpp
@@ -1,13 +1,18 @@
-#include <protomol/module/ConfigurationModule.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/config/CommandLine.h>
 #include <protomol/config/Configuration.h>
 #include <protomol/io/ConfigurationReader.h>
-
-#include <protomol/config/CommandLine.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/config/InputValue.h>
-
+#include <protomol/module/ConfigurationModule.h>
 #include <iostream>
+#include <map>
 #include <string>
+#include <utility>
+
+#include "protomol/base/Exception.h"
+#include "protomol/base/StringUtilities.h"
+#include "protomol/config/CommandLineOption.h"
+#include "protomol/config/Value.h"
+#include "protomol/io/File.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/ConfigurationModule.h b/protomol/module/ConfigurationModule.h
index 7c1040c..fe41b4f 100644
--- a/protomol/module/ConfigurationModule.h
+++ b/protomol/module/ConfigurationModule.h
@@ -3,13 +3,14 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
-
-#include <vector>
 #include <string>
+#include <vector>
+
+#include "protomol/config/InputValueMacros.h"
 
 namespace ProtoMol {
-  class ProtoMolApp;
   class Configuration;
+  class ProtoMolApp;
 
   declareInputValue(InputConfig, STRING, NOTEMPTY)
 
diff --git a/protomol/module/HessianIntegratorModule.cpp b/protomol/module/HessianIntegratorModule.cpp
index 4134140..4c26904 100644
--- a/protomol/module/HessianIntegratorModule.cpp
+++ b/protomol/module/HessianIntegratorModule.cpp
@@ -1,7 +1,8 @@
-#include <protomol/module/HessianIntegratorModule.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/integrator/hessian/HessianInt.h>
+#include <protomol/module/HessianIntegratorModule.h>
 
-#include <protomol/ProtoMolApp.h>
+#include "protomol/factory/IntegratorFactory.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/IOModule.cpp b/protomol/module/IOModule.cpp
index cb82dac..d416335 100644
--- a/protomol/module/IOModule.cpp
+++ b/protomol/module/IOModule.cpp
@@ -1,23 +1,35 @@
-#include <protomol/module/IOModule.h>
-
-#include <protomol/io/PosVelReader.h>
-#include <protomol/io/PSFReader.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/Exception.h>
+#include <protomol/base/PMConstants.h>
+//
+#include <protomol/config/Configuration.h>
 #include <protomol/io/PARReader.h>
-
+#include <protomol/io/PSFReader.h>
+#include <protomol/io/PosVelReader.h>
+#include <protomol/io/SCPISMReader.h>
 //for GROMACS
 #include <protomol/io/gromacs/PortGromacsParameters.h>
-#include <protomol/type/GromacsTopology.h>
-#include <protomol/type/GromacsParameters.h>
-//
-#include <protomol/config/Configuration.h>
-#include <protomol/base/Exception.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/PMConstants.h>
-#include <protomol/type/String.h>
-#include <protomol/type/PDB.h>
+#include <protomol/module/IOModule.h>
 #include <protomol/module/MainModule.h>
-#include <protomol/io/SCPISMReader.h>
 #include <protomol/topology/CoulombSCPISMParameterTable.h>
+#include <protomol/type/GromacsParameters.h>
+#include <protomol/type/GromacsTopology.h>
+#include <protomol/type/PDB.h>
+#include <ostream>
+#include <vector>
+
+#include "protomol/base/Report.h"
+#include "protomol/config/Value.h"
+#include "protomol/io/File.h"
+#include "protomol/io/PosVelReaderType.h"
+#include "protomol/output/OutputCache.h"
+#include "protomol/type/AbstractEnumType.h"
+#include "protomol/type/PAR.h"
+#include "protomol/type/PSF.h"
+#include "protomol/type/Vector.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
+#include "protomol/type/XYZ.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/IOModule.h b/protomol/module/IOModule.h
index bf7710f..014a14c 100644
--- a/protomol/module/IOModule.h
+++ b/protomol/module/IOModule.h
@@ -3,9 +3,10 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
-
 #include <string>
 
+#include "protomol/config/InputValueMacros.h"
+
 namespace ProtoMol {
   class ProtoMolApp;
 
diff --git a/protomol/module/IntegratorBaseModule.cpp b/protomol/module/IntegratorBaseModule.cpp
index 1ae328a..09a2da0 100644
--- a/protomol/module/IntegratorBaseModule.cpp
+++ b/protomol/module/IntegratorBaseModule.cpp
@@ -1,15 +1,15 @@
-#include <protomol/module/IntegratorBaseModule.h>
-
+#include <protomol/ProtoMolApp.h>
+#include <protomol/integrator/base/CGMinimizerIntegrator.h>
 #include <protomol/integrator/base/LangevinImpulseIntegrator.h>
 #include <protomol/integrator/base/LangevinLeapfrogIntegrator.h>
 #include <protomol/integrator/base/LangevinLeapfrogSwitchingIntegrator.h>
 #include <protomol/integrator/base/LangevinVVVRIntegrator.h>
-#include <protomol/integrator/base/CGMinimizerIntegrator.h>
 #include <protomol/integrator/base/NumericalDifferentiation.h>
 #include <protomol/integrator/base/NumericallyDifferentiatedHessian.h>
 #include <protomol/integrator/base/RMTIntegrator.h>
+#include <protomol/module/IntegratorBaseModule.h>
 
-#include <protomol/ProtoMolApp.h>
+#include "protomol/factory/IntegratorFactory.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/IntegratorOpenMMModule.cpp b/protomol/module/IntegratorOpenMMModule.cpp
index 1f9a148..67a3250 100644
--- a/protomol/module/IntegratorOpenMMModule.cpp
+++ b/protomol/module/IntegratorOpenMMModule.cpp
@@ -15,6 +15,8 @@
 
 #include <protomol/ProtoMolApp.h>
 
+#include "protomol/factory/IntegratorFactory.h"
+
 using namespace std;
 using namespace ProtoMol;
 
diff --git a/protomol/module/LeapfrogModule.cpp b/protomol/module/LeapfrogModule.cpp
index 5de4816..1a1fa2d 100644
--- a/protomol/module/LeapfrogModule.cpp
+++ b/protomol/module/LeapfrogModule.cpp
@@ -1,15 +1,14 @@
-#include <protomol/module/LeapfrogModule.h>
-
 #include <protomol/ProtoMolApp.h>
-
+#include <protomol/integrator/leapfrog/DMDLeapfrogIntegrator.h>
+#include <protomol/integrator/leapfrog/GPU.h>
+#include <protomol/integrator/leapfrog/LeapfrogDataAcquisition.h>
 #include <protomol/integrator/leapfrog/LeapfrogIntegrator.h>
 #include <protomol/integrator/leapfrog/LeapfrogTruncatedShadow.h>
-#include <protomol/integrator/leapfrog/DMDLeapfrogIntegrator.h>
-#include <protomol/integrator/leapfrog/PLeapfrogIntegrator.h>
 #include <protomol/integrator/leapfrog/NoseNVTLeapfrogIntegrator.h>
+#include <protomol/integrator/leapfrog/PLeapfrogIntegrator.h>
+#include <protomol/module/LeapfrogModule.h>
 
-#include <protomol/integrator/leapfrog/LeapfrogDataAcquisition.h>
-#include <protomol/integrator/leapfrog/GPU.h>
+#include "protomol/factory/IntegratorFactory.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/MainModule.cpp b/protomol/module/MainModule.cpp
index f2dbb4c..93ec5bf 100644
--- a/protomol/module/MainModule.cpp
+++ b/protomol/module/MainModule.cpp
@@ -1,12 +1,17 @@
-#include <protomol/module/MainModule.h>
-
-#include <protomol/module/IOModule.h>
 #include <protomol/ProtoMolApp.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/base/Report.h>
 #include <protomol/base/Exception.h>
+#include <protomol/base/Report.h>
+#include <protomol/config/Configuration.h>
+#include <protomol/module/IOModule.h>
+#include <protomol/module/MainModule.h>
 #include <protomol/parallel/Parallel.h>
+#include <protomol/topology/TopologyUtilities.h>
+#include <ostream>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/Value.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/MainModule.h b/protomol/module/MainModule.h
index 8603ccf..2b42344 100644
--- a/protomol/module/MainModule.h
+++ b/protomol/module/MainModule.h
@@ -3,6 +3,9 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
+#include <string>
+
+#include "protomol/config/InputValueMacros.h"
 
 namespace ProtoMol {
   class ProtoMolApp;
diff --git a/protomol/module/ModifierModule.cpp b/protomol/module/ModifierModule.cpp
index 3114976..7a31a64 100644
--- a/protomol/module/ModifierModule.cpp
+++ b/protomol/module/ModifierModule.cpp
@@ -1,16 +1,25 @@
-#include <protomol/module/ModifierModule.h>
-
-#include <protomol/modifier/ModifierIncrementTimestep.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/Report.h>
 #include <protomol/modifier/ModifierRattle.h>
-#include <protomol/modifier/ModifierShake.h>
-#include <protomol/modifier/ModifierShadow.h>
 #include <protomol/modifier/ModifierRemoveAngularMomentum.h>
 #include <protomol/modifier/ModifierRemoveLinearMomentum.h>
-
-#include <protomol/base/Report.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/modifier/ModifierShadow.h>
+#include <protomol/modifier/ModifierShake.h>
+#include <protomol/module/ModifierModule.h>
 #include <protomol/topology/TopologyUtilities.h>
 
+#include "protomol/base/PMConstants.h"
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector.h"
+#include "protomol/type/Vector3D.h"
+
+namespace ProtoMol {
+class Modifier;
+}  // namespace ProtoMol
+
 using namespace std;
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/module/ModifierModule.h b/protomol/module/ModifierModule.h
index 5727433..646e801 100644
--- a/protomol/module/ModifierModule.h
+++ b/protomol/module/ModifierModule.h
@@ -3,9 +3,10 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
-
 #include <string>
 
+#include "protomol/config/InputValueMacros.h"
+
 namespace ProtoMol {
   class ProtoMolApp;
 
diff --git a/protomol/module/NonbondedCutoffForceModule.cpp b/protomol/module/NonbondedCutoffForceModule.cpp
index 1b0b5e6..c43f977 100644
--- a/protomol/module/NonbondedCutoffForceModule.cpp
+++ b/protomol/module/NonbondedCutoffForceModule.cpp
@@ -1,38 +1,41 @@
-#include <protomol/module/NonbondedCutoffForceModule.h>
-
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/StringUtilities.h>
-#include <protomol/module/TopologyModule.h>
-#include <protomol/topology/PeriodicBoundaryConditions.h>
-#include <protomol/topology/VacuumBoundaryConditions.h>
-
-#include <protomol/force/OneAtomPair.h>
-#include <protomol/force/OneAtomPairTwo.h>
-#include <protomol/force/OneAtomPairThree.h>
-#include <protomol/force/OneAtomPairNoExclusion.h>
 #include <protomol/force/CoulombForce.h>
+#include <protomol/force/GB/GBACEForce.h>
+#include <protomol/force/GB/GBBornRadii.h>
+//GB
+#include <protomol/force/GB/GBForce.h>
+#include <protomol/force/GB/GBPartialSum.h>
 #include <protomol/force/LennardJonesForce.h>
-#include <protomol/force/coulomb/CoulombSCPISMForce.h>
+#include <protomol/force/OneAtomPair.h>
+#include <protomol/force/OneAtomPairNoExclusion.h>
+#include <protomol/force/OneAtomPairThree.h>
+#include <protomol/force/OneAtomPairTwo.h>
 #include <protomol/force/born/BornRadii.h>
 #include <protomol/force/born/BornSelfForce.h>
+#include <protomol/force/coulomb/CoulombSCPISMForce.h>
 #include <protomol/force/nonbonded/NonbondedCutoffSystemForce.h>
 #include <protomol/force/table/LennardJonesTableForce.h>
-
+#include <protomol/module/NonbondedCutoffForceModule.h>
+#include <protomol/module/TopologyModule.h>
 #include <protomol/switch/C1SwitchingFunction.h>
 #include <protomol/switch/C2SwitchingFunction.h>
 #include <protomol/switch/CmpCnCnSwitchingFunction.h>
 #include <protomol/switch/CnSwitchingFunction.h>
-#include <protomol/switch/UniversalSwitchingFunction.h>
 #include <protomol/switch/CutoffSwitchingFunction.h>
-
-#include <protomol/topology/CellListEnumeratorPeriodicBoundaries.h>
-#include <protomol/topology/CellListEnumeratorStandard.h>
-
-//GB
-#include <protomol/force/GB/GBForce.h>
-#include <protomol/force/GB/GBACEForce.h>
-#include <protomol/force/GB/GBBornRadii.h>
-#include <protomol/force/GB/GBPartialSum.h>
+#include <protomol/switch/UniversalSwitchingFunction.h>
+#include <protomol/topology/PeriodicBoundaryConditions.h>
+#include <protomol/topology/VacuumBoundaryConditions.h>
+#include <vector>
+
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/ForceFactory.h"
+#include "protomol/force/Force.h"
+#include "protomol/topology/CubicCellManager.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Real.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/NonbondedFullElectrostaticForceModule.cpp b/protomol/module/NonbondedFullElectrostaticForceModule.cpp
index 73389c8..605ee34 100644
--- a/protomol/module/NonbondedFullElectrostaticForceModule.cpp
+++ b/protomol/module/NonbondedFullElectrostaticForceModule.cpp
@@ -1,18 +1,20 @@
-#include <protomol/module/NonbondedFullElectrostaticForceModule.h>
-
+#include <math.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/StringUtilities.h>
-#include <protomol/module/TopologyModule.h>
-#include <protomol/topology/PeriodicBoundaryConditions.h>
-
 #include <protomol/force/nonbonded/NonbondedFullEwaldSystemForce.h>
-
+#include <protomol/module/NonbondedFullElectrostaticForceModule.h>
+#include <protomol/module/TopologyModule.h>
 #include <protomol/switch/CutoffSwitchingFunction.h>
-
-#include <protomol/topology/CellListEnumeratorPeriodicBoundaries.h>
-#include <protomol/topology/CellListEnumeratorStandard.h>
-#include <protomol/topology/CellListEnumerator.h>
 #include <protomol/topology/CubicCellManager.h>
+#include <protomol/topology/PeriodicBoundaryConditions.h>
+
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/ForceFactory.h"
+#include "protomol/force/Force.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/NonbondedFullForceModule.cpp b/protomol/module/NonbondedFullForceModule.cpp
index 7565e84..5261e5c 100644
--- a/protomol/module/NonbondedFullForceModule.cpp
+++ b/protomol/module/NonbondedFullForceModule.cpp
@@ -1,24 +1,23 @@
-#include <protomol/module/NonbondedFullForceModule.h>
-
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/StringUtilities.h>
-#include <protomol/module/TopologyModule.h>
-#include <protomol/topology/PeriodicBoundaryConditions.h>
-#include <protomol/topology/VacuumBoundaryConditions.h>
-
-#include <protomol/force/OneAtomPairFull.h>
 #include <protomol/force/CoulombForce.h>
 #include <protomol/force/LennardJonesForce.h>
-
+#include <protomol/force/OneAtomPairFull.h>
+#include <protomol/force/nonbonded/NonbondedFullSystemForce.h>
+#include <protomol/module/NonbondedFullForceModule.h>
+#include <protomol/module/TopologyModule.h>
 #include <protomol/switch/C1SwitchingFunction.h>
 #include <protomol/switch/C2SwitchingFunction.h>
 #include <protomol/switch/CmpCnCnSwitchingFunction.h>
 #include <protomol/switch/CnSwitchingFunction.h>
+#include <protomol/topology/PeriodicBoundaryConditions.h>
+#include <protomol/topology/VacuumBoundaryConditions.h>
+#include <vector>
 
-#include <protomol/force/nonbonded/NonbondedFullSystemForce.h>
-
-#include <protomol/topology/CellListEnumeratorPeriodicBoundaries.h>
-#include <protomol/topology/CellListEnumeratorStandard.h>
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/ForceFactory.h"
+#include "protomol/force/Force.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/NonbondedIntermittentFullForceModule.cpp b/protomol/module/NonbondedIntermittentFullForceModule.cpp
index 64e6005..80f405b 100644
--- a/protomol/module/NonbondedIntermittentFullForceModule.cpp
+++ b/protomol/module/NonbondedIntermittentFullForceModule.cpp
@@ -1,28 +1,25 @@
-#include <protomol/module/NonbondedIntermittentFullForceModule.h>
-
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/StringUtilities.h>
-#include <protomol/module/TopologyModule.h>
-#include <protomol/topology/PeriodicBoundaryConditions.h>
-#include <protomol/topology/VacuumBoundaryConditions.h>
-
+//GB
+#include <protomol/force/GB/GBBornRadii.h>
+#include <protomol/force/GB/GBPartialSum.h>
 #include <protomol/force/OneAtomPairNoExclusion.h>
-
-#include <protomol/switch/UniversalSwitchingFunction.h>
-#include <protomol/switch/CutoffSwitchingFunction.h>
-
-#include <protomol/force/nonbonded/NonbondedIntermittentFullSystemForce.h>
-
-#include <protomol/topology/CellListEnumeratorPeriodicBoundaries.h>
-#include <protomol/topology/CellListEnumeratorStandard.h>
-
 //SCPISM
 #include <protomol/force/born/BornRadii.h>
 #include <protomol/force/born/BornSelfForce.h>
+#include <protomol/force/nonbonded/NonbondedIntermittentFullSystemForce.h>
+#include <protomol/module/NonbondedIntermittentFullForceModule.h>
+#include <protomol/module/TopologyModule.h>
+#include <protomol/switch/CutoffSwitchingFunction.h>
+#include <protomol/switch/UniversalSwitchingFunction.h>
+#include <protomol/topology/PeriodicBoundaryConditions.h>
+#include <protomol/topology/VacuumBoundaryConditions.h>
+#include <vector>
 
-//GB
-#include <protomol/force/GB/GBBornRadii.h>
-#include <protomol/force/GB/GBPartialSum.h>
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/ForceFactory.h"
+#include "protomol/force/Force.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/NonbondedSimpleFullForceModule.cpp b/protomol/module/NonbondedSimpleFullForceModule.cpp
index ecdf7c3..d5e55ee 100644
--- a/protomol/module/NonbondedSimpleFullForceModule.cpp
+++ b/protomol/module/NonbondedSimpleFullForceModule.cpp
@@ -1,39 +1,37 @@
-#include <protomol/module/NonbondedSimpleFullForceModule.h>
-
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/StringUtilities.h>
-#include <protomol/module/TopologyModule.h>
-#include <protomol/topology/PeriodicBoundaryConditions.h>
-#include <protomol/topology/VacuumBoundaryConditions.h>
-
-#include <protomol/force/OneAtomPair.h>
-#include <protomol/force/OneAtomPairNoExclusion.h>
-#include <protomol/force/OneAtomPairTwo.h>
 #include <protomol/force/CoulombForce.h>
+#include <protomol/force/GB/GBACEForce.h>
+//GB
+#include <protomol/force/GB/GBBornRadii.h>
+#include <protomol/force/GB/GBForce.h>
+#include <protomol/force/GB/GBPartialSum.h>
+#include <protomol/force/HarmonicRestraintForce.h>
 #include <protomol/force/LennardJonesForce.h>
 #include <protomol/force/LennardJonesVDWForce.h>
-#include <protomol/force/HarmonicRestraintForce.h>
+#include <protomol/force/OneAtomPair.h>
+#include <protomol/force/OneAtomPairNoExclusion.h>
+#include <protomol/force/OneAtomPairTwo.h>
 #include <protomol/force/ProteinRestraintForce.h>
-#include <protomol/force/coulomb/CoulombSCPISMForce.h>
 #include <protomol/force/coulomb/CoulombForceDiElec.h>
-
+#include <protomol/force/coulomb/CoulombSCPISMForce.h>
+#include <protomol/force/nonbonded/NonbondedSimpleFullSystemForce.h>
+#include <protomol/module/NonbondedSimpleFullForceModule.h>
+#include <protomol/module/TopologyModule.h>
 #include <protomol/switch/C1SwitchingFunction.h>
 #include <protomol/switch/C2SwitchingFunction.h>
 #include <protomol/switch/CmpCnCnSwitchingFunction.h>
 #include <protomol/switch/CnSwitchingFunction.h>
 #include <protomol/switch/ComplementSwitchingFunction.h>
 #include <protomol/switch/UniversalSwitchingFunction.h>
+#include <protomol/topology/PeriodicBoundaryConditions.h>
+#include <protomol/topology/VacuumBoundaryConditions.h>
+#include <vector>
 
-#include <protomol/force/nonbonded/NonbondedSimpleFullSystemForce.h>
-
-#include <protomol/topology/CellListEnumeratorPeriodicBoundaries.h>
-#include <protomol/topology/CellListEnumeratorStandard.h>
-
-//GB
-#include <protomol/force/GB/GBBornRadii.h>
-#include <protomol/force/GB/GBForce.h>
-#include <protomol/force/GB/GBACEForce.h>
-#include <protomol/force/GB/GBPartialSum.h>
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/ForceFactory.h"
+#include "protomol/force/Force.h"
 
 
 using namespace std;
diff --git a/protomol/module/NormalModeModule.cpp b/protomol/module/NormalModeModule.cpp
index 22e3914..fb3bd97 100644
--- a/protomol/module/NormalModeModule.cpp
+++ b/protomol/module/NormalModeModule.cpp
@@ -1,24 +1,32 @@
-#include <protomol/module/NormalModeModule.h>
-
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/Exception.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/type/String.h>
-#include <protomol/io/EigenvectorReader.h>
-#include <protomol/io/EigenvectorTextReader.h>
-#include <protomol/io/XYZReader.h>
-#include <protomol/integrator/normal/NormalModeLangevin.h>
+#include <protomol/integrator/normal/NormalModeBrownian.h>
+#include <protomol/integrator/normal/NormalModeCompLang.h>
+#include <protomol/integrator/normal/NormalModeDamping.h> 
+#include <protomol/integrator/normal/NormalModeDiagonalize.h>
 #include <protomol/integrator/normal/NormalModeLangLf.h>
+#include <protomol/integrator/normal/NormalModeLangevin.h>
 #include <protomol/integrator/normal/NormalModeLangevinLeapfrogSwitching.h>
 #include <protomol/integrator/normal/NormalModeMinimizer.h>
-#include <protomol/integrator/normal/NormalModeDiagonalize.h>
 #include <protomol/integrator/normal/NormalModeMori.h>
-#include <protomol/integrator/normal/NormalModeRelax.h>
-#include <protomol/integrator/normal/NormalModeBrownian.h>
-#include <protomol/integrator/normal/NormalModeDamping.h> 
 #include <protomol/integrator/normal/NormalModeQuadratic.h>
+#include <protomol/integrator/normal/NormalModeRelax.h>
 #include <protomol/integrator/normal/NormalModeSubspaceSampling.h>
-#include <protomol/integrator/normal/NormalModeCompLang.h>
+#include <protomol/io/EigenvectorReader.h>
+#include <protomol/io/EigenvectorTextReader.h>
+#include <protomol/io/XYZReader.h>
+#include <protomol/module/NormalModeModule.h>
+#include <ostream>
+#include <vector>
+
+#include "protomol/base/Report.h"
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/factory/IntegratorFactory.h"
+#include "protomol/io/File.h"
+#include "protomol/type/EigenvectorInfo.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/NormalModeModule.h b/protomol/module/NormalModeModule.h
index b276fa0..314881a 100644
--- a/protomol/module/NormalModeModule.h
+++ b/protomol/module/NormalModeModule.h
@@ -3,9 +3,10 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
-
 #include <string>
 
+#include "protomol/config/InputValueMacros.h"
+
 namespace ProtoMol {
   class ProtoMolApp;
 
diff --git a/protomol/module/OutputModule.cpp b/protomol/module/OutputModule.cpp
index 26dd628..521f1e0 100644
--- a/protomol/module/OutputModule.cpp
+++ b/protomol/module/OutputModule.cpp
@@ -1,25 +1,20 @@
-#include <protomol/module/OutputModule.h>
-
 #include <protomol/ProtoMolApp.h>
-#include <protomol/config/Configuration.h>
 #include <protomol/factory/OutputFactory.h>
-
+#include <protomol/module/OutputModule.h>
 #include <protomol/output/OutputDCDTrajectory.h>
-#include <protomol/output/OutputDCDTrajectoryVel.h>
 #include <protomol/output/OutputDCDTrajectoryForces.h>
+#include <protomol/output/OutputDCDTrajectoryVel.h>
+#include <protomol/output/OutputDihedrals.h>
+#include <protomol/output/OutputEnergies.h>
+#include <protomol/output/OutputFAHFile.h>
 #include <protomol/output/OutputFinalPDBPos.h>
 #include <protomol/output/OutputFinalXYZPos.h>
 #include <protomol/output/OutputFinalXYZVel.h>
 #include <protomol/output/OutputScreen.h>
+#include <protomol/output/OutputXTCTrajectory.h>
 #include <protomol/output/OutputXYZTrajectoryForce.h>
 #include <protomol/output/OutputXYZTrajectoryPos.h>
 #include <protomol/output/OutputXYZTrajectoryVel.h>
-#include <protomol/output/OutputEnergies.h>
-#include <protomol/output/OutputFAHGUI.h>
-#include <protomol/output/OutputFAHFile.h>
-#include <protomol/output/OutputScreen.h>
-#include <protomol/output/OutputXTCTrajectory.h>
-#include <protomol/output/OutputDihedrals.h>
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/OutputModule.h b/protomol/module/OutputModule.h
index 67057f2..b1c9a22 100644
--- a/protomol/module/OutputModule.h
+++ b/protomol/module/OutputModule.h
@@ -3,7 +3,6 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
-
 #include <string>
 
 namespace ProtoMol {
diff --git a/protomol/module/TopologyModule.cpp b/protomol/module/TopologyModule.cpp
index bb4ee81..c49c99a 100644
--- a/protomol/module/TopologyModule.cpp
+++ b/protomol/module/TopologyModule.cpp
@@ -1,14 +1,16 @@
-#include <protomol/module/TopologyModule.h>
-
-#include <protomol/topology/Topology.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/factory/TopologyFactory.h>
+#include <protomol/module/TopologyModule.h>
 #include <protomol/topology/CubicCellManager.h>
-#include <protomol/topology/VacuumBoundaryConditions.h>
 #include <protomol/topology/PeriodicBoundaryConditions.h>
+#include <protomol/topology/Topology.h>
+#include <protomol/topology/VacuumBoundaryConditions.h>
+#include <vector>
 
