/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * G R O M A C S
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
*
- * GROningen MAchine for Chemical Simulations
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \internal \file
* \brief
* Implements classes in analysisdata.h.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/analysisdata.h"
+#include "gmxpre.h"
+
+#include "analysisdata.h"
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/analysisdata/datastorage.h"
#include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
-
-#include "analysisdata-impl.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/uniqueptr.h"
namespace gmx
{
/********************************************************************
- * AnalysisData::Impl
+ * AnalysisDataHandleImpl
*/
-AnalysisData::Impl::Impl()
+namespace internal
{
-}
-
-AnalysisData::Impl::~Impl()
+/*! \internal \brief
+ * Private implementation class for AnalysisDataHandle.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataHandleImpl
{
-}
+ public:
+ //! Creates a handle associated with the given data object.
+ explicit AnalysisDataHandleImpl(AnalysisData *data)
+ : data_(*data), currentFrame_(NULL)
+ {
+ }
+
+ //! The data object that this handle belongs to.
+ AnalysisData &data_;
+ //! Current storage frame object, or NULL if no current frame.
+ AnalysisDataStorageFrame *currentFrame_;
+};
+
+} // namespace internal
+/********************************************************************
+ * AnalysisData::Impl
+ */
+
+/*! \internal \brief
+ * Private implementation class for AnalysisData.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisData::Impl
+{
+ public:
+ //! Smart pointer type to manage a data handle implementation.
+ typedef gmx_unique_ptr<internal::AnalysisDataHandleImpl>::type
+ HandlePointer;
+ //! Shorthand for a list of data handles.
+ typedef std::vector<HandlePointer> HandleList;
+
+ //! Storage implementation.
+ AnalysisDataStorage storage_;
+ /*! \brief
+ * List of handles for this data object.
+ *
+ * Note that AnalysisDataHandle objects also contain (raw) pointers
+ * to these objects.
+ */
+ HandleList handles_;
+};
/********************************************************************
* AnalysisData
void
-AnalysisData::setColumns(int ncol, bool multipoint)
+AnalysisData::setDataSetCount(int dataSetCount)
{
- GMX_RELEASE_ASSERT(ncol > 0, "Number of columns must be positive");
GMX_RELEASE_ASSERT(impl_->handles_.empty(),
"Cannot change data dimensionality after creating handles");
- setColumnCount(ncol);
- setMultipoint(multipoint);
- impl_->storage_.setMultipoint(multipoint);
+ AbstractAnalysisData::setDataSetCount(dataSetCount);
+}
+
+
+void
+AnalysisData::setColumnCount(int dataSet, int columnCount)
+{
+ GMX_RELEASE_ASSERT(impl_->handles_.empty(),
+ "Cannot change data dimensionality after creating handles");
+ AbstractAnalysisData::setColumnCount(dataSet, columnCount);
+}
+
+
+void
+AnalysisData::setMultipoint(bool bMultipoint)
+{
+ GMX_RELEASE_ASSERT(impl_->handles_.empty(),
+ "Cannot change data type after creating handles");
+ AbstractAnalysisData::setMultipoint(bMultipoint);
+}
+
+
+int
+AnalysisData::frameCount() const
+{
+ return impl_->storage_.frameCount();
}
"Too many calls to startData() compared to provided options");
if (impl_->handles_.empty())
{
- notifyDataStart();
- impl_->storage_.setParallelOptions(opt);
- impl_->storage_.startDataStorage(this);
- }
- else if (isMultipoint())
- {
- GMX_THROW(NotImplementedError("Parallelism not supported for multipoint data"));
+ impl_->storage_.startParallelDataStorage(this, &moduleManager(), opt);
}
Impl::HandlePointer handle(new internal::AnalysisDataHandleImpl(this));
if (impl_->handles_.empty())
{
- notifyDataFinish();
+ impl_->storage_.finishDataStorage();
}
}
}
-/********************************************************************
- * AnalysisDataHandleImpl
- */
-
-internal::AnalysisDataHandleImpl::AnalysisDataHandleImpl(AnalysisData *data)
- : data_(*data), currentFrame_(NULL)
-{
-}
-
-
/********************************************************************
* AnalysisDataHandle
*/
void
-AnalysisDataHandle::setPoint(int col, real y, real dy, bool present)
+AnalysisDataHandle::selectDataSet(int index)
+{
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ "selectDataSet() called without calling startFrame()");
+ impl_->currentFrame_->selectDataSet(index);
+}
+
+
+void
+AnalysisDataHandle::setPoint(int column, real value, bool bPresent)
+{
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ "setPoint() called without calling startFrame()");
+ impl_->currentFrame_->setValue(column, value, bPresent);
+}
+
+
+void
+AnalysisDataHandle::setPoint(int column, real value, real error, bool bPresent)
{
GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
"setPoint() called without calling startFrame()");
- impl_->currentFrame_->setValue(col, y, dy, present);
+ impl_->currentFrame_->setValue(column, value, error, bPresent);
}
void
-AnalysisDataHandle::setPoints(int firstcol, int n, const real *y)
+AnalysisDataHandle::setPoints(int firstColumn, int count, const real *values)
{
GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
"setPoints() called without calling startFrame()");
- for (int i = 0; i < n; ++i)
+ for (int i = 0; i < count; ++i)
{
- impl_->currentFrame_->setValue(firstcol + i, y[i]);
+ impl_->currentFrame_->setValue(firstColumn + i, values[i]);
}
}
GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
"finishFrame() called without calling startFrame()");
- int index = impl_->currentFrame_->frameIndex();
+ AnalysisDataStorageFrame *frame = impl_->currentFrame_;
impl_->currentFrame_ = NULL;
- impl_->data_.impl_->storage_.finishFrame(index);
+ frame->finishFrame();
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff