#Following ones are undecided/TODO
"-Wno-disabled-macro-expansion"
"-Wno-cast-align"
- "-Wno-undefined-reinterpret-cast"
"-Wno-reserved-id-macro"
"-Wno-global-constructors"
- "-Wno-comma"
"-Wno-exit-time-destructors"
"-Wno-unused-macros"
"-Wno-weak-vtables"
- "-Wno-extra-semi"
"-Wno-conditional-uninitialized"
"-Wno-format-nonliteral"
"-Wno-shadow"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2018, 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.
efAllowMultipleDataSets = 1<<4
};
- virtual ~IAnalysisDataModule() {};
+ virtual ~IAnalysisDataModule() {}
/*! \brief
* Returns properties supported by the module.
const awh_dvec coordValue)
{
coordState_.setCoordValue(grid, coordValue);
- };
+ }
/*! \brief
* Performs an update of the bias.
const CoordState &coordState() const
{
return coordState_;
- };
+ }
/*! \brief Returns a const reference to the point state.
*/
const std::vector<PointState> &points() const
{
return points_;
- };
+ }
/*! \brief Returns true if we are in the initial stage.
*/
bool inInitialStage() const
{
return histogramSize_.inInitialStage();
- };
+ }
/*! \brief Returns the current histogram size.
*/
inline HistogramSize histogramSize() const
{
return histogramSize_;
- };
+ }
/* Data members */
private:
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
const awh_dvec &coordValue() const
{
return coordValue_;
- };
+ }
/*! \brief Returns the grid point index for the current coordinate value.
*/
int umbrellaGridpoint() const
{
return umbrellaGridpoint_;
- };
+ }
private:
awh_dvec coordValue_; /**< Current coordinate value in (nm or rad) */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
double t)
{
tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
- };
+ }
/*! \brief Restores the correlation grid state from the correlation grid history.
*
blockSumWeightX(0),
sumOverBlocksBlockWeightBlockWeightX(0)
{
- };
+ }
double blockSumWeightX; /**< Weighted sum of x for current block. */
double sumOverBlocksBlockWeightBlockWeightX; /**< Sum over all blocks in the simulation of block weight times sum_wx. */
coordData_(numDim),
correlationIntegral_(numDim*(numDim + 1)/2)
{
- };
+ }
/*! \brief Restore the state from history.
*
{
coordData_[d].blockSumWeightX += weight*data[d];
}
- };
+ }
/*! \brief Adds a filled data block to correlation time integral.
*/
double blockSumWeight() const
{
return blockSumWeight_;
- };
+ }
/*! \brief Returns the sum weights^2 for current block. */
double blockSumSquareWeight() const
{
return blockSumSquareWeight_;
- };
+ }
/*! \brief Returns the sum over blocks of block weight^2. */
double sumOverBlocksSquareBlockWeight() const
{
return sumOverBlocksSquareBlockWeight_;
- };
+ }
/*! \brief Returns the sum over blocks of weight^2. */
double sumOverBlocksBlockSquareWeight() const
{
return sumOverBlocksBlockSquareWeight_;
- };
+ }
/*! \brief Returns the length of each block used for block averaging. */
double blockLength() const
{
return blockLength_;
- };
+ }
/*! \brief Double the length of each block used for block averaging. */
void doubleBlockLength()
{
blockLength_ *= 2;
- };
+ }
/*! \brief Return the last block index data was added to (needed only for block length in terms of time). */
int previousBlockIndex() const
const std::vector<CoordData> &coordData() const
{
return coordData_;
- };
+ }
/*! \brief Return the correlation integral tensor. */
const std::vector<double> &correlationIntegral() const
{
return correlationIntegral_;
- };
+ }
private:
/* Weight sum data, indentical for all dimensions */
{
/* The last blockdata has only 1 block containing all data */
return blockDataList().back().blockSumWeight();
- };
+ }
/*! \brief Restore a correlation element from history.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
betak(beta*forceConstant),
userCoordUnitsToInternal(conversionFactor)
{
- };
+ }
/*! \brief Convert internal coordinate units to external, user coordinate units.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
int numUpdates() const
{
return numUpdates_;
- };
+ }
/*! \brief Increments the number of updates by 1.
*/
double histogramSize() const
{
return histogramSize_;
- };
+ }
/*! \brief Sets the histogram size.
*
bool inInitialStage() const
{
return inInitialStage_;
- };
+ }
/*! \brief Returns The log of the current sample weight, scaled because of the histogram rescaling.
*/
double logScaledSampleWeight() const
{
return logScaledSampleWeight_;
- };
+ }
private:
gmx_int64_t numUpdates_; /**< The number of updates performed since the start of the simulation. */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
numVisitsIteration_(0),
numVisitsTot_(0)
{
- };
+ }
/*! \brief
* Set all values in the state to those from a history.
//! Shorthand for a list of modules contained in a group.
typedef CommandLineModuleGroupData::ModuleList ModuleGroupContents;
- virtual ~IHelpExport() {};
+ virtual ~IHelpExport() {}
/*! \brief
* Called once before exporting individual modules.