-#include <protomol/ProtoMolApp.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/base/Exception.h>
+#include "protomol/config/Configuration.h"
+#include "protomol/config/Value.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/module/TopologyModule.h b/protomol/module/TopologyModule.h
index 5112d85..3d44acb 100644
--- a/protomol/module/TopologyModule.h
+++ b/protomol/module/TopologyModule.h
@@ -3,9 +3,10 @@
 
 #include <protomol/base/Module.h>
 #include <protomol/config/InputValue.h>
-
-#include <vector>
 #include <string>
+#include <vector>
+
+#include "protomol/config/InputValueMacros.h"
 
 namespace ProtoMol {
   class ProtoMolApp;
diff --git a/protomol/output/GUIServer.cpp b/protomol/output/GUIServer.cpp
index 0434834..9c5b9ce 100755
--- a/protomol/output/GUIServer.cpp
+++ b/protomol/output/GUIServer.cpp
@@ -1,24 +1,26 @@
 #include "GUIServer.h"
 
+#include <netinet/in.h>
 #include <protomol/base/Exception.h>
-
-#include <iostream>
-
-#include <errno.h>
-#include <stdlib.h>
-#include <string.h>
+#include <pthread.h>
 #include <stdio.h>
+#include <string.h>
+#include <sys/_endian.h>
+#include <sys/_select.h>
+#include <sys/_types/_fd_isset.h>
+#include <sys/_types/_fd_set.h>
+#include <sys/_types/_fd_zero.h>
+#include <sys/errno.h>
+#include <sys/fcntl.h>
 #include <time.h>
+#include <iostream>
+#include <string>
+
+#include "protomol/base/Report.h"
 
 #ifndef _WIN32
-#include <sched.h>
-#include <unistd.h>
-#include <netdb.h>
-#include <sys/types.h>
 #include <sys/socket.h>
-#include <arpa/inet.h>
-// #include <errno.h>
-#include <fcntl.h>
+#include <unistd.h>
 #endif
 
 //  Redefine some types and constants based on OS
diff --git a/protomol/output/GUIServer.h b/protomol/output/GUIServer.h
index 90bd095..0882c07 100755
--- a/protomol/output/GUIServer.h
+++ b/protomol/output/GUIServer.h
@@ -7,13 +7,22 @@
 #define COMM_NNCOORD 050363
 #define NUMCONN      20
 
-#include "stdtypes.h"
+#include <_types/_uint32_t.h>
+#include <_types/_uint64_t.h>
+#include <_types/_uint8_t.h>
+#include <sys/_pthread/_pthread_mutex_t.h>
+#include <sys/_pthread/_pthread_t.h>
+#include <sys/_types/_fd_def.h>
+#include <sys/_types/_int64_t.h>
 #include <sys/types.h>
 
+#include "stdtypes.h"
+
 #if defined _WIN32
 #define WIN32_LEAN_AND_MEAN
 #include <windows.h>
 #include <winsock.h>
+
 typedef int socklen_t;  //  Unix socket length
 
 #else
diff --git a/protomol/output/Output.cpp b/protomol/output/Output.cpp
index 06646b6..2fa10fa 100644
--- a/protomol/output/Output.cpp
+++ b/protomol/output/Output.cpp
@@ -1,9 +1,14 @@
-#include <protomol/output/Output.h>
+#include <protomol/ProtoMolApp.h>
 #include <protomol/config/Configuration.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
 #include <protomol/module/MainModule.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/output/Output.h>
+#include <algorithm>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/output/Output.h b/protomol/output/Output.h
index 3758cf3..a5cb22e 100644
--- a/protomol/output/Output.h
+++ b/protomol/output/Output.h
@@ -3,9 +3,14 @@
 #define PROTOMOL_OUTPUT_H
 
 #include <protomol/base/Makeable.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class ProtoMolApp;
+class Configuration;
+class Value;
+struct Parameter;
 
   /***
      Base class of all Output classes to dump data at a given
diff --git a/protomol/output/OutputCache.cpp b/protomol/output/OutputCache.cpp
index 251cde1..c54da4b 100644
--- a/protomol/output/OutputCache.cpp
+++ b/protomol/output/OutputCache.cpp
@@ -1,24 +1,22 @@
+#include <math.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/MathUtilities.h>
+#include <protomol/base/PMConstants.h>
+#include <protomol/base/Report.h>
+#include <protomol/base/SystemUtilities.h>
+#include <protomol/base/Zap.h>
 #include <protomol/output/OutputCache.h>
-#include <protomol/output/Output.h>
-#include <protomol/config/Configuration.h>
 #include <protomol/topology/GenericTopology.h>
+#include <protomol/topology/TopologyUtilities.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/integrator/Integrator.h>
-
-#include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
-#include <protomol/base/SystemUtilities.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/base/PMConstants.h>
-
-#include <protomol/ProtoMolApp.h>
-
-#include <protomol/base/Zap.h>
-#include <protomol/base/Exception.h>
-
 #include <limits>
 
+#include "protomol/topology/Atom.h"
+#include "protomol/type/PDB.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+
 using namespace std;
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/output/OutputCache.h b/protomol/output/OutputCache.h
index b1e6cec..05470a0 100644
--- a/protomol/output/OutputCache.h
+++ b/protomol/output/OutputCache.h
@@ -2,23 +2,24 @@
 #ifndef PROTOMOL_OUTPUT_CACHE_H
 #define PROTOMOL_OUTPUT_CACHE_H
 
-#include <protomol/type/Real.h>
-#include <protomol/type/PDB.h>
 #include <protomol/type/PAR.h>
+#include <protomol/type/PDB.h>
 #include <protomol/type/PSF.h>
+#include <protomol/type/Real.h>
 #include <protomol/type/Vector3D.h>
+#include <vector>
 
 namespace ProtoMol {
-  class ProtoMolApp;
-  class Output;
   class Configuration;
   class GenericTopology;
+  class Integrator;
+  class Output;
+  class OutputFactory;
+  class ProtoMolApp;
   class ScalarStructure;
   class Vector3DBlock;
-  class OutputFactory;
-  class Integrator;
-  struct PDB;
   struct Atom;
+  struct PDB;
 
   /**
      OutputCache caches all kind of values, which may be needed
diff --git a/protomol/output/OutputCheckpoint.cpp b/protomol/output/OutputCheckpoint.cpp
index 925bea8..3be5a5f 100644
--- a/protomol/output/OutputCheckpoint.cpp
+++ b/protomol/output/OutputCheckpoint.cpp
@@ -1,24 +1,32 @@
-#include <protomol/output/OutputCheckpoint.h>
-
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/module/MainModule.h>
 #include <protomol/ProtoMolApp.h>
-
-#include <protomol/base/MathUtilities.h>
 #include <protomol/base/StringUtilities.h>
 #include <protomol/base/SystemUtilities.h>
-
-#include <protomol/io/XYZWriter.h>
 #include <protomol/io/CheckpointConfigWriter.h>
-
-#include <sstream>
+#include <protomol/io/XYZWriter.h>
+#include <protomol/module/MainModule.h>
+#include <protomol/output/OutputCheckpoint.h>
 #include <iostream>
 
+#include "protomol/base/Exception.h"
+#include "protomol/base/Random.h"
+#include "protomol/config/Configuration.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
+#include "protomol/output/OutputCache.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/SimpleTypes.h"
+
+namespace ProtoMol {
+class Vector3DBlock;
+}  // namespace ProtoMol
+
 #ifdef HAVE_LIBFAH
 #include <cbang/os/File.h>
+
 typedef cb::File fileStream;
 #else
-#include <fstream>
 typedef std::fstream fileStream;
 #endif
 
diff --git a/protomol/output/OutputCheckpoint.h b/protomol/output/OutputCheckpoint.h
index a238616..f3b7b1e 100644
--- a/protomol/output/OutputCheckpoint.h
+++ b/protomol/output/OutputCheckpoint.h
@@ -3,11 +3,15 @@
 #define PROTOMOL_OUTPUT_CHECKPIINT_H
 
 #include <protomol/base/StringUtilities.h>
-#include <protomol/output/Output.h>
 #include <protomol/base/Timer.h>
+#include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class Configuration;
+class Value;
+struct Parameter;
 
   class OutputCheckpoint : public Output {
   public:
diff --git a/protomol/output/OutputCollection.cpp b/protomol/output/OutputCollection.cpp
index 65ea0dc..5119387 100644
--- a/protomol/output/OutputCollection.cpp
+++ b/protomol/output/OutputCollection.cpp
@@ -1,15 +1,13 @@
-#include <protomol/output/OutputCollection.h>
-#include <protomol/output/Output.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/integrator/Integrator.h>
-#include <protomol/base/Report.h>
-#include <protomol/base/MathUtilities.h>
-#include <protomol/topology/TopologyUtilities.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/Exception.h>
+#include <protomol/base/MathUtilities.h>
+#include <protomol/output/Output.h>
+#include <protomol/output/OutputCollection.h>
+#include <algorithm>
+#include <string>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/output/OutputCache.h"
 
 using namespace ProtoMol;
 
diff --git a/protomol/output/OutputDCDTrajectory.cpp b/protomol/output/OutputDCDTrajectory.cpp
index 72f3c25..3ae99ef 100644
--- a/protomol/output/OutputDCDTrajectory.cpp
+++ b/protomol/output/OutputDCDTrajectory.cpp
@@ -1,12 +1,26 @@
-#include <protomol/output/OutputDCDTrajectory.h>
+#include <ctype.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/Exception.h>
+#include <protomol/base/StringUtilities.h>
 #include <protomol/config/Configuration.h>
-#include <protomol/output/OutputCache.h>
+#include <protomol/io/DCDTrajectoryWriter.h>
 #include <protomol/module/MainModule.h>
-#include <protomol/base/StringUtilities.h>
+#include <protomol/output/OutputCache.h>
+#include <protomol/output/OutputDCDTrajectory.h>
 #include <protomol/topology/GenericTopology.h>
-#include <protomol/io/DCDTrajectoryWriter.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/Exception.h>
+#include <stddef.h>
+#include <algorithm>
+#include <iostream>
+
+#include "protomol/base/Report.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputDCDTrajectory.h b/protomol/output/OutputDCDTrajectory.h
index b20d451..f23c894 100644
--- a/protomol/output/OutputDCDTrajectory.h
+++ b/protomol/output/OutputDCDTrajectory.h
@@ -4,9 +4,14 @@
 
 #include <protomol/output/Output.h>
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class DCDTrajectoryWriter;
+class Configuration;
+class Value;
+struct Parameter;
 
   class OutputDCDTrajectory : public Output {
   public:
diff --git a/protomol/output/OutputDCDTrajectoryForces.cpp b/protomol/output/OutputDCDTrajectoryForces.cpp
index 583c2d6..7e39fcd 100644
--- a/protomol/output/OutputDCDTrajectoryForces.cpp
+++ b/protomol/output/OutputDCDTrajectoryForces.cpp
@@ -1,12 +1,17 @@
-#include <protomol/output/OutputDCDTrajectoryForces.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/Exception.h>
 #include <protomol/config/Configuration.h>
-#include <protomol/output/OutputCache.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/topology/GenericTopology.h>
 #include <protomol/io/DCDTrajectoryWriter.h>
-#include <protomol/base/Exception.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/module/MainModule.h>
+#include <protomol/output/OutputDCDTrajectoryForces.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/integrator/Integrator.h"
+#include "protomol/output/Output.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputDCDTrajectoryForces.h b/protomol/output/OutputDCDTrajectoryForces.h
index f359799..96323ea 100644
--- a/protomol/output/OutputDCDTrajectoryForces.h
+++ b/protomol/output/OutputDCDTrajectoryForces.h
@@ -3,9 +3,14 @@
 #define PROTOMOL_OUTPUT_DCD_TRAJECTORY_FORCE_H
 
 #include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class DCDTrajectoryWriter;
+class Configuration;
+class Value;
+struct Parameter;
 
   class OutputDCDTrajectoryForces : public Output {
   public:
diff --git a/protomol/output/OutputDCDTrajectoryVel.cpp b/protomol/output/OutputDCDTrajectoryVel.cpp
index 778128c..cf648f1 100644
--- a/protomol/output/OutputDCDTrajectoryVel.cpp
+++ b/protomol/output/OutputDCDTrajectoryVel.cpp
@@ -1,12 +1,16 @@
-#include <protomol/output/OutputDCDTrajectoryVel.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/Exception.h>
 #include <protomol/config/Configuration.h>
-#include <protomol/output/OutputCache.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/topology/GenericTopology.h>
 #include <protomol/io/DCDTrajectoryWriter.h>
-#include <protomol/base/Exception.h>
-#include <protomol/ProtoMolApp.h>
+#include <protomol/module/MainModule.h>
+#include <protomol/output/OutputDCDTrajectoryVel.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputDCDTrajectoryVel.h b/protomol/output/OutputDCDTrajectoryVel.h
index 6c7f611..f3bc442 100644
--- a/protomol/output/OutputDCDTrajectoryVel.h
+++ b/protomol/output/OutputDCDTrajectoryVel.h
@@ -3,9 +3,14 @@
 #define PROTOMOL_OUTPUT_DCD_TRAJECTORY_VEL_H
 
 #include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class DCDTrajectoryWriter;
+class Configuration;
+class Value;
+struct Parameter;
 
   class OutputDCDTrajectoryVel : public Output {
   public:
diff --git a/protomol/output/OutputDihedrals.cpp b/protomol/output/OutputDihedrals.cpp
index 6807165..e06d961 100644
--- a/protomol/output/OutputDihedrals.cpp
+++ b/protomol/output/OutputDihedrals.cpp
@@ -1,16 +1,18 @@
 #include "OutputDihedrals.h"
 
-#include <protomol/config/Configuration.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/output/OutputCache.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/base/SystemUtilities.h>
 #include <protomol/ProtoMolApp.h>
-
+#include <protomol/output/OutputCache.h>
+#include <protomol/topology/GenericTopology.h>
 #include <iomanip>
-#include <algorithm>
+#include <set>
+
+#include "protomol/base/Exception.h"
+#include "protomol/base/Report.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
+#include "protomol/type/Real.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputDihedrals.h b/protomol/output/OutputDihedrals.h
index 85c149a..a98a484 100644
--- a/protomol/output/OutputDihedrals.h
+++ b/protomol/output/OutputDihedrals.h
@@ -2,13 +2,17 @@
 #ifndef OUTPUTDIHEDRALS_H
 #define OUTPUTDIHEDRALS_H
 
+#include <protomol/output/Output.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <algorithm>
+#include <set>
 #include <string>
 #include <vector>
-#include <set>
-#include <algorithm>
 
-#include <protomol/output/Output.h>
-#include <protomol/type/Vector3DBlock.h>
+namespace ProtoMol {
+class Value;
+struct Parameter;
+}  // namespace ProtoMol
 
 #ifdef HAVE_LIBFAH
 #include <cbang/os/File.h>
diff --git a/protomol/output/OutputEnergies.cpp b/protomol/output/OutputEnergies.cpp
index 3735600..d6eb77c 100644
--- a/protomol/output/OutputEnergies.cpp
+++ b/protomol/output/OutputEnergies.cpp
@@ -1,16 +1,17 @@
 #include "OutputEnergies.h"
 
-#include <protomol/config/Configuration.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/output/OutputCache.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/base/SystemUtilities.h>
 #include <protomol/ProtoMolApp.h>
-
+#include <protomol/base/SystemUtilities.h>
+#include <protomol/output/OutputCache.h>
+#include <protomol/type/ScalarStructure.h>
 #include <iomanip>
 
+#include "protomol/base/Exception.h"
+#include "protomol/base/Report.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+
 using namespace std;
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/output/OutputEnergies.h b/protomol/output/OutputEnergies.h
index cca7030..45c2f4e 100644
--- a/protomol/output/OutputEnergies.h
+++ b/protomol/output/OutputEnergies.h
@@ -2,7 +2,16 @@
 #ifndef PROTOMOL_OUTPUT_ENERGIES_H
 #define PROTOMOL_OUTPUT_ENERGIES_H
 
+#include <string>
+#include <vector>
+
 #include "Output.h"
+#include "protomol/output/Output.h"
+
+namespace ProtoMol {
+class Value;
+struct Parameter;
+}  // namespace ProtoMol
 
 #ifdef HAVE_LIBFAH
 #include <cbang/os/File.h>
diff --git a/protomol/output/OutputFAHFile.cpp b/protomol/output/OutputFAHFile.cpp
index 62a26ca..2e86f2b 100644
--- a/protomol/output/OutputFAHFile.cpp
+++ b/protomol/output/OutputFAHFile.cpp
@@ -1,8 +1,18 @@
-#include <protomol/output/OutputFAHFile.h>
 #include <protomol/ProtoMolApp.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/module/OutputModule.h>
+#include <protomol/output/OutputFAHFile.h>
 #include <protomol/type/String.h>
+#include <iostream>
+
+#include "protomol/config/Configuration.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputFAHFile.h b/protomol/output/OutputFAHFile.h
index 7fa5cc8..8f29c35 100644
--- a/protomol/output/OutputFAHFile.h
+++ b/protomol/output/OutputFAHFile.h
@@ -2,12 +2,15 @@
 #ifndef PROTOMOL_OUTPUT_FAH_FILE_H
 #define PROTOMOL_OUTPUT_FAH_FILE_H
 
-#include <protomol/output/Output.h>
 #include <protomol/io/File.h>
+#include <protomol/output/Output.h>
 #include <string>
+#include <vector>
 
 namespace ProtoMol {
   class Configuration;
+class Value;
+struct Parameter;
 
   class OutputFAHFile : public Output, public File {
   public:
diff --git a/protomol/output/OutputFinalPDBPos.cpp b/protomol/output/OutputFinalPDBPos.cpp
index 000aaac..3a0e9a0 100644
--- a/protomol/output/OutputFinalPDBPos.cpp
+++ b/protomol/output/OutputFinalPDBPos.cpp
@@ -1,12 +1,21 @@
-#include <protomol/output/OutputFinalPDBPos.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/output/OutputCache.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/io/PDBWriter.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/Exception.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/config/Configuration.h>
+#include <protomol/io/PDBWriter.h>
+#include <protomol/module/MainModule.h>
+#include <protomol/output/OutputCache.h>
+#include <protomol/output/OutputFinalPDBPos.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+
+namespace ProtoMol {
+class Vector3DBlock;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputFinalPDBPos.h b/protomol/output/OutputFinalPDBPos.h
index ea226ae..21b6546 100644
--- a/protomol/output/OutputFinalPDBPos.h
+++ b/protomol/output/OutputFinalPDBPos.h
@@ -2,10 +2,16 @@
 #ifndef PROTOMOL_OUTPUT_FINAL_PDB_POS_H
 #define PROTOMOL_OUTPUT_FINAL_PDB_POS_H
 
+#include <string>
+#include <vector>
+
 #include "Output.h"
+#include "protomol/output/Output.h"
 
 namespace ProtoMol {
   class Configuration;
+class Value;
+struct Parameter;
 
   class OutputFinalPDBPos : public Output {
     static const std::string keyword;
diff --git a/protomol/output/OutputFinalXYZPos.cpp b/protomol/output/OutputFinalXYZPos.cpp
index 1d51e0f..bc0c4cc 100644
--- a/protomol/output/OutputFinalXYZPos.cpp
+++ b/protomol/output/OutputFinalXYZPos.cpp
@@ -1,12 +1,23 @@
-#include <protomol/output/OutputFinalXYZPos.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/Exception.h>
+#include <protomol/base/StringUtilities.h>
 #include <protomol/config/Configuration.h>
-#include <protomol/output/OutputCache.h>
+#include <protomol/io/XYZWriter.h>
 #include <protomol/module/MainModule.h>
-#include <protomol/base/StringUtilities.h>
+#include <protomol/output/OutputCache.h>
+#include <protomol/output/OutputFinalXYZPos.h>
 #include <protomol/topology/GenericTopology.h>
-#include <protomol/io/XYZWriter.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/base/Exception.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
+#include "protomol/type/SimpleTypes.h"
+
+namespace ProtoMol {
+class Vector3DBlock;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputFinalXYZPos.h b/protomol/output/OutputFinalXYZPos.h
index 76c360d..5b8da1d 100644
--- a/protomol/output/OutputFinalXYZPos.h
+++ b/protomol/output/OutputFinalXYZPos.h
@@ -3,9 +3,13 @@
 #define PROTOMOL_OUTPUT_FINAL_XYZ_POS_H
 
 #include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class Configuration;
+class Value;
+struct Parameter;
 
   class OutputFinalXYZPos : public Output {
   public:
diff --git a/protomol/output/OutputFinalXYZVel.cpp b/protomol/output/OutputFinalXYZVel.cpp
index 320fc34..cdb49d1 100644
--- a/protomol/output/OutputFinalXYZVel.cpp
+++ b/protomol/output/OutputFinalXYZVel.cpp
@@ -1,11 +1,16 @@
-#include <protomol/output/OutputFinalXYZVel.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/output/OutputCache.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/io/XYZWriter.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/Exception.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/io/XYZWriter.h>
+#include <protomol/output/OutputCache.h>
+#include <protomol/output/OutputFinalXYZVel.h>
+#include <protomol/topology/GenericTopology.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputFinalXYZVel.h b/protomol/output/OutputFinalXYZVel.h
index f8e0edc..165bc5b 100644
--- a/protomol/output/OutputFinalXYZVel.h
+++ b/protomol/output/OutputFinalXYZVel.h
@@ -3,9 +3,13 @@
 #define PROTOMOL_OUTPUT_FINAL_XYZ_VEL_H
 
 #include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class Configuration;
+class Value;
+struct Parameter;
 
   class OutputFinalXYZVel : public Output {
   public:
diff --git a/protomol/output/OutputScreen.cpp b/protomol/output/OutputScreen.cpp
index 1dc169a..11ef4f5 100644
--- a/protomol/output/OutputScreen.cpp
+++ b/protomol/output/OutputScreen.cpp
@@ -1,13 +1,16 @@
-#include <protomol/output/OutputScreen.h>
-#include <protomol/output/OutputCache.h>
-#include <protomol/integrator/Integrator.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/module/MainModule.h>
 #include <protomol/ProtoMolApp.h>
-#include <protomol/module/OutputModule.h>
+#include <protomol/config/Configuration.h>
+#include <protomol/integrator/Integrator.h>
+#include <protomol/output/OutputCache.h>
+#include <protomol/output/OutputScreen.h>
+#include <algorithm>
+#include <iostream>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/base/Report.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputScreen.h b/protomol/output/OutputScreen.h
index f35b643..431a340 100644
--- a/protomol/output/OutputScreen.h
+++ b/protomol/output/OutputScreen.h
@@ -3,9 +3,15 @@
 #define PROTOMOL_OUTPUT_SCREEN_H
 
 #include <protomol/output/Output.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   class Configuration;
+class Value;
+struct Parameter;
 
   class OutputScreen : public Output {
   public:
diff --git a/protomol/output/OutputXTCTrajectory.cpp b/protomol/output/OutputXTCTrajectory.cpp
index c4d5d53..1eafd05 100644
--- a/protomol/output/OutputXTCTrajectory.cpp
+++ b/protomol/output/OutputXTCTrajectory.cpp
@@ -1,11 +1,25 @@
 #include "OutputXTCTrajectory.h"
 
-#include "OutputCache.h"
-
-#include <protomol/module/MainModule.h>
-#include <protomol/base/StringUtilities.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/Exception.h>
+#include <protomol/base/StringUtilities.h>
+#include <protomol/module/MainModule.h>
+#include <ostream>
+
+#include "gromacs/gmxfio.h"
+#include "gromacs/types/simple.h"
+#include "protomol/base/PMConstants.h"
+#include "protomol/base/Report.h"
+#include "protomol/base/SmartPointer.h"
+#include "protomol/config/Configuration.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/OutputCache.h"
+#include "protomol/topology/GenericTopology.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
+#include "protomol/type/Vector3DBlock.h"
 
 #ifdef HAVE_GROMACS
 extern "C" {
diff --git a/protomol/output/OutputXTCTrajectory.h b/protomol/output/OutputXTCTrajectory.h
index 80e02ac..2f587e7 100644
--- a/protomol/output/OutputXTCTrajectory.h
+++ b/protomol/output/OutputXTCTrajectory.h
@@ -1,9 +1,17 @@
 #ifndef PROTOMOL_OUTPUT_XTC_TRAJECTORY_H
 #define PROTOMOL_OUTPUT_XTC_TRAJECTORY_H
 
+#include <string>
+#include <vector>
+
 #include "Output.h"
+#include "protomol/output/Output.h"
 
 namespace ProtoMol {
+class Configuration;
+class Value;
+struct Parameter;
+
   class OutputXTCTrajectory : public Output {
     void *fxtc;
     bool minimalImage;
diff --git a/protomol/output/OutputXYZTrajectoryForce.cpp b/protomol/output/OutputXYZTrajectoryForce.cpp
index 8bda5c9..ccaf248 100644
--- a/protomol/output/OutputXYZTrajectoryForce.cpp
+++ b/protomol/output/OutputXYZTrajectoryForce.cpp
@@ -1,12 +1,16 @@
-#include <protomol/output/OutputXYZTrajectoryForce.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/integrator/Integrator.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/io/XYZTrajectoryWriter.h>
 #include <protomol/ProtoMolApp.h>
 #include <protomol/base/Exception.h>
+#include <protomol/integrator/Integrator.h>
+#include <protomol/io/XYZTrajectoryWriter.h>
+#include <protomol/output/OutputXYZTrajectoryForce.h>
+#include <protomol/topology/GenericTopology.h>
+#include <stddef.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputXYZTrajectoryForce.h b/protomol/output/OutputXYZTrajectoryForce.h
index 4552705..5aeb613 100644
--- a/protomol/output/OutputXYZTrajectoryForce.h
+++ b/protomol/output/OutputXYZTrajectoryForce.h
@@ -3,9 +3,13 @@
 #define PROTOMOL_OUTPUT_XYZ_TRAJECTORY_FORCE_H
 
 #include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class XYZTrajectoryWriter;
+class Value;
+struct Parameter;
 
   class OutputXYZTrajectoryForce : public Output {
   public:
diff --git a/protomol/output/OutputXYZTrajectoryPos.cpp b/protomol/output/OutputXYZTrajectoryPos.cpp
index 8f02098..ae9dba2 100644
--- a/protomol/output/OutputXYZTrajectoryPos.cpp
+++ b/protomol/output/OutputXYZTrajectoryPos.cpp
@@ -1,12 +1,23 @@
-#include <protomol/output/OutputXYZTrajectoryPos.h>
+#include <protomol/ProtoMolApp.h>
+#include <protomol/base/Exception.h>
+#include <protomol/config/Configuration.h>
+#include <protomol/io/XYZTrajectoryWriter.h>
 #include <protomol/module/MainModule.h>
 #include <protomol/output/OutputCache.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/base/StringUtilities.h>
+#include <protomol/output/OutputXYZTrajectoryPos.h>
 #include <protomol/topology/GenericTopology.h>
-#include <protomol/base/Exception.h>
-#include <protomol/ProtoMolApp.h>
-#include <protomol/io/XYZTrajectoryWriter.h>
+#include <stddef.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
+#include "protomol/type/SimpleTypes.h"
+
+namespace ProtoMol {
+class Vector3DBlock;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputXYZTrajectoryPos.h b/protomol/output/OutputXYZTrajectoryPos.h
index 0f996c4..b2cdfc9 100644
--- a/protomol/output/OutputXYZTrajectoryPos.h
+++ b/protomol/output/OutputXYZTrajectoryPos.h
@@ -3,9 +3,14 @@
 #define PROTOMOL_OUTPUT_XYZ_TRAJECTORY_POS_H
 
 #include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class XYZTrajectoryWriter;
+class Configuration;
+class Value;
+struct Parameter;
 
   class OutputXYZTrajectoryPos : public Output {
   public:
diff --git a/protomol/output/OutputXYZTrajectoryVel.cpp b/protomol/output/OutputXYZTrajectoryVel.cpp
index 857ad03..a4d30e0 100644
--- a/protomol/output/OutputXYZTrajectoryVel.cpp
+++ b/protomol/output/OutputXYZTrajectoryVel.cpp
@@ -1,11 +1,15 @@
-#include <protomol/output/OutputXYZTrajectoryVel.h>
-#include <protomol/config/Configuration.h>
-#include <protomol/base/StringUtilities.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/module/MainModule.h>
-#include <protomol/base/Exception.h>
 #include <protomol/ProtoMolApp.h>
+#include <protomol/base/Exception.h>
 #include <protomol/io/XYZTrajectoryWriter.h>
+#include <protomol/output/OutputXYZTrajectoryVel.h>
+#include <protomol/topology/GenericTopology.h>
+#include <stddef.h>
+#include <ostream>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/output/Output.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/output/OutputXYZTrajectoryVel.h b/protomol/output/OutputXYZTrajectoryVel.h
index ca88f0b..b91a6ac 100644
--- a/protomol/output/OutputXYZTrajectoryVel.h
+++ b/protomol/output/OutputXYZTrajectoryVel.h
@@ -3,9 +3,13 @@
 #define PROTOMOL_OUTPUT_XYZ_TRAJECTORY_VEL_H
 
 #include <protomol/output/Output.h>
+#include <string>
+#include <vector>
 
 namespace ProtoMol {
   class XYZTrajectoryWriter;
+class Value;
+struct Parameter;
 
   class OutputXYZTrajectoryVel : public Output {
   public:
diff --git a/protomol/parallel/FFTComplex.cpp b/protomol/parallel/FFTComplex.cpp
index e592278..8a418a6 100644
--- a/protomol/parallel/FFTComplex.cpp
+++ b/protomol/parallel/FFTComplex.cpp
@@ -1,6 +1,7 @@
 //
 // FFT includes and forward declarations
 //
+#include <stdlib.h>
 #ifdef HAVE_FFT_SGI
 #  include <protomol/parallel/FFTComplex.h> !!!
                    // We use the definition of zomplex in <fft.h>
@@ -20,6 +21,7 @@
 #           include <fftw_mpi.h>
 #         else /* ZFFT */
 #           include <protomol/parallel/FFTComplex.h>     // Defines zomplex
+
 extern "C" {
   extern zomplex *zfftm1di(int m, zomplex *save);
   extern int zfftm1d(int sign, int m, int n, zomplex *array, 
@@ -39,13 +41,6 @@ extern "C" {
 #  endif
 #endif
 
-//
-// Other includes
-//
-#include <protomol/parallel/FFTComplex.h>
-#include <protomol/base/Timer.h>
-#include <protomol/base/MathUtilities.h>
-#include <protomol/base/Report.h>
 using namespace ProtoMol::Report;
 
 namespace ProtoMol {
diff --git a/protomol/parallel/Parallel.cpp b/protomol/parallel/Parallel.cpp
index f4a2993..ac2d478 100644
--- a/protomol/parallel/Parallel.cpp
+++ b/protomol/parallel/Parallel.cpp
@@ -3,19 +3,22 @@
 #include <mpi.h>
 #endif
 
-#include <iostream>
-#include <vector>
-#include <algorithm>
-
-#include <protomol/parallel/Parallel.h>
-#include <protomol/type/ScalarStructure.h>
-#include <protomol/type/Vector3DBlock.h>
 #include <protomol/base/MathUtilities.h>
+#include <protomol/base/Report.h>
 #include <protomol/base/SystemUtilities.h>
 #include <protomol/base/TimerStatistic.h>
-#include <protomol/base/Report.h>
+#include <protomol/parallel/Parallel.h>
+#include <algorithm>
+#include <string>
+#include <vector>
 
-#include <unistd.h>
+#include "protomol/parallel/ParallelType.h"
+#include "protomol/type/Real.h"
+
+namespace ProtoMol {
+class ScalarStructure;
+class Vector3DBlock;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol::Report;
@@ -86,10 +89,6 @@ static void mpiEndSerial(bool exludeMaster) {
 }
 #endif
 
-//____ MPITypeTraits
-template<typename T>
-struct MPITypeTraits;
-
 #ifdef HAVE_MPI
 template<>
 struct MPITypeTraits<Real> {
diff --git a/protomol/parallel/ParallelType.h b/protomol/parallel/ParallelType.h
index 1ea8b0a..3e591ba 100644
--- a/protomol/parallel/ParallelType.h
+++ b/protomol/parallel/ParallelType.h
@@ -3,6 +3,7 @@
 #define PARALLELTYPE_H
 
 #include <protomol/type/AbstractEnumType.h>
+#include <string>
 
 namespace ProtoMol {
   //____ ParallelEnum
diff --git a/protomol/switch/C1SwitchingFunction.cpp b/protomol/switch/C1SwitchingFunction.cpp
index 368c16c..dfcfa2f 100644
--- a/protomol/switch/C1SwitchingFunction.cpp
+++ b/protomol/switch/C1SwitchingFunction.cpp
@@ -1,5 +1,10 @@
 #include <protomol/switch/C1SwitchingFunction.h>
-#include <protomol/base/StringUtilities.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/switch/C1SwitchingFunction.h b/protomol/switch/C1SwitchingFunction.h
index f113c85..82c2974 100644
--- a/protomol/switch/C1SwitchingFunction.h
+++ b/protomol/switch/C1SwitchingFunction.h
@@ -2,10 +2,14 @@
 #ifndef C1SWITCHINGFUNCTION_H
 #define C1SWITCHINGFUNCTION_H
 
-#include <vector>
-
+#include <math.h>
 #include <protomol/config/Parameter.h>
 #include <protomol/type/Matrix3By3.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //____ C1SwitchingFunction
@@ -13,6 +17,9 @@ namespace ProtoMol {
   /**
    * The switching function provide C1 continues
    */
+class Value;
+struct Parameter;
+
   class C1SwitchingFunction {
   public:
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/switch/C2SwitchingFunction.cpp b/protomol/switch/C2SwitchingFunction.cpp
index bd36260..7dcd450 100644
--- a/protomol/switch/C2SwitchingFunction.cpp
+++ b/protomol/switch/C2SwitchingFunction.cpp
@@ -1,6 +1,12 @@
-#include <protomol/switch/C2SwitchingFunction.h>
-#include <protomol/base/MathUtilities.h>
 #include <protomol/base/Exception.h>
+#include <protomol/base/MathUtilities.h>
+#include <protomol/switch/C2SwitchingFunction.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/switch/C2SwitchingFunction.h b/protomol/switch/C2SwitchingFunction.h
index eb6d904..aa1b28a 100644
--- a/protomol/switch/C2SwitchingFunction.h
+++ b/protomol/switch/C2SwitchingFunction.h
@@ -2,11 +2,13 @@
 #ifndef C2SWITCHINGFUNCTION_H
 #define C2SWITCHINGFUNCTION_H
 
-#include <vector>
-#include <string>
-
 #include <protomol/config/Parameter.h>
 #include <protomol/type/Matrix3By3.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //____ C2SwitchingFunction
@@ -14,6 +16,9 @@ namespace ProtoMol {
   /**
    * The switching function provide C2 continues
    */
+class Value;
+struct Parameter;
+
   class C2SwitchingFunction {
   public:
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/switch/CmpCnCnSwitchingFunction.cpp b/protomol/switch/CmpCnCnSwitchingFunction.cpp
index 25dc85b..ebfec98 100644
--- a/protomol/switch/CmpCnCnSwitchingFunction.cpp
+++ b/protomol/switch/CmpCnCnSwitchingFunction.cpp
@@ -1,6 +1,11 @@
-#include <protomol/switch/CmpCnCnSwitchingFunction.h>
-#include <protomol/base/MathUtilities.h>
 #include <protomol/base/Exception.h>
+#include <protomol/switch/CmpCnCnSwitchingFunction.h>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/switch/CmpCnCnSwitchingFunction.h b/protomol/switch/CmpCnCnSwitchingFunction.h
index b43c208..182da1e 100644
--- a/protomol/switch/CmpCnCnSwitchingFunction.h
+++ b/protomol/switch/CmpCnCnSwitchingFunction.h
@@ -2,11 +2,14 @@
 #ifndef CMPCNCNSWITCHINGFUNCTION_H
 #define CMPCNCNSWITCHINGFUNCTION_H
 
-#include <vector>
-#include <string>
-
 #include <protomol/config/Parameter.h>
 #include <protomol/type/Matrix3By3.h>
+#include <cmath>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //____ CmpCnCnSwitchingFunction
@@ -14,6 +17,9 @@ namespace ProtoMol {
   /**
    * The switching function provide C2,3,4 or 6 with compliment continuous
    */
+class Value;
+struct Parameter;
+
   class CmpCnCnSwitchingFunction {
 
   public:
diff --git a/protomol/switch/CnSwitchingFunction.cpp b/protomol/switch/CnSwitchingFunction.cpp
index 344cbb4..5a2aeea 100644
--- a/protomol/switch/CnSwitchingFunction.cpp
+++ b/protomol/switch/CnSwitchingFunction.cpp
@@ -1,6 +1,12 @@
-#include <protomol/switch/CnSwitchingFunction.h>
-#include <protomol/base/MathUtilities.h>
 #include <protomol/base/Exception.h>
+#include <protomol/switch/CnSwitchingFunction.h>
+#include <cmath>
+
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/switch/CnSwitchingFunction.h b/protomol/switch/CnSwitchingFunction.h
index d99dd91..a3dbed2 100644
--- a/protomol/switch/CnSwitchingFunction.h
+++ b/protomol/switch/CnSwitchingFunction.h
@@ -2,11 +2,13 @@
 #ifndef CnSWITCHINGFUNCTION_H
 #define CnSWITCHINGFUNCTION_H
 
-#include <vector>
-#include <string>
-
 #include <protomol/config/Parameter.h>
 #include <protomol/type/Matrix3By3.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //____ CnSwitchingFunction
@@ -14,6 +16,9 @@ namespace ProtoMol {
   /**
    * The switching function provide C2, 3, 4 0r 6 continuous
    */
+class Value;
+struct Parameter;
+
   class CnSwitchingFunction {
 
   public:
diff --git a/protomol/topology/AngleInfo.cpp b/protomol/topology/AngleInfo.cpp
index bc5a5e2..9ad4640 100644
--- a/protomol/topology/AngleInfo.cpp
+++ b/protomol/topology/AngleInfo.cpp
@@ -1,5 +1,7 @@
 #include <protomol/topology/AngleInfo.h>
 
+#include "protomol/type/Real.h"
+
 using namespace ProtoMol;
 AngleInfo::AngleInfo() {
   my_angle = 0.0;
diff --git a/protomol/topology/ArrayCellListStructure.cpp b/protomol/topology/ArrayCellListStructure.cpp
index 6f9b807..0dfbeee 100644
--- a/protomol/topology/ArrayCellListStructure.cpp
+++ b/protomol/topology/ArrayCellListStructure.cpp
@@ -1,7 +1,14 @@
-#include <protomol/topology/ArrayCellListStructure.h>
-#include <protomol/base/Exception.h>
 #include <protomol/base/Report.h>
-#include <exception>
+#include <protomol/topology/ArrayCellListStructure.h>
+#include <stddef.h>
+#include <algorithm>
+#include <cmath>
+#include <new>
+
+#include "protomol/base/MathUtilities.h"
+#include "protomol/base/PMConstants.h"
+#include "protomol/topology/CubicCellLocation.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/topology/ArrayCellListStructure.h b/protomol/topology/ArrayCellListStructure.h
index c8f9346..2acce99 100644
--- a/protomol/topology/ArrayCellListStructure.h
+++ b/protomol/topology/ArrayCellListStructure.h
@@ -3,8 +3,11 @@
 
