AWH data structures modular checkpointing

diff --git a/src/gromacs/mdtypes/CMakeLists.txt b/src/gromacs/mdtypes/CMakeLists.txt
index f4517b6cdcddf3f9a4123c865014bd3113eee829..a9ee14787a7b079ca1e99219d41d7afa73b1cef8 100644 (file)
--- a/src/gromacs/mdtypes/CMakeLists.txt
+++ b/src/gromacs/mdtypes/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2015,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2015,2019,2020,2021, 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.
@@ -36,6 +36,7 @@
 add_library(mdtypes INTERFACE)
 
 file(GLOB MDTYPES_SOURCES
+    awh_history.cpp
     checkpointdata.cpp
     df_history.cpp
     energyhistory.cpp

diff --git a/src/gromacs/mdtypes/awh_history.cpp b/src/gromacs/mdtypes/awh_history.cpp
new file mode 100644 (file)
index 0000000..1f14f38
--- /dev/null
+++ b/src/gromacs/mdtypes/awh_history.cpp
@@ -0,0 +1,192 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * 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 to GROMACS, please
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+ * 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 research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief Defines functions of the AWH history used by modular checkpointing
+ *
+ * \author Pascal Merz <pascal.merz@me.com>
+ */
+
+#include "gmxpre.h"
+
+#include "awh_history.h"
+
+#include "gromacs/utility/strconvert.h"
+
+#include "checkpointdata.h"
+
+namespace gmx
+{
+
+namespace
+{
+/*!
+ * \brief Enum describing the contents all AWH history classes implemented in this file
+ *        write to modular checkpoint
+ *
+ * When changing the checkpoint content, add a new element just above Count, and adjust the
+ * checkpoint functionality.
+ */
+enum class CheckpointVersion
+{
+    Base, //!< First version of modular checkpointing
+    Count //!< Number of entries. Add new versions right above this!
+};
+constexpr auto c_currentVersion = CheckpointVersion(int(CheckpointVersion::Count) - 1);
+
+template<CheckpointDataOperation operation>
+static void doCheckpoint(CheckpointData<operation> checkpointData, AwhPointStateHistory* awhPointStateHistory)
+{
+    checkpointData.scalar("bias", &awhPointStateHistory->bias);
+    checkpointData.scalar("free_energy", &awhPointStateHistory->free_energy);
+    checkpointData.scalar("target", &awhPointStateHistory->target);
+    checkpointData.scalar("weightsum_iteration", &awhPointStateHistory->weightsum_iteration);
+    checkpointData.scalar("weightsum_covering", &awhPointStateHistory->weightsum_covering);
+    checkpointData.scalar("weightsum_tot", &awhPointStateHistory->weightsum_tot);
+    checkpointData.scalar("weightsum_ref", &awhPointStateHistory->weightsum_ref);
+    checkpointData.scalar("last_update_index", &awhPointStateHistory->last_update_index);
+    checkpointData.scalar("log_pmfsum", &awhPointStateHistory->log_pmfsum);
+    checkpointData.scalar("visits_iteration", &awhPointStateHistory->visits_iteration);
+    checkpointData.scalar("visits_tot", &awhPointStateHistory->visits_tot);
+}
+
+template<CheckpointDataOperation operation>
+static void doCheckpoint(CheckpointData<operation> checkpointData, AwhBiasStateHistory* awhBiasStateHistory)
+{
+    checkpointData.scalar("umbrellaGridpoint", &awhBiasStateHistory->umbrellaGridpoint);
+    checkpointData.scalar("origin_index_updatelist", &awhBiasStateHistory->origin_index_updatelist);
+    checkpointData.scalar("end_index_updatelist", &awhBiasStateHistory->end_index_updatelist);
+    checkpointData.scalar("in_initial", &awhBiasStateHistory->in_initial);
+    checkpointData.scalar("equilibrateHistogram", &awhBiasStateHistory->equilibrateHistogram);
+    checkpointData.scalar("histSize", &awhBiasStateHistory->histSize);
+    checkpointData.scalar("logScaledSampleWeight", &awhBiasStateHistory->logScaledSampleWeight);
+    checkpointData.scalar("maxLogScaledSampleWeight", &awhBiasStateHistory->maxLogScaledSampleWeight);
+    checkpointData.scalar("numUpdates", &awhBiasStateHistory->numUpdates);
+}
+
+template<CheckpointDataOperation operation>
+void doCheckpoint(CheckpointData<operation>    checkpointData,
+                  CorrelationBlockDataHistory* correlationBlockDataHistory)
+{
+    checkpointData.scalar("blockSumWeight", &correlationBlockDataHistory->blockSumWeight);
+    checkpointData.scalar("blockSumSquareWeight", &correlationBlockDataHistory->blockSumSquareWeight);
+    checkpointData.scalar("blockSumWeightX", &correlationBlockDataHistory->blockSumWeightX);
+    checkpointData.scalar("blockSumWeightY", &correlationBlockDataHistory->blockSumWeightY);
+    checkpointData.scalar("sumOverBlocksSquareBlockWeight",
+                          &correlationBlockDataHistory->sumOverBlocksSquareBlockWeight);
+    checkpointData.scalar("sumOverBlocksBlockSquareWeight",
+                          &correlationBlockDataHistory->sumOverBlocksBlockSquareWeight);
+    checkpointData.scalar("sumOverBlocksBlockWeightBlockWeightX",
+                          &correlationBlockDataHistory->sumOverBlocksBlockWeightBlockWeightX);
+    checkpointData.scalar("sumOverBlocksBlockWeightBlockWeightY",
+                          &correlationBlockDataHistory->sumOverBlocksBlockWeightBlockWeightY);
+    checkpointData.scalar("blockLength", &correlationBlockDataHistory->blockLength);
+    checkpointData.scalar("previousBlockIndex", &correlationBlockDataHistory->previousBlockIndex);
+    checkpointData.scalar("correlationIntegral", &correlationBlockDataHistory->correlationIntegral);
+}
+
+template<CheckpointDataOperation operation>
+static void doCheckpoint(CheckpointData<operation> checkpointData, CorrelationGridHistory* correlationGridHistory)
+{
+    checkpointData.scalar("numCorrelationTensors", &correlationGridHistory->numCorrelationTensors);
+    checkpointData.scalar("tensorSize", &correlationGridHistory->tensorSize);
+    checkpointData.scalar("blockDataListSize", &correlationGridHistory->blockDataListSize);
+
+    int blockDataBufferSize = correlationGridHistory->blockDataBuffer.size();
+    checkpointData.scalar("blockDataBufferSize", &blockDataBufferSize);
+    if (operation == CheckpointDataOperation::Read)
+    {
+        correlationGridHistory->blockDataBuffer.resize(blockDataBufferSize);
+    }
+    int counter = 0;
+    for (auto& buffer : correlationGridHistory->blockDataBuffer)
+    {
+        doCheckpoint(checkpointData.subCheckpointData("blockDataBuffer " + toString(counter)), &buffer);
+        counter++;
+    }
+}
+
+template<CheckpointDataOperation operation>
+void doCheckpointData(CheckpointData<operation> checkpointData, AwhBiasHistory* awhBiasHistory)
+{
+    int pointStateSize = awhBiasHistory->pointState.size();
+    checkpointData.scalar("pointStateSize", &pointStateSize);
+    if (operation == CheckpointDataOperation::Read)
+    {
+        awhBiasHistory->pointState.resize(pointStateSize);
+    }
+
+    int counter = 0;
+    for (auto& point : awhBiasHistory->pointState)
+    {
+        doCheckpoint(checkpointData.subCheckpointData("pointState " + toString(counter)), &point);
+        counter++;
+    }
+    doCheckpoint(checkpointData.subCheckpointData("state"), &awhBiasHistory->state);
+    doCheckpoint(checkpointData.subCheckpointData("forceCorrelationGrid"),
+                 &awhBiasHistory->forceCorrelationGrid);
+}
+} // namespace
+
+// This trips doxygen up
+//! \cond
+template<CheckpointDataOperation operation>
+void AwhHistory::doCheckpoint(CheckpointData<operation> checkpointData)
+{
+    // Keep one version for all objects in this file
+    checkpointVersion(&checkpointData, "AwhHistory version", c_currentVersion);
+
+    checkpointData.scalar("potentialOffset", &potentialOffset);
+
+    int biasSize = bias.size();
+    checkpointData.scalar("biasSize", &biasSize);
+    if (operation == CheckpointDataOperation::Read)
+    {
+        bias.resize(biasSize);
+    }
+    int counter = 0;
+    for (auto& b : bias)
+    {
+        doCheckpointData(checkpointData.subCheckpointData("bias " + toString(counter)), &b);
+        counter++;
+    }
+}
+
+// explicit template instantiation
+template void AwhHistory::doCheckpoint(CheckpointData<CheckpointDataOperation::Read>);
+template void AwhHistory::doCheckpoint(CheckpointData<CheckpointDataOperation::Write>);
+//! \endcond
+
+} // namespace gmx

