file headers for sampler classes

src/Sample/FromFile.h

+//
+// Class FromFile
+//   This class parses a file that contains design variable values.
+//   Each column belongs to a design variable.
+//   The first line is considered as header and consists of the
+//   design variable name. The name has to agree with the string
+//   in the input file.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_SEQUENCE_H
 #define OPAL_SEQUENCE_H
 
@@ -11,13 +35,6 @@
 
 #include <vector>
 
-/**
- * Parse file that contains design variable values.
- * Each column belongs to a design variable.
- * The first line is considered as header and consists of the
- * design variable name. The name has to agree with the string
- * in the input file.
- */
 class FromFile : public SamplingMethod
 {
 

src/Sample/LatinHyperCube.h

+//
+// Class LatinHyperCube
+//   This class does Latin hypercube sampling.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_LATIN_HYPERCUBE_H
 #define OPAL_LATIN_HYPERCUBE_H
 

src/Sample/Normal.h

+//
+// Class Normal
+//   This class provides normally distributed samples.
+//
+// Copyright (c) 2018, Christof Metzger-Kraus, Open Sourcerer
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_NORMAL_RANDOM_SAMPLING_H
 #define OPAL_NORMAL_RANDOM_SAMPLING_H
 

src/Sample/OpalSample.cpp

+//
+// Class OpalSample
+//   The SAMPLING definition.
+//   A SAMPLING definition is used to run the optimizer in sample mode.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #include "Sample/OpalSample.h"
 
 #include "AbstractObjects/OpalData.h"
@@ -14,9 +35,6 @@
 #include "Sample/SampleRandomizedSequence.h"
 
 
-// Class OpalSample
-// ------------------------------------------------------------------------
-
 // The attributes of class OpalSample.
 namespace {
     enum {

src/Sample/OpalSample.h

+//
+// Class OpalSample
+//   The SAMPLING definition.
+//   A SAMPLING definition is used to run the optimizer in sample mode.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_SAMPLE_H
 #define OPAL_SAMPLE_H
 
@@ -7,11 +28,6 @@
 
 #include "Sample/SamplingMethod.h"
 
-// Class OpalSample
-// ------------------------------------------------------------------------
-/// The SAMPLING definition.
-//  A SAMPLING definition is used run the optimizer in sample mode.
-
 class OpalSample: public Definition {
 
 public:

src/Sample/RNGStream.cpp

+//
+// Class RNGStream
+//   This class takes care of RNG generator instances.
+//
+// Copyright (c) 2018, Christof Metzger-Kraus, Open Sourcerer
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #include "Sample/RNGStream.h"
 
 #include <iostream>

src/Sample/RNGStream.h

+//
+// Class RNGStream
+//   This class takes care of RNG generator instances.
+//
+// Copyright (c) 2018, Christof Metzger-Kraus, Open Sourcerer
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef RNGSTREAM_H
 #define RNGSTREAM_H
 

src/Sample/SampleCmd.cpp

+//
+// Class SampleCmd
+//   This class defines the SAMPLE command.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #include "Sample/SampleCmd.h"
 #include "Sample/Sampler.h"
 #include "Sample/OpalSample.h"

src/Sample/SampleCmd.h

+//
+// Class SampleCmd
+//   This class defines the SAMPLE command.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_SampleCmd_HH
 #define OPAL_SampleCmd_HH
 
@@ -5,10 +25,6 @@
 
 #include <string>
 
-// Class SampleCmd
-// ------------------------------------------------------------------------
-/// The SAMPLE command.
-
 class SampleCmd: public Action {
 
 public:

src/Sample/SampleGaussianSequence.h

+//
+// Class SampleGaussianSequence
+//   This class provides a sequence of sampling points that have a Gaussian distribution
+//   with
+//         mean = 0.5 * (upper + lower)
+//         sigma = (upper - lower) / 10
+//   This can be achieved if the integral of the Gaussian between the sampling
+//   points are all equal. The sampling points are therefore computed using
+//   the inverse error function at equally distributed arguments between
+//   -1 and 1.
+//
+// Copyright (c) 2018, Christof Metzger-Kraus, Open Sourcerer
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_SAMPLE_GAUSSIAN_SEQUENCE_H
 #define OPAL_SAMPLE_GAUSSIAN_SEQUENCE_H
 
@@ -10,14 +34,6 @@
 
 class SampleGaussianSequence : public SamplingMethod
 {
-    // provides a sequence of sampling points that have a Gaussian distribution
-    // with
-    //      mean = 0.5 * (upper + lower)
-    //      sigma = (upper - lower) / 10
-    // This can be achieved if the integral of the Gaussian between the sampling
-    // points are all equal. The sampling points are therefore computed using
-    // the inverse error function at equally distributed arguments between
-    // -1 and 1.
 
 public:
 

src/Sample/SampleIndividual.h

+//
+// Class SampleIndividual
+//   Structure for an individual in the population holding genes values.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef __SAMPLE_INDIVIDUAL_H__
 #define __SAMPLE_INDIVIDUAL_H__
 
@@ -13,13 +33,6 @@
 
 #include "boost/smart_ptr.hpp"
 