 #include <protomol/base/StringUtilities.h>
 #include <protomol/topology/CubicCellLocation.h>
-#include <protomol/type/Vector3D.h>
 #include <protomol/type/Array.h>
+#include <protomol/type/Vector3D.h>
+#include <utility>
+
+#include "protomol/type/ArrayFastest.h"
 
 namespace ProtoMol {
 	/**
diff --git a/protomol/topology/BuildTopology.cpp b/protomol/topology/BuildTopology.cpp
index 0d137d2..d98eacb 100644
--- a/protomol/topology/BuildTopology.cpp
+++ b/protomol/topology/BuildTopology.cpp
@@ -1,16 +1,41 @@
-#include <protomol/topology/BuildTopology.h>
-
+#include <ctype.h>
+#include <math.h>
 #include <protomol/base/Exception.h>
+#include <protomol/topology/BuildTopology.h>
+#include <protomol/topology/CoulombSCPISMParameterTable.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/topology/LennardJonesParameterTable.h>
+#include <protomol/topology/TopologyUtilities.h>
 #include <protomol/type/PAR.h>
 #include <protomol/type/PSF.h>
 #include <protomol/type/String.h>
-#include <protomol/topology/TopologyUtilities.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/topology/CoulombSCPISMParameterTable.h>
-#include <protomol/topology/LennardJonesParameterTable.h>
-
+#include <stdlib.h>
+#include <algorithm>
+#include <map>
+#include <ostream>
+#include <set>
+#include <string>
+#include <utility>
 #include <vector>
 
+#include "protomol/base/MathUtilities.h"
+#include "protomol/base/PMConstants.h"
+#include "protomol/base/Report.h"
+#include "protomol/base/StringUtilities.h"
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/CoulombSCPISMParameters.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/ExclusionType.h"
+#include "protomol/topology/LennardJonesParameters.h"
+#include "protomol/topology/Molecule.h"
+#include "protomol/topology/RBTorsion.h"
+#include "protomol/topology/Torsion.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/SimpleTypes.h"
+
 using namespace std;
 using namespace ProtoMol;
 using namespace ProtoMol::Report;
diff --git a/protomol/topology/BuildTopology.h b/protomol/topology/BuildTopology.h
index cf3d2b1..f23afc1 100644
--- a/protomol/topology/BuildTopology.h
+++ b/protomol/topology/BuildTopology.h
@@ -1,13 +1,14 @@
 #ifndef BUILD_TOPOLOGY_H
 #define BUILD_TOPOLOGY_H
 
-#include <protomol/topology/ExclusionType.h>
 #include <protomol/topology/CoulombSCPISMParameterTable.h>
+#include <protomol/topology/ExclusionType.h>
 
 namespace ProtoMol {
   class GenericTopology;
-  class PSF;
   class PAR;
+  class PSF;
+struct CoulombSCPISMParameterTable;
 
   void buildExclusionTable(GenericTopology *topo,
                            const ExclusionType &exclusionType);
diff --git a/protomol/topology/BuildTopologyFromTpr.cpp b/protomol/topology/BuildTopologyFromTpr.cpp
index 29daf4d..56427c4 100644
--- a/protomol/topology/BuildTopologyFromTpr.cpp
+++ b/protomol/topology/BuildTopologyFromTpr.cpp
@@ -1,17 +1,37 @@
-#include <protomol/topology/BuildTopologyFromTpr.h>
-
-#include <protomol/topology/BuildTopology.h>
-
+#include <ctype.h>
+#include <math.h>
 #include <protomol/base/Exception.h>
 #include <protomol/base/SystemUtilities.h>
-#include <protomol/type/String.h>
-#include <protomol/topology/TopologyUtilities.h>
+#include <protomol/topology/BuildTopology.h>
+#include <protomol/topology/BuildTopologyFromTpr.h>
 #include <protomol/topology/GenericTopology.h>
 #include <protomol/topology/LennardJonesParameterTable.h>
+#include <stdlib.h>
+#include <iomanip>
+#include <iostream>
 #include <vector>
 
-#include <sstream>
-#include <iomanip>
+#include "gromacs/types/atoms.h"
+#include "gromacs/types/block.h"
+#include "gromacs/types/idef.h"
+#include "gromacs/types/ifunc.h"
+#include "gromacs/types/inputrec.h"
+#include "gromacs/types/simple.h"
+#include "gromacs/types/state.h"
+#include "gromacs/types/topology.h"
+#include "protomol/base/MathUtilities.h"
+#include "protomol/base/PMConstants.h"
+#include "protomol/base/Report.h"
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/ExclusionTable.h"
+#include "protomol/topology/LennardJonesParameters.h"
+#include "protomol/topology/RBTorsion.h"
+#include "protomol/topology/Torsion.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3DBlock.h"
 
 // GROMACS headers
 #if defined(HAVE_GROMACS)
diff --git a/protomol/topology/BuildTopologyFromTpr.h b/protomol/topology/BuildTopologyFromTpr.h
index 3de20f4..45e77c6 100644
--- a/protomol/topology/BuildTopologyFromTpr.h
+++ b/protomol/topology/BuildTopologyFromTpr.h
@@ -3,13 +3,14 @@
 
 #include <protomol/topology/ExclusionType.h>
 #include <protomol/type/Vector3DBlock.h>
-
-#include <vector>
+#include <iosfwd>
 #include <string>
+#include <vector>
 
 
 namespace ProtoMol {
   class GenericTopology;
+class Vector3DBlock;
 
   //build topo from TPR file
   void buildTopologyFromTpr(GenericTopology *topo,
diff --git a/protomol/topology/CoulombSCPISMParameterTable.cpp b/protomol/topology/CoulombSCPISMParameterTable.cpp
index a90cc02..17e360f 100644
--- a/protomol/topology/CoulombSCPISMParameterTable.cpp
+++ b/protomol/topology/CoulombSCPISMParameterTable.cpp
@@ -1,6 +1,12 @@
-#include <protomol/topology/CoulombSCPISMParameters.h>
-#include <protomol/topology/CoulombSCPISMParameterTable.h>
 #include <protomol/base/Report.h>
+#include <protomol/topology/CoulombSCPISMParameterTable.h>
+#include <protomol/topology/CoulombSCPISMParameters.h>
+#include <map>
+#include <ostream>
+#include <string>
+#include <utility>
+
+#include "protomol/topology/AtomType.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
@@ -11,8 +17,8 @@ void CoulombSCPISMParameterTable::populateTable() {
 
 //  if(!scpismFile.empty()) {
 
-//    SCPISMReader mReader(scpismFile);
-
+//    SCPISMReader mReader(scpismFile);
+
 //    if(!mReader.read( myData ))
 //      report << error << "Invalid SCPISM parameter file " << scpismFile << "." << endr;
 
diff --git a/protomol/topology/CubicCellManager.cpp b/protomol/topology/CubicCellManager.cpp
index 571c157..157dae4 100644
--- a/protomol/topology/CubicCellManager.cpp
+++ b/protomol/topology/CubicCellManager.cpp
@@ -1,7 +1,13 @@
+#include <math.h>
+#include <protomol/base/Report.h>
 #include <protomol/topology/CubicCellManager.h>
+#include <algorithm>
 
-#include <protomol/base/Report.h>
-#include <protomol/base/Exception.h>
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/SimpleTypes.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
 	using namespace ProtoMol::Report;
diff --git a/protomol/topology/CubicCellManager.h b/protomol/topology/CubicCellManager.h
index 7018538..aac1305 100644
--- a/protomol/topology/CubicCellManager.h
+++ b/protomol/topology/CubicCellManager.h
@@ -1,18 +1,24 @@
 #ifndef CUBICCELLMANAGER_H
 #define CUBICCELLMANAGER_H
 
-#include <protomol/topology/ArrayCellListStructure.h>
 #include <protomol/config/Parameter.h>
+#include <protomol/topology/ArrayCellListStructure.h>
 #include <protomol/type/Vector3D.h>
-
+#include <string>
 #include <vector>
 
+#include "protomol/topology/CubicCellLocation.h"
+#include "protomol/type/Real.h"
+
 namespace ProtoMol {
 	/**
 	 * The cell manager for equal-sized (cubic) cells. For optimization reasons
 	 * in case of periodic boundary conditions the cells are not cubic any more
 	 * in order to fit the system by multiples of the cell dimensions.
 	 */
+class Value;
+struct Parameter;
+
 	class CubicCellManager {
 		public:
 			/// topology and cell location structure of the cell
diff --git a/protomol/topology/ExclusionTable.cpp b/protomol/topology/ExclusionTable.cpp
index f4061fe..6e3f9c0 100644
--- a/protomol/topology/ExclusionTable.cpp
+++ b/protomol/topology/ExclusionTable.cpp
@@ -1,5 +1,9 @@
 #include <protomol/topology/ExclusionTable.h>
 #include <protomol/base/Report.h>
+#include <stddef.h>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/type/SimpleTypes.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/topology/ExclusionTable.h b/protomol/topology/ExclusionTable.h
index d65b774..9107c44 100644
--- a/protomol/topology/ExclusionTable.h
+++ b/protomol/topology/ExclusionTable.h
@@ -2,12 +2,13 @@
 #ifndef EXCLUSIONTABLE_H
 #define EXCLUSIONTABLE_H
 
-#include <vector>
-#include <map>
-#include <set>
-
 #include <protomol/base/PMConstants.h>
 #include <protomol/type/SimpleTypes.h>
+#include <algorithm>
+#include <map>
+#include <set>
+#include <utility>
+#include <vector>
 
 namespace ProtoMol {
   //________________________________________ ExclusionClass
diff --git a/protomol/topology/ExclusionType.h b/protomol/topology/ExclusionType.h
index 0067aad..d0cc15b 100644
--- a/protomol/topology/ExclusionType.h
+++ b/protomol/topology/ExclusionType.h
@@ -3,6 +3,7 @@
 #define EXCLUSIONTYPE_H
 
 #include <protomol/type/AbstractEnumType.h>
+#include <string>
 
 namespace ProtoMol {
   //________________________________________ ExclusionEnum
diff --git a/protomol/topology/GenericTopology.cpp b/protomol/topology/GenericTopology.cpp
index 2a8ac2d..a632968 100644
--- a/protomol/topology/GenericTopology.cpp
+++ b/protomol/topology/GenericTopology.cpp
@@ -1,6 +1,18 @@
 #include <protomol/topology/GenericTopology.h>
 
-#include <protomol/base/Exception.h>
+#include "protomol/base/PMConstants.h"
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/AtomType.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/ExclusionType.h"
+#include "protomol/topology/Molecule.h"
+#include "protomol/topology/RBTorsion.h"
+#include "protomol/topology/Torsion.h"
+
+namespace ProtoMol {
+class Value;
+}  // namespace ProtoMol
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/topology/GenericTopology.h b/protomol/topology/GenericTopology.h
index 5c11083..c94776f 100644
--- a/protomol/topology/GenericTopology.h
+++ b/protomol/topology/GenericTopology.h
@@ -2,22 +2,26 @@
 #ifndef GENERICTOPOLOGY_H
 #define GENERICTOPOLOGY_H
 
+#include <protomol/base/Makeable.h>
+#include <protomol/base/Zap.h>
+#include <protomol/topology/Angle.h>
 #include <protomol/topology/Atom.h>
 #include <protomol/topology/AtomType.h>
-#include <protomol/topology/Angle.h>
+#include <protomol/topology/BankLennardJonesParameterTable.h>
 #include <protomol/topology/Bond.h>
-#include <protomol/topology/Torsion.h>
 #include <protomol/topology/ExclusionTable.h>
 #include <protomol/topology/ExclusionType.h>
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/base/Makeable.h>
+#include <protomol/topology/LennardJonesParameterTable.h>
 #include <protomol/topology/Molecule.h>
-#include <protomol/base/Zap.h>
-
 #include <protomol/topology/RBTorsion.h>
+#include <protomol/topology/Torsion.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
+#include <string>
+#include <vector>
 
-#include <protomol/topology/LennardJonesParameterTable.h>
-#include <protomol/topology/BankLennardJonesParameterTable.h>
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //________________________________________ GenericTopology
@@ -50,6 +54,10 @@ namespace ProtoMol {
    */
 
   ///Available force fields
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   enum ForceFieldType {
     CHARMM,
     GROMACS
diff --git a/protomol/topology/LennardJonesParameterTable.cpp b/protomol/topology/LennardJonesParameterTable.cpp
index 71676ad..2eda8b7 100644
--- a/protomol/topology/LennardJonesParameterTable.cpp
+++ b/protomol/topology/LennardJonesParameterTable.cpp
@@ -1,5 +1,9 @@
-#include <protomol/topology/LennardJonesParameterTable.h>
 #include <protomol/base/Report.h>
+#include <protomol/topology/LennardJonesParameterTable.h>
+#include <stddef.h>
+
+#include "protomol/topology/LennardJonesParameters.h"
+
 using namespace ProtoMol::Report;
 
 using namespace ProtoMol;
diff --git a/protomol/topology/PeriodicBoundaryConditions.cpp b/protomol/topology/PeriodicBoundaryConditions.cpp
index 7200440..79d5832 100644
--- a/protomol/topology/PeriodicBoundaryConditions.cpp
+++ b/protomol/topology/PeriodicBoundaryConditions.cpp
@@ -1,10 +1,15 @@
-#include <protomol/topology/PeriodicBoundaryConditions.h>
-
 #include <protomol/base/Exception.h>
 #include <protomol/base/MathUtilities.h>
 #include <protomol/base/Report.h>
+#include <protomol/topology/PeriodicBoundaryConditions.h>
 #include <algorithm>
 
+#include "protomol/base/PMConstants.h"
+#include "protomol/config/ConstraintValueType.h"
+#include "protomol/config/Parameter.h"
+#include "protomol/config/Value.h"
+#include "protomol/type/Vector3DBlock.h"
+
 using namespace std;
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/topology/PeriodicBoundaryConditions.h b/protomol/topology/PeriodicBoundaryConditions.h
index b97b7e9..c61fd43 100644
--- a/protomol/topology/PeriodicBoundaryConditions.h
+++ b/protomol/topology/PeriodicBoundaryConditions.h
@@ -2,10 +2,14 @@
 #ifndef PERODICBOUNDARYCONDITIONS_H
 #define PERODICBOUNDARYCONDITIONS_H
 
-#include <string>
-
+#include <math.h>
 #include <protomol/config/Parameter.h>
 #include <protomol/type/Vector3DBlock.h>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //________________________________________ PeriodicBoundaryConditions
@@ -16,6 +20,10 @@ namespace ProtoMol {
    * The class use a couple of shorts cut's to avoid rint and to many div's and
    * mul's.
    */
+class Value;
+class Vector3DBlock;
+struct Parameter;
+
   class PeriodicBoundaryConditions {
     //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     // Constructors, destructors, assignment
diff --git a/protomol/topology/TopologyUtilities.cpp b/protomol/topology/TopologyUtilities.cpp
index 5b3b207..0925cb2 100644
--- a/protomol/topology/TopologyUtilities.cpp
+++ b/protomol/topology/TopologyUtilities.cpp
@@ -1,17 +1,27 @@
-#include <protomol/topology/TopologyUtilities.h>
-
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/topology/GenericTopology.h>
-#include <protomol/base/Report.h>
-#include <protomol/topology/Topology.h>
+#include <math.h>
 #include <protomol/base/MathUtilities.h>
 #include <protomol/base/PMConstants.h>
+#include <protomol/base/Report.h>
 #include <protomol/base/StringUtilities.h>
+#include <protomol/topology/GenericTopology.h>
+#include <protomol/topology/TopologyUtilities.h>
 #include <protomol/type/ScalarStructure.h>
-
-#include <vector>
+#include <protomol/type/Vector3DBlock.h>
 #include <algorithm>
+#include <functional>
 #include <set>
+#include <vector>
+
+#include "protomol/topology/Angle.h"
+#include "protomol/topology/AngleInfo.h"
+#include "protomol/topology/Atom.h"
+#include "protomol/topology/Bond.h"
+#include "protomol/topology/Molecule.h"
+#include "protomol/topology/Torsion.h"
+#include "protomol/type/Matrix3By3.h"
+#include "protomol/type/Real.h"
+#include "protomol/type/Stack.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace ProtoMol::Report;
 using namespace std;
diff --git a/protomol/topology/TopologyUtilities.h b/protomol/topology/TopologyUtilities.h
index 4793004..7ec1d68 100644
--- a/protomol/topology/TopologyUtilities.h
+++ b/protomol/topology/TopologyUtilities.h
@@ -2,22 +2,25 @@
 #ifndef TOPOLOGYUTILITIES_H
 #define TOPOLOGYUTILITIES_H
 
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/type/Vector3D.h>
+#include <protomol/topology/AngleInfo.h>
+#include <protomol/topology/Bond.h>
+#include <protomol/topology/Torsion.h>
 #include <protomol/type/Matrix3By3.h>
 #include <protomol/type/Real.h>
-#include <protomol/topology/Torsion.h>
 #include <protomol/type/Stack.h>
-#include <protomol/topology/AngleInfo.h>
-#include <protomol/topology/Bond.h>
-
+#include <protomol/type/Vector3D.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <set>
 #include <string>
 #include <vector>
-#include <set>
 
 
 
 namespace ProtoMol {
+class AngleInfo;
+class Vector3DBlock;
+template <class T> class Stack;
+
   enum {X_AXIS, Y_AXIS, Z_AXIS};
 
   class GenericTopology;
diff --git a/protomol/topology/VacuumBoundaryConditions.cpp b/protomol/topology/VacuumBoundaryConditions.cpp
index d796917..8878118 100644
--- a/protomol/topology/VacuumBoundaryConditions.cpp
+++ b/protomol/topology/VacuumBoundaryConditions.cpp
@@ -1,5 +1,8 @@
 #include <protomol/topology/VacuumBoundaryConditions.h>
 
+#include "protomol/base/PMConstants.h"
+#include "protomol/config/Value.h"
+
 using namespace std;
 using namespace ProtoMol;
 //____ VacuumBoundaryConditions
diff --git a/protomol/topology/VacuumBoundaryConditions.h b/protomol/topology/VacuumBoundaryConditions.h
index e38b735..b0b488c 100644
--- a/protomol/topology/VacuumBoundaryConditions.h
+++ b/protomol/topology/VacuumBoundaryConditions.h
@@ -4,8 +4,18 @@
 
 #include <protomol/config/Parameter.h>
 #include <protomol/type/Vector3DBlock.h>
-#include <string>
 #include <iostream>
+#include <string>
+#include <vector>
+
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
+
+namespace ProtoMol {
+class Value;
+class Vector3DBlock;
+}  // namespace ProtoMol
+
 using namespace std;
 
 namespace ProtoMol {
diff --git a/protomol/type/BlockMatrix.cpp b/protomol/type/BlockMatrix.cpp
index e0c322c..8562554 100644
--- a/protomol/type/BlockMatrix.cpp
+++ b/protomol/type/BlockMatrix.cpp
@@ -1,6 +1,9 @@
+#include <protomol/base/Lapack.h>
 #include <protomol/type/BlockMatrix.h>
+#include <algorithm>
 
-#include <protomol/base/Lapack.h>
+#include "protomol/base/Report.h"
+#include "protomol/type/Real.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/type/BlockMatrix.h b/protomol/type/BlockMatrix.h
index 9274ca9..51fab5e 100644
--- a/protomol/type/BlockMatrix.h
+++ b/protomol/type/BlockMatrix.h
@@ -2,10 +2,10 @@
 #ifndef BLOCKMATRIX_H
 #define BLOCKMATRIX_H
 
-#include <vector>
-#include <algorithm>
 #include <protomol/base/Report.h>
 #include <protomol/type/Real.h>
+#include <algorithm>
+#include <vector>
 
 using namespace std;
 
diff --git a/protomol/type/EigenvectorInfo.cpp b/protomol/type/EigenvectorInfo.cpp
index 7a30cb3..fe773ab 100644
--- a/protomol/type/EigenvectorInfo.cpp
+++ b/protomol/type/EigenvectorInfo.cpp
@@ -1,5 +1,7 @@
 #include "protomol/type/EigenvectorInfo.h"
 
+#include <new>
+
 using namespace ProtoMol;
 
 //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/protomol/type/Matrix3By3.cpp b/protomol/type/Matrix3By3.cpp
index f188c56..7ad7873 100644
--- a/protomol/type/Matrix3By3.cpp
+++ b/protomol/type/Matrix3By3.cpp
@@ -1,6 +1,11 @@
-#include <protomol/type/Matrix3By3.h>
+#include <math.h>
 #include <protomol/base/MathUtilities.h>
 #include <protomol/base/Report.h>
+#include <protomol/type/Matrix3By3.h>
+#include <algorithm>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol::Report;
diff --git a/protomol/type/Matrix3By3.h b/protomol/type/Matrix3By3.h
index 204392f..e25e2d2 100644
--- a/protomol/type/Matrix3By3.h
+++ b/protomol/type/Matrix3By3.h
@@ -2,8 +2,10 @@
 #ifndef MATRIX3BY3_H
 #define MATRIX3BY3_H
 
-#include <iostream>
 #include <protomol/type/Vector3D.h>
+#include <iostream>
+
+#include "protomol/type/Real.h"
 
 namespace ProtoMol {
   /*________________________________________ Matrix3By3
diff --git a/protomol/type/PAR.cpp b/protomol/type/PAR.cpp
index 2186bd8..ac099e8 100644
--- a/protomol/type/PAR.cpp
+++ b/protomol/type/PAR.cpp
@@ -1,6 +1,7 @@
+#include <math.h>
 #include <protomol/type/PAR.h>
 
-#include <protomol/base/MathUtilities.h>
+#include "protomol/type/Real.h"
 
 using namespace ProtoMol;
 //____ PAR
diff --git a/protomol/type/PAR.h b/protomol/type/PAR.h
index c10a217..9c5b6b1 100644
--- a/protomol/type/PAR.h
+++ b/protomol/type/PAR.h
@@ -2,12 +2,11 @@
 #ifndef PAR_H
 #define PAR_H
 
+#include <protomol/base/Report.h>
+#include <protomol/type/Real.h>
+#include <map>
 #include <string>
 #include <vector>
-#include <map>
-
-#include <protomol/type/Real.h>
-#include <protomol/base/Report.h>
 
 namespace ProtoMol {
   //_________________________________________________________________PAR
@@ -18,6 +17,10 @@ namespace ProtoMol {
    * - angles are always kept in degrees
    * - simga's for Nonbonded are asummed to be Charmm28
    */
+namespace Report {
+class MyStreamer;
+}  // namespace Report
+
   class PAR {
   public:
     //______________________________________________________________________Bond
diff --git a/protomol/type/PDB.cpp b/protomol/type/PDB.cpp
index 0eb567a..ad71e09 100644
--- a/protomol/type/PDB.cpp
+++ b/protomol/type/PDB.cpp
@@ -1,5 +1,8 @@
 #include <protomol/type/PDB.h>
 
+#include "protomol/base/Report.h"
+#include "protomol/type/Vector3DBlock.h"
+
 using namespace std;
 using namespace ProtoMol::Report;
 using namespace ProtoMol;
diff --git a/protomol/type/PDB.h b/protomol/type/PDB.h
index 9105e0c..60be7a5 100644
--- a/protomol/type/PDB.h
+++ b/protomol/type/PDB.h
@@ -2,17 +2,24 @@
 #ifndef PDB_H
 #define PDB_H
 
+#include <protomol/base/Report.h>
+#include <protomol/type/Vector3DBlock.h>
+#include <stddef.h>
 #include <string>
 #include <vector>
 
-#include <protomol/type/Vector3DBlock.h>
-#include <protomol/base/Report.h>
+#include "protomol/type/Real.h"
+#include "protomol/type/Vector3D.h"
 
 namespace ProtoMol {
   //___________________________________________________________________PDB
   /**
    * PDB container holding Atom's and coordinates
    */
+namespace Report {
+class MyStreamer;
+}  // namespace Report
+
   struct PDB {
     //___________________________________________________________________Atom
     /**
diff --git a/protomol/type/ScalarStructure.cpp b/protomol/type/ScalarStructure.cpp
index 178a424..c440d9c 100644
--- a/protomol/type/ScalarStructure.cpp
+++ b/protomol/type/ScalarStructure.cpp
@@ -1,5 +1,8 @@
 #include <protomol/type/ScalarStructure.h>
 
+#include "protomol/base/Proxy.h"
+#include "protomol/type/Vector3D.h"
+
 using namespace ProtoMol;
 //____ ScalarStructure
 ScalarStructure::ScalarStructure() :
diff --git a/protomol/type/ScalarStructure.h b/protomol/type/ScalarStructure.h
index bb5a6b9..9f3c9b3 100644
--- a/protomol/type/ScalarStructure.h
+++ b/protomol/type/ScalarStructure.h
@@ -2,11 +2,13 @@
 #ifndef ENERGYSTRUCTURE_H
 #define ENERGYSTRUCTURE_H
 
+#include <protomol/base/PMConstants.h>
 #include <protomol/base/Proxy.h>
 #include <protomol/type/Vector3D.h>
-#include <protomol/base/PMConstants.h>
-
 #include <iostream>
+
+#include "protomol/type/Real.h"
+
 using namespace std;
 
 namespace ProtoMol {
diff --git a/protomol/type/String.cpp b/protomol/type/String.cpp
index 6cd6995..f9a04a1 100644
--- a/protomol/type/String.cpp
+++ b/protomol/type/String.cpp
@@ -21,12 +21,12 @@
                    jcofflan@users.sourceforge.net
 
 \*******************************************************************/
-#include <protomol/type/String.h>
+#include <ctype.h>
 #include <protomol/base/Exception.h>
-
+#include <protomol/type/String.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <errno.h>
+#include <sys/errno.h>
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/type/Vector3DBlock.cpp b/protomol/type/Vector3DBlock.cpp
index 0c4c9a6..33cc909 100644
--- a/protomol/type/Vector3DBlock.cpp
+++ b/protomol/type/Vector3DBlock.cpp
@@ -1,5 +1,7 @@
 #include <protomol/type/Vector3DBlock.h>
-#include <protomol/type/Array.h>
+
+#include "protomol/base/PMConstants.h"
+#include "protomol/type/Vector3D.h"
 
 using namespace std;
 using namespace ProtoMol;
diff --git a/protomol/type/Vector3DBlock.h b/protomol/type/Vector3DBlock.h
index a4b00d5..7c81c53 100644
--- a/protomol/type/Vector3DBlock.h
+++ b/protomol/type/Vector3DBlock.h
@@ -2,11 +2,14 @@
 #ifndef VECTOR3DBLOCK_H
 #define VECTOR3DBLOCK_H
 
-#include <vector>
 #include <iostream>
+#include <vector>
+
+#include "protomol/type/Real.h"
+
 using namespace std;
-#include <protomol/type/Vector3D.h>
 #include <protomol/base/Proxy.h>
+#include <protomol/type/Vector3D.h>
 
 
 namespace ProtoMol {
@@ -246,7 +249,7 @@ namespace ProtoMol {
       unsigned int blkSz;
 
       OS >> blkSz;
-
+
       vblock.resize( blkSz );
       for (unsigned int i=0; i< blkSz; i++) {
         OS >> vblock[i];

From c5e462cf4d99648154c2cb88206e37bebf5cf7a4 Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 20:58:27 -0500
Subject: [PATCH 03/10] Fix incorrect include

---
 protomol/base/SystemUtilities.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protomol/base/SystemUtilities.cpp b/protomol/base/SystemUtilities.cpp
index 0ace4a3..9e5a580 100644
--- a/protomol/base/SystemUtilities.cpp
+++ b/protomol/base/SystemUtilities.cpp
@@ -38,7 +38,7 @@
 #include <sys/stat.h>
 #include <fstream>
 
-#include "/Users/Omegaice/Documents/Code/ProtoMol/protomol/base/Exception.h"
+#include "protomol/base/Exception.h"
 
 #ifdef HAVE_LIBFAH
 #include <fah/checksum/overrides.h>

From 208bec746f1109487f2741e2eb14a7bc383ec277 Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 21:01:00 -0500
Subject: [PATCH 04/10] More include fixes

---
 protomol/base/Timer.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/protomol/base/Timer.cpp b/protomol/base/Timer.cpp
index a6dc38e..0c1a06c 100644
--- a/protomol/base/Timer.cpp
+++ b/protomol/base/Timer.cpp
@@ -34,7 +34,6 @@
 
 #include <protomol/base/Timer.h>
 #include <stddef.h>
-#include <sys/_types/_timeval.h>
 #include <iostream>
 
 #include "protomol/base/Report.h"
@@ -232,4 +231,3 @@ TimeRep Timer::getCurrentTime() {
 
   return TimeRep(realTime, userTime, sysTime);
 }
-

From abc430d0598e3d9afda277450464542d0c88e344 Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 21:09:40 -0500
Subject: [PATCH 05/10] Missing include

---
 protomol/force/bonded/AngleSystemForce.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/protomol/force/bonded/AngleSystemForce.h b/protomol/force/bonded/AngleSystemForce.h
index f646296..8f05176 100644
--- a/protomol/force/bonded/AngleSystemForce.h
+++ b/protomol/force/bonded/AngleSystemForce.h
@@ -5,6 +5,7 @@
 #include <protomol/force/system/SystemForce.h>
 #include <protomol/type/ScalarStructure.h>
 #include <protomol/parallel/Parallel.h>
+#include <protomol/topology/SemiGenericTopology.h>
 
 namespace ProtoMol {
   //____ AngleSystemForce

From 7d516b67901c1b323ce6f81465b3d255a0809d9d Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 21:15:23 -0500
Subject: [PATCH 06/10] Missing includes

---
 protomol/module/NonbondedCutoffForceModule.cpp | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/protomol/module/NonbondedCutoffForceModule.cpp b/protomol/module/NonbondedCutoffForceModule.cpp
index c43f977..089b952 100644
--- a/protomol/module/NonbondedCutoffForceModule.cpp
+++ b/protomol/module/NonbondedCutoffForceModule.cpp
@@ -4,7 +4,6 @@
 #include <protomol/force/CoulombForce.h>
 #include <protomol/force/GB/GBACEForce.h>
 #include <protomol/force/GB/GBBornRadii.h>
-//GB
 #include <protomol/force/GB/GBForce.h>
 #include <protomol/force/GB/GBPartialSum.h>
 #include <protomol/force/LennardJonesForce.h>
@@ -29,6 +28,9 @@
 #include <protomol/topology/VacuumBoundaryConditions.h>
 #include <vector>
 
+#include <protomol/topology/CellListEnumeratorPeriodicBoundaries.h>
+#include <protomol/topology/CellListEnumeratorStandard.h>
+
 #include "protomol/config/Configuration.h"
 #include "protomol/config/Value.h"
 #include "protomol/factory/ForceFactory.h"
@@ -62,7 +64,7 @@ void NonbondedCutoffForceModule::registerForces(ProtoMolApp *app) {
     f.reg(new CutoffSystem<CCM, OneAtomPair<PBC, C2, CoulombForce> >());
     f.reg(new CutoffSystem<CCM, OneAtomPair<PBC, Cn, CoulombForce> >());
     f.reg(new CutoffSystem<CCM, OneAtomPair<PBC, CmpCnCn, CoulombForce> >());
-    
+
     // NonbondedCutoffSystemForce LennardJonesForce
     f.reg(new CutoffSystem<CCM, OneAtomPair<PBC, C1, LennardJonesForce> >());
     f.reg(new CutoffSystem<CCM, OneAtomPair<PBC, C2, LennardJonesForce> >());
@@ -75,7 +77,7 @@ void NonbondedCutoffForceModule::registerForces(ProtoMolApp *app) {
           LennardJonesTableForce<Cn, 7 ,Real> > >());
     f.reg(new CutoffSystem<CCM, OneAtomPair<PBC, Universal,
           LennardJonesTableForce<CmpCnCn, 7 ,Real> > >());
-    
+
     // NonbondedCutoffSystemForce LennardJonesForce CoulombForce
     f.reg(new CutoffSystem<CCM, OneAtomPairTwo<PBC, C2, LennardJonesForce,
           C1, CoulombForce> >());
@@ -129,7 +131,7 @@ void NonbondedCutoffForceModule::registerForces(ProtoMolApp *app) {
           LennardJonesTableForce<Cn, 7 ,Real> > >());
     f.reg(new CutoffSystem<CCM, OneAtomPair<VBC, Universal,
           LennardJonesTableForce<CmpCnCn, 7 ,Real> > >());
-    
+
     // NonbondedCutoffSystemForce LennardJonesForce CoulombForce
     f.reg(new CutoffSystem<CCM, OneAtomPairTwo<VBC, C2, LennardJonesForce, C1,
           CoulombForce> >());
@@ -156,7 +158,7 @@ void NonbondedCutoffForceModule::registerForces(ProtoMolApp *app) {
     f.reg(new CutoffSystem<CCM, OneAtomPair<VBC, Cn, CoulombSCPISMForce> >());
     f.reg(new CutoffSystem<CCM, OneAtomPair<VBC, CmpCnCn,
           CoulombSCPISMForce> >());
-    
+
     // GB
     f.reg(new CutoffSystem<CCM, OneAtomPairNoExclusion<VBC, Universal, GBForce> >());
     f.reg(new CutoffSystem<CCM, OneAtomPairNoExclusion<VBC, Universal, GBACEForce> >());
@@ -166,7 +168,7 @@ void NonbondedCutoffForceModule::registerForces(ProtoMolApp *app) {
     f.reg(new CutoffSystem<CCM, OneAtomPairNoExclusion<VBC, Cn, GBACEForce> >());
     f.reg(new CutoffSystem<CCM, OneAtomPairNoExclusion<VBC, Universal, GBBornRadii> >());
     f.reg(new CutoffSystem<CCM, OneAtomPairNoExclusion<VBC, Universal, GBPartialSum> >());
-    
+
     // OneAtomPairThree (forces): LennardJonesForce CoulombSCPISMForce BornRadii
 
     f.reg(new CutoffSystem<CCM, OneAtomPairThree<VBC, C2, LennardJonesForce, C1,

From 5d97a453c34997ef48571c741781ef92ab4240d1 Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 21:15:31 -0500
Subject: [PATCH 07/10] Unneeded includes

---
 protomol/output/GUIServer.cpp | 5 -----
 protomol/output/GUIServer.h   | 7 -------
 2 files changed, 12 deletions(-)

diff --git a/protomol/output/GUIServer.cpp b/protomol/output/GUIServer.cpp
index 9c5b9ce..5bec67a 100755
--- a/protomol/output/GUIServer.cpp
+++ b/protomol/output/GUIServer.cpp
@@ -5,11 +5,6 @@
 #include <pthread.h>
 #include <stdio.h>
 #include <string.h>
-#include <sys/_endian.h>
-#include <sys/_select.h>
-#include <sys/_types/_fd_isset.h>
-#include <sys/_types/_fd_set.h>
-#include <sys/_types/_fd_zero.h>
 #include <sys/errno.h>
 #include <sys/fcntl.h>
 #include <time.h>
diff --git a/protomol/output/GUIServer.h b/protomol/output/GUIServer.h
index 0882c07..4dce7a7 100755
--- a/protomol/output/GUIServer.h
+++ b/protomol/output/GUIServer.h
@@ -7,13 +7,6 @@
 #define COMM_NNCOORD 050363
 #define NUMCONN      20
 
-#include <_types/_uint32_t.h>
-#include <_types/_uint64_t.h>
-#include <_types/_uint8_t.h>
-#include <sys/_pthread/_pthread_mutex_t.h>
-#include <sys/_pthread/_pthread_t.h>
-#include <sys/_types/_fd_def.h>
-#include <sys/_types/_int64_t.h>
 #include <sys/types.h>
 
 #include "stdtypes.h"

From 1918793db2308449e1072ffef277b80a5889ca47 Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 21:16:26 -0500
Subject: [PATCH 08/10] Unneeded using namespace

---
 protomol/parallel/FFTComplex.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/protomol/parallel/FFTComplex.cpp b/protomol/parallel/FFTComplex.cpp
index 8a418a6..761a60a 100644
--- a/protomol/parallel/FFTComplex.cpp
+++ b/protomol/parallel/FFTComplex.cpp
@@ -41,8 +41,6 @@ extern "C" {
 #  endif
 #endif
 
-using namespace ProtoMol::Report;
-
 namespace ProtoMol {
 
   //

From 64f32b8a11448c1e170e2edb8559932d5a670f35 Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 21:20:06 -0500
Subject: [PATCH 09/10] Removed unused imports

---
 protomol/topology/BuildTopologyFromTpr.cpp | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/protomol/topology/BuildTopologyFromTpr.cpp b/protomol/topology/BuildTopologyFromTpr.cpp
index 56427c4..1a9f1df 100644
--- a/protomol/topology/BuildTopologyFromTpr.cpp
+++ b/protomol/topology/BuildTopologyFromTpr.cpp
@@ -11,14 +11,6 @@
 #include <iostream>
 #include <vector>
 
-#include "gromacs/types/atoms.h"
-#include "gromacs/types/block.h"
-#include "gromacs/types/idef.h"
-#include "gromacs/types/ifunc.h"
-#include "gromacs/types/inputrec.h"
-#include "gromacs/types/simple.h"
-#include "gromacs/types/state.h"
-#include "gromacs/types/topology.h"
 #include "protomol/base/MathUtilities.h"
 #include "protomol/base/PMConstants.h"
 #include "protomol/base/Report.h"

From 4c2d82b75caef03d184065db14aeabdddaaf7283 Mon Sep 17 00:00:00 2001
From: James Sweet <james.sweet88@googlemail.com>
Date: Fri, 6 Nov 2015 22:44:16 -0500
Subject: [PATCH 10/10] Fix parallel build issues

---
 protomol/integrator/normal/NormalModeDiagonalize.cpp |  1 +
 protomol/parallel/Parallel.cpp                       | 11 +++++++----
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/protomol/integrator/normal/NormalModeDiagonalize.cpp b/protomol/integrator/normal/NormalModeDiagonalize.cpp
index f8aaf1e..10be800 100644
--- a/protomol/integrator/normal/NormalModeDiagonalize.cpp
+++ b/protomol/integrator/normal/NormalModeDiagonalize.cpp
@@ -8,6 +8,7 @@
 #include <cmath>
 #include <fstream>
 
+#include <protomol/parallel/Parallel.h>
 #include "protomol/base/Timer.h"
 #include "protomol/config/ConstraintValueType.h"
 #include "protomol/config/Parameter.h"
diff --git a/protomol/parallel/Parallel.cpp b/protomol/parallel/Parallel.cpp
index ac2d478..4b8a33a 100644
--- a/protomol/parallel/Parallel.cpp
+++ b/protomol/parallel/Parallel.cpp
@@ -3,6 +3,7 @@
 #include <mpi.h>
 #endif
 
+#include <unistd.h>
 #include <protomol/base/MathUtilities.h>
 #include <protomol/base/Report.h>
 #include <protomol/base/SystemUtilities.h>
@@ -15,10 +16,8 @@
 #include "protomol/parallel/ParallelType.h"
 #include "protomol/type/Real.h"
 
-namespace ProtoMol {
-class ScalarStructure;
-class Vector3DBlock;
-}  // namespace ProtoMol
+#include <protomol/type/ScalarStructure.h>
+#include <protomol/type/Vector3DBlock.h>
 
 using namespace std;
 using namespace ProtoMol::Report;
@@ -89,6 +88,10 @@ static void mpiEndSerial(bool exludeMaster) {
 }
 #endif
 
+//____ MPITypeTraits
+template<typename T>
+struct MPITypeTraits;
+
 #ifdef HAVE_MPI
 template<>
 struct MPITypeTraits<Real> {