/usr/include/votca/csg/csgapplication.h is in libvotca-csg-dev 1.4.1-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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* Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*/
#ifndef __VOTCA_CSGAPPLICATION_H
#define __VOTCA_CSGAPPLICATION_H
#include <votca/tools/application.h>
#include "topology.h"
#include "topologymap.h"
#include "cgobserver.h"
#include <votca/tools/thread.h>
#include <votca/tools/mutex.h>
#include "trajectoryreader.h"
namespace votca {
namespace csg {
using namespace votca::tools;
class CsgApplication
: public Application {
public:
CsgApplication();
~CsgApplication();
void Initialize();
bool EvaluateOptions();
void Run(void);
void ShowHelpText(std::ostream &out);
/// \brief overload and return true to enable mapping command line options
virtual bool DoMapping(void) {
return false;
}
/// \brief if DoMapping is true, will by default require mapping or not
virtual bool DoMappingDefault(void) {
return true;
}
/// \brief overload and return true to enable trajectory command line options
virtual bool DoTrajectory(void) {
return false;
}
/* \brief overload and return true to enable threaded calculations */
virtual bool DoThreaded(void) {
return false;
}
/* \brief overload and return false to disable synchronized (while threaded) calculations */
virtual bool SynchronizeThreads(void) {
if (DoThreaded())
return true;
else
return false;
}
/// \brief if topology is always needed
virtual bool NeedsTopology(void) {
return true;
}
/// \brief called after topology was loaded
virtual bool EvaluateTopology(Topology *top, Topology *top_ref = 0) {
return true;
}
void AddObserver(CGObserver *observer);
/// \brief called before the first frame
virtual void BeginEvaluate(Topology *top, Topology *top_ref = 0);
/// \brief called after the last frame
virtual void EndEvaluate();
// \brief called for each frame which is mapped
virtual void EvalConfiguration(Topology *top, Topology *top_ref = 0);
// thread related stuff follows
/**
\brief Worker, derived from Thread, does the work.
*
* Worker holds the information about the current frame, either in its
* own copy (e.g. Topology), or, by reference, from the parent CsgApplication.
* The computation is shifted from Run() into EvalConfiguration. The
* user is required to overload ForkWorker and Mergeworker and thereby
* define the initialization and merging of workers. By default, workers
* will be executed in correct order according to the frames. Also,
* output will follow the same order.
* Mutexes handle the locking of input/output and are also used to impose
* the correct order of frames for in/output.
*
*/
class Worker : public Thread {
public:
Worker();
~Worker();
/// \brief overload with the actual computation
virtual void EvalConfiguration(Topology *top, Topology *top_ref = 0) = 0;
/// \brief returns worker id
int getId() {
return _id;
}
protected:
CsgApplication *_app;
Topology _top, _top_cg;
TopologyMap * _map;
int _id;
void Run(void);
void setApplication(CsgApplication *app) {
_app = app;
}
void setId(int id) {
_id = id;
}
friend class CsgApplication;
};
/**
* \brief Gets frames from TrajectoryReader in an ordered way and, if successful,
* calls Worker::EvalConfiguration for that frame.
*
* @param worker
* @return True if frames left for calculation, else False
*/
bool ProcessData(Worker * worker);
/**
*
* User is required to overload ForkWorker and initialize workers.
* @return worker
*/
virtual Worker *ForkWorker(void);
/**
* User is required to overload MergeWorker and merge data from each worker.
* @param worker
*/
virtual void MergeWorker(Worker *worker);
protected:
list<CGObserver *> _observers;
bool _do_mapping;
std::vector<Worker*> _myWorkers;
int _nframes;
bool _is_first_frame;
int _nthreads;
Mutex _nframesMutex;
Mutex _traj_readerMutex;
/// \brief stores Mutexes used to impose order for input
std::vector<Mutex*> _threadsMutexesIn;
/// \brief stores Mutexes used to impose order for output
std::vector<Mutex*> _threadsMutexesOut;
TrajectoryReader * _traj_reader;
};
inline void CsgApplication::AddObserver(CGObserver *observer) {
_observers.push_back(observer);
}
inline CsgApplication::Worker::Worker()
: _app(NULL), _map(NULL) , _id(-1) {
}
}
}
#endif /* __VOTCA_CSGAPPLICATION_H */
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