diff --git a/src/gromacs/mdtypes/awh_history.h b/src/gromacs/mdtypes/awh_history.h
index b3ce1dd905faf9d5d8cf5e61ad4a10187c1941e2..7e1a4e46801e7025247ccfa22aa3185eff483dbd 100644 (file)
--- a/src/gromacs/mdtypes/awh_history.h
+++ b/src/gromacs/mdtypes/awh_history.h
@@ -47,12 +47,17 @@
 #ifndef GMX_MDTYPES_AWHHISTORY_H
 #define GMX_MDTYPES_AWHHISTORY_H
 
+#include <cstdint>
+
 #include <vector>
 
 #include "gromacs/mdtypes/awh_correlation_history.h"
 
 namespace gmx
 {
+enum class CheckpointDataOperation;
+template<CheckpointDataOperation operation>
+class CheckpointData;
 
 /*! \cond INTERNAL */
 
@@ -117,6 +122,14 @@ struct AwhHistory
 
     /*! \brief Constructor. */
     AwhHistory() : potentialOffset(0) {}
+
+    /*! \brief Allows to read and write checkpoint within modular simulator
+     *
+     * \tparam operation  Whether we're reading or writing
+     * \param checkpointData  The CheckpointData object
+     */
+    template<CheckpointDataOperation operation>
+    void doCheckpoint(CheckpointData<operation> checkpointData);
 };
 
 /*! \endcond */