LCLS · Omegaice · Nov 7, 2015 · Nov 7, 2015 · Nov 7, 2015 · Nov 7, 2015
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,5 @@
 
 test/ProtoMol*
 test/tests/output
+
+*.gch
diff --git 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
@@ -1,30 +1,30 @@
 #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;
   class AnalysisCollection;
   class Integrator;
   class GenericTopology;
   class ModuleManager;
+  struct CoulombSCPISMParameterTable;
 
   class ProtoMolApp {
   public:

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,8 +1,7 @@
 #include <protomol/base/Report.h>
-
-#include <iomanip>
-
 #include <protomol/base/SystemUtilities.h>
+#include <stddef.h>
+#include <algorithm>
 
 using namespace std;