{
return end_[static_cast<int>(rangeType) - 1];
}
- };
+ }
/*! \brief Returns the end atom index for range \p rangeType */
int end(Type rangeType) const
{
return end_[static_cast<int>(rangeType)];
- };
+ }
/*! \brief Returns the number of home atoms */
int numHomeAtoms() const
{
return end_[static_cast<int>(Type::Home)];
- };
+ }
/*! \brief Returns the total number of atoms */
int numAtomsTotal() const
}
lastTypeSet_ = rangeType;
- };
+ }
private:
/*! \brief The list of end atom indices */
kkk[i].Jc = 0;
kkk[i].Jcsig = 0;
}
- tdc = 0, tds = 0;
+ tdc = 0; tds = 0;
for (j = 0; (j < nh); j++)
{
d = invth*histo[j];
}
fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
- rgblo.r = rlo[XX], rgblo.g = rlo[YY], rgblo.b = rlo[ZZ];
- rgbhi.r = rhi[XX], rgbhi.g = rhi[YY], rgbhi.b = rhi[ZZ];
+ rgblo.r = rlo[XX]; rgblo.g = rlo[YY]; rgblo.b = rlo[ZZ];
+ rgbhi.r = rhi[XX]; rgbhi.g = rhi[YY]; rgbhi.b = rhi[ZZ];
fnTPR = ftp2fn_null(efTPR, NFILE, fnm);
if (bMol && !fnTPR)
{
groupnr[i] = i+1;
}
- rlo.r = 1.0, rlo.g = 0.0, rlo.b = 0.0;
- rmid.r = 1.0, rmid.g = 1.0, rmid.b = 1.0;
- rhi.r = 0.0, rhi.g = 0.0, rhi.b = 1.0;
+ rlo.r = 1.0; rlo.g = 0.0; rlo.b = 0.0;
+ rmid.r = 1.0; rmid.g = 1.0; rmid.b = 1.0;
+ rhi.r = 0.0; rhi.g = 0.0; rhi.b = 1.0;
if (bMeanEmtx)
{
snew(e, ngroups);
nframes = 0;
- rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
- rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
+ rlo.r = 1.0; rlo.g = 1.0; rlo.b = 1.0;
+ rhi.r = 0.0; rhi.g = 0.0; rhi.b = 0.0;
gpbc = gmx_rmpbc_init(&top.idef, ePBC, trxnat);
calc_noe(isize, noe_index, dtot1_3, dtot1_6, gnr, noe);
}
- rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
- rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
+ rlo.r = 1.0; rlo.g = 1.0; rlo.b = 1.0;
+ rhi.r = 0.0; rhi.g = 0.0; rhi.b = 0.0;
if (bRMS)
{
snew(bb, rnr);
for (i = 0; (i < rnr); i++)
{
- bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1, bb[i].resno = res0+i;
+ bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1; bb[i].resno = res0+i;
}
for (i = j = 0; (i < gnx); i++)
}
else
{
- haveX2Apic = false,
+ haveX2Apic = false;
haveApic = false;
}
numExchanges(0),
randomSeed(-1)
{
- };
+ }
int exchangeInterval; /* Interval in steps at which to attempt exchanges, 0 means no replica exchange */
int numExchanges; /* The number of exchanges to attempt at an exchange step */
{
public:
//! Constructor
- SimulationSignal(bool isSignalLocal = true) : sig(0), set(0), isLocal(isSignalLocal) {};
+ SimulationSignal(bool isSignalLocal = true) : sig(0), set(0), isLocal(isSignalLocal) {}
//! The signal set by this rank in do_md().
signed char sig;
//! The communicated signal that triggers action, which will be equal for all ranks, once communication has occured.
: x_(x), mdatoms_(mdatoms), t_(time), cr_(cr)
{
copy_mat(box, box_);
- };
+ }
ArrayRef<const RVec> x_; //!< The atomic positions
const t_mdatoms &mdatoms_; //!< Atomic data
gmx_enerdata_t *enerd)
: forceWithVirial_(makeRefFromPointer(forceWithVirial)), enerd_(makeRefFromPointer(enerd))
{
- };
+ }
ForceWithVirial &forceWithVirial_; //!< Container for force and virial
gmx_enerdata_t &enerd_; //!< Structure containing energy data
scalarForce(0),
bExternalPotentialProviderHasBeenRegistered(false)
{
- };
+ }
const t_pull_coord params; /* Pull coordinate parameters */
* \{
*/
+#ifdef __clang__
+#pragma clang diagnostic push
+/* reinterpret_cast is used for SIMD->scalar conversion
+ *
+ * In general using reinterpret_cast for bit_cast is UB but
+ * for intrinsics types it works for all known compilers
+ * and not all compilers produce as good code for memcpy.
+ */
+#pragma clang diagnostic ignored "-Wundefined-reinterpret-cast"
+#endif
+
#if GMX_SIMD_X86_SSE2
# include "impl_x86_sse2/impl_x86_sse2.h"
#elif GMX_SIMD_X86_SSE4_1
# include "impl_none/impl_none.h"
#endif
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
+
// The scalar SIMD-mimicking functions are always included so we can use
// templated functions even without SIMD support.
#include "gromacs/simd/scalar/scalar.h"
}
/*! \brief Begin iterator/value */
- const iterator begin() const { return begin_; };
+ const iterator begin() const { return begin_; }
/*! \brief End iterator/value */
- const iterator end() const { return end_; };
+ const iterator end() const { return end_; }
/*! \brief The number of items in the block */
int size() const
{
public:
FreeVolume();
- virtual ~FreeVolume() {};
+ virtual ~FreeVolume() {}
virtual void initOptions(IOptionsContainer *options,
TrajectoryAnalysisSettings *settings);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018, 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.
// From TextInputStream
virtual bool readLine(std::string *line);
- virtual void close() {};
+ virtual void close() {}
private:
std::string input_;
size_t pos_;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff