Fix random typos

diff --git a/api/legacy/include/gromacs/fileio/confio.h b/api/legacy/include/gromacs/fileio/confio.h
index bd69125d2efc884dc358ae3920cb252e5b05d630..f75b238fd54538c16ea2ba5694c734f8b5976187 100644 (file)
--- a/api/legacy/include/gromacs/fileio/confio.h
+++ b/api/legacy/include/gromacs/fileio/confio.h
@@ -141,7 +141,8 @@ void readConfAndAtoms(const char* infile,
  * \param[in,out] v             Velocities will be stored when *v!=NULL
  * \param[out]    box           Box dimensions
  * \param[in]     requireMasses Require masses to be present, either from tpr or from the mass
- * database \returns if a topology is available
+ *                              database
+ * \returns if a topology is available
  */
 gmx_bool read_tps_conf(const char*        infile,
                        struct t_topology* top,

diff --git a/api/legacy/include/gromacs/math/functions.h b/api/legacy/include/gromacs/math/functions.h
index af557fb6adde0cd37262f2b659a1ca92de888c82..91305221678384c686be2f62d94604376adaa0e1 100644 (file)
--- a/api/legacy/include/gromacs/math/functions.h
+++ b/api/legacy/include/gromacs/math/functions.h
@@ -442,8 +442,8 @@ constexpr int64_t exactDiv(int64_t a, int64_t b)
 
 /*! \brief Round float to int
  *
- * Rounding behavior is round to nearest. Rounding of halfway cases is implemention defined
- * (either halway to even or halway away from zero).
+ * Rounding behavior is round to nearest. Rounding of halfway cases is implementation defined
+ * (either halfway to even or halfway away from zero).
  */
 /* Implementation details: It is assumed that FE_TONEAREST is default and not changed by anyone.
  * Currently the implementation is using rint(f) because 1) on all known HW that is faster than

diff --git a/docs/reference-manual/analysis/radial-distribution-function.rst b/docs/reference-manual/analysis/radial-distribution-function.rst
index 0d106e488ece483418e441d8b949f6f9f9279d9c..38be10c5498dc7c0187b745b2108f53148fb71b0 100644 (file)
--- a/docs/reference-manual/analysis/radial-distribution-function.rst
+++ b/docs/reference-manual/analysis/radial-distribution-function.rst
@@ -37,7 +37,7 @@ averaging is also performed in time. In practice the analysis program
 into spherical slices (from :math:`r` to :math:`r+dr`, see
 :numref:`Fig. %s <fig-rdfex>` A) and makes a histogram in stead of
 the :math:`\delta`-function. An example of the RDF of oxygen-oxygen in
-SPC water \ :ref::ref:`80 <refBerendsen81>` is given in :numref:`Fig. %s <fig-rdf>`
+SPC water \ :ref:`80 <refBerendsen81>` is given in :numref:`Fig. %s <fig-rdf>`
 
 .. _fig-rdf:
 

diff --git a/docs/reference-manual/functions/polarization.rst b/docs/reference-manual/functions/polarization.rst
index c332a3df563d0abd739fa3049bd1fc135df57c9c..ccdd526f5f5c45182b6c499017e9c4b0994c6cc9 100644 (file)
--- a/docs/reference-manual/functions/polarization.rst
+++ b/docs/reference-manual/functions/polarization.rst
@@ -68,7 +68,7 @@ Thole polarization
 
 Based on early work by Thole :ref:`95 <refThole81>`, Roux and coworkers
 have implemented potentials for molecules like
-ethanol \ :ref:`96 <refLamoureux2003a>`\ :ref:`98 <refNoskov2005a>`.
+ethanol \ :ref:`96 <refLamoureux2003a>`, :ref:`98 <refNoskov2005a>`.
 Within such molecules, there are intra-molecular interactions between
 shell particles, however these must be screened because full Coulomb
 would be too strong. The potential between two shell particles :math:`i`