-/**
- * \class SampleIndividual
- *  Structure for an individual in the population holding genes
- *  values.
- *
- *  @see Types.h
- */
 class SampleIndividual {
 
 public:

src/Sample/SamplePilot.h

+//
+// Class SamplePilot
+//   The sample Pilot (Master): Coordinates requests by sampler to workers.
+//   Every worker thread notifies the master here if idle or not. When
+//   available the master dispatches one of the pending simulations to the
+//   worker who will run the specified simulation and report results back to
+//   the master.
+//   @see SampleWorker
+//   @see Sampler
+//   @tparam Opt_t type of the sampler
+//   @tparam Sim_t type of the simulation
+//   @tparam SolPropagationGraph_t strategy to distribute solution between
+//           master islands
+//   @tparam Comm_t comm splitter strategy
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef __SAMPLE_PILOT_H__
 #define __SAMPLE_PILOT_H__
 
@@ -5,25 +36,6 @@
 #include "Sample/SampleWorker.h"
 #include "Expression/Parser/function.hpp"
 
-/**
- *  \class SamplePilot
- *  \brief The sample Pilot (Master): Coordinates requests by sampler
- *  to workers.
- *
- *  Every worker thread notifies the master here if idle or not. When
- *  available the master dispatches one of the pending simulations to the
- *  worker who will run the specified simulation and report results back to
- *  the master.
- *
- *  @see SampleWorker
- *  @see Sampler
- *
- *  @tparam Opt_t type of the sampler
- *  @tparam Sim_t type of the simulation
- *  @tparam SolPropagationGraph_t strategy to distribute solution between
- *          master islands
- *  @tparam Comm_t comm splitter strategy
- */
 template <
       class Opt_t
     , class Sim_t

src/Sample/SampleRandomizedSequence.h

+//
+// Class SampleRandomizedSequence
+//   This class creates randomized sequences, i.e., it randomly picks values from
+//   a sequence.
+//
+// Copyright (c) 2019, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_SAMPLE_WEIGHTED_SEQUENCE_H
 #define OPAL_SAMPLE_WEIGHTED_SEQUENCE_H
 

src/Sample/SampleSequence.h

+//
+// Class SampleSequence
+//   This class provides a sequence of equidistant sampling points. It
+//   can't be garanteed that the sampling is equidistant if
+//   an integer type is chosen and the difference between
+//   the upper and lower limit isn't divisible by the number
+//   of sampling points.
+//
+// Copyright (c) 2018, Christof Metzger-Kraus, Open Sourcerer
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_SAMPLE_SEQUENCE_H
 #define OPAL_SAMPLE_SEQUENCE_H
 
@@ -6,11 +27,6 @@
 template <typename T>
 class SampleSequence : public SamplingMethod
 {
-    // provides a sequence of equidistant sampling points. It
-    // can't be garanteed that the sampling is equidistant if
-    // an integer type is chosen and the difference between
-    // the upper and lower limit isn't divisible by the number
-    // of sampling points.
 
 public:
 

src/Sample/SampleWorker.h

+//
+// Class SampleWorker
+//   A worker MPI entity consists of a processor group that runs a
+//   simulation of type Sim_t. The main loop in run() accepts new jobs from the
+//   master process runs the simulation and reports back the results.
+//
+//   @see SamplePilot
+//   @see Worker
+//   @see MPIHelper.h
+//
+//   @tparam Sim_T type of simulation to run
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef __SAMPLE_WORKER_H__
 #define __SAMPLE_WORKER_H__
 
 #include "Pilot/Worker.h"
 
-
-/**
- *  \class SampleWorker
- *  \brief A worker MPI entity consists of a processor group that runs a
- *  simulation of type Sim_t. The main loop in run() accepts new jobs from the
- *  master process runs the simulation and reports back the results.
- *
- *  @see SamplePilot
- *  @see Worker
- *  @see MPIHelper.h
- *
- *  @tparam Sim_T type of simulation to run
- */
 template <class Sim_t>
 class SampleWorker : protected Worker<Sim_t> {
 

src/Sample/Sampler.cpp

+//
+// Class Sampler
+//   This class creates, dispatches and dumps new individuals.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #include <iostream>
 #include <string>
 #include <limits>

src/Sample/Sampler.h

+//
+// Class Sampler
+//   This class creates, dispatches and dumps new individuals.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef __OPAL_SAMPLER_H__
 #define __OPAL_SAMPLER_H__
 
@@ -31,13 +51,6 @@
 #include <boost/property_tree/ptree.hpp>
 
 
-/**
- *  \class Sampler
- *  \brief Implementing sampling
- */
-// template<
-//       template <class> class SamplingOperator
-// >
 class Sampler : public Optimizer {
 
 public:

src/Sample/SamplingMethod.h

+//
+// Class SamplingMethod
+//   Base class for all sampling methods.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_SAMPLING_METHOD_H
 #define OPAL_SAMPLING_METHOD_H
 

src/Sample/Uniform.h

+//
+// Class Uniform
+//   This class creates uniformly distributed samples.
+//
+// Copyright (c) 2018, Matthias Frey, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// Implemented as part of the PhD thesis
+// "Precise Simulations of Multibunches in High Intensity Cyclotrons"
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
 #ifndef OPAL_UNIFORM_H
 #define OPAL_UNIFORM_H