diff --git a/src/gromacs/applied_forces/awh/biasstate.cpp b/src/gromacs/applied_forces/awh/biasstate.cpp
index 7c8b1d0e2bfa5e1affef6e3cd8299ae39211d4b4..08fbd29a92d935581da766e491b2900dd9b7576d 100644 (file)
--- a/src/gromacs/applied_forces/awh/biasstate.cpp
+++ b/src/gromacs/applied_forces/awh/biasstate.cpp
@@ -690,8 +690,10 @@ void mergeSharedUpdateLists(std::vector<int>*  updateList,
  * \param[in] grid              The AWH bias.
  * \param[in] points            The point state.
  * \param[in] originUpdatelist  The origin of the rectangular region that has been sampled since
- * last update. \param[in] endUpdatelist     The end of the rectangular that has been sampled since
- * last update. \param[in,out] updateList    Local update list to set (assumed >= npoints long).
+ *                              last update.
+ * \param[in] endUpdatelist     The end of the rectangular that has been sampled since
+ *                              last update.
+ * \param[in,out] updateList    Local update list to set (assumed >= npoints long).
  */
 void makeLocalUpdateList(const BiasGrid&            grid,
                          ArrayRef<const PointState> points,

diff --git a/src/gromacs/applied_forces/awh/correlationtensor.h b/src/gromacs/applied_forces/awh/correlationtensor.h
index 9da3928dc9ef0fcfaa985c6e445393017cadf1c9..96f680428d80d288dee41e48795ffa80b9a71373 100644 (file)
--- a/src/gromacs/applied_forces/awh/correlationtensor.h
+++ b/src/gromacs/applied_forces/awh/correlationtensor.h
@@ -1,7 +1,8 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
+ * Copyright (c) 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.
@@ -251,7 +252,8 @@ public:
      * \param[in] weight               The weight of the data.
      * \param[in] data                 One data point for each grid dimension.
      * \param[in] blockLengthInWeight  If true, a block is measured in probability weight, otherwise
-     * in time. \param[in] t                    The simulation time.
+     *                                 in time.
+     * \param[in] t                    The simulation time.
      */
     void addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t);
 

diff --git a/src/gromacs/applied_forces/awh/histogramsize.h b/src/gromacs/applied_forces/awh/histogramsize.h
index f0c5725d33026d3587a347065b8b06d3bdc7bb3b..7861e794bcd4a127b78d353af6dc18da0bc4e1aa 100644 (file)
--- a/src/gromacs/applied_forces/awh/histogramsize.h
+++ b/src/gromacs/applied_forces/awh/histogramsize.h
@@ -98,7 +98,8 @@ private:
      * \param[in]     params             The bias parameters.
      * \param[in]     t                  Time.
      * \param[in]     detectedCovering   True if we detected that the sampling interval has been
-     * sufficiently covered. \param[in,out] weightsumCovering  The weight sum for checking covering.
+     *                                   sufficiently covered.
+     * \param[in,out] weightsumCovering  The weight sum for checking covering.
      * \param[in,out] fplog              Log file.
      * \returns the new histogram size.
      */

diff --git a/src/gromacs/domdec/gpuhaloexchange_impl.cu b/src/gromacs/domdec/gpuhaloexchange_impl.cu
index 4a62a895324c1a98ea742cf109137e22a22f192c..f8950c13f6093d28dc4bbfe6bf1ac40814d61a43 100644 (file)
--- a/src/gromacs/domdec/gpuhaloexchange_impl.cu
+++ b/src/gromacs/domdec/gpuhaloexchange_impl.cu
@@ -100,9 +100,11 @@ __global__ void packSendBufKernel(float3* __restrict__ dataPacked,
 }
 
 /*! \brief unpack non-local force data buffer on the GPU using pre-populated "map" containing index
- * information \param[out] data        full array of force values \param[in]  dataPacked  packed
- * array of force values to be transferred \param[in]  map         array of indices defining mapping
- * from full to packed array \param[in]  mapSize     number of elements in map array
+ * information
+ * \param[out] data        full array of force values
+ * \param[in]  dataPacked  packed array of force values to be transferred
+ * \param[in]  map         array of indices defining mapping from full to packed array
+ * \param[in]  mapSize     number of elements in map array
  */
 template<bool accumulate>
 __global__ void unpackRecvBufKernel(float3* __restrict__ data,
@@ -140,7 +142,7 @@ void GpuHaloExchange::Impl::reinitHalo(float3* d_coordinatesBuffer, float3* d_fo
     const gmx_domdec_comm_dim_t& cd   = comm.cd[dimIndex_];
     const gmx_domdec_ind_t&      ind  = cd.ind[pulse_];
 
-    numHomeAtoms_ = comm.atomRanges.numHomeAtoms(); // offset for data recieved by this rank
+    numHomeAtoms_ = comm.atomRanges.numHomeAtoms(); // offset for data received by this rank
 
     // Determine receive offset for the dimension index and pulse of this halo exchange object
     int numZoneTemp   = 1;

diff --git a/src/gromacs/ewald/pme_gpu_types_host_impl.h b/src/gromacs/ewald/pme_gpu_types_host_impl.h
index e1f7f17b90f5bde2dcd32a25181328e520d9e144..69121ab07a81bb0e0ffc682ea69b73249ffbcaf3 100644 (file)
--- a/src/gromacs/ewald/pme_gpu_types_host_impl.h
+++ b/src/gromacs/ewald/pme_gpu_types_host_impl.h
@@ -107,7 +107,7 @@ struct PmeGpuSpecific
     GpuEventSynchronizer syncSpreadGridD2H;
 
     /* Settings which are set at the start of the run */
-    /*! \brief A boolean which tells whether the complex and real grids for cu/clFFT are different or same. Currenty true. */
+    /*! \brief A boolean which tells whether the complex and real grids for cu/clFFT are different or same. Currently true. */
     bool performOutOfPlaceFFT = false;
     /*! \brief A boolean which tells if the GPU timing events are enabled.
      *  False by default, can be enabled by setting the environment variable GMX_ENABLE_GPU_TIMING.

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index 4c9fbf8d93d4ee2683d65002bad612ccbe9a9be5..899b5008c2becadbe5008ba31f7652865f5c7fa8 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -1577,7 +1577,7 @@ static bool haveDecoupledModeInMol(const gmx_moltype_t&           molt,
 
 /*! \brief Checks if the Verlet buffer and constraint accuracy is sufficient for decoupled dynamic modes.
  *
- * When decoupled modes are present and the accuray in insufficient,
+ * When decoupled modes are present and the accuracy in insufficient,
  * this routine issues a warning if the accuracy is insufficient.
  */
 static void checkDecoupledModeAccuracy(const gmx_mtop_t* mtop, const t_inputrec* ir, warninp* wi)

diff --git a/src/gromacs/gpu_utils/cudautils.cuh b/src/gromacs/gpu_utils/cudautils.cuh
index 0c4507d809dfcf69b1ef7c1e352e4e92fe2ae0d4..f1f1c57cfcdcaeea7f22b8c588db8a07457200b9 100644 (file)
--- a/src/gromacs/gpu_utils/cudautils.cuh
+++ b/src/gromacs/gpu_utils/cudautils.cuh
@@ -272,7 +272,8 @@ std::array<void*, sizeof...(Args)> prepareGpuKernelArguments(KernelPtr kernel,
  * \param[in] deviceStream    GPU stream to launch kernel in
  * \param[in] kernelName      Human readable kernel description, for error handling only
  * \param[in] kernelArgs      Array of the pointers to the kernel arguments, prepared by
- * prepareGpuKernelArguments() \throws gmx::InternalError on kernel launch failure
+ *                            prepareGpuKernelArguments()
+ * \throws gmx::InternalError on kernel launch failure
  */
 template<typename... Args>
 void launchGpuKernel(void (*kernel)(Args...),

diff --git a/src/gromacs/gpu_utils/gpuregiontimer.h b/src/gromacs/gpu_utils/gpuregiontimer.h
index f0860b164d9cbdbe61aade8bf3d5e127c5ed08cc..a6614c1bba505ccd34cd3c907c3d20f3815e20a5 100644 (file)
--- a/src/gromacs/gpu_utils/gpuregiontimer.h
+++ b/src/gromacs/gpu_utils/gpuregiontimer.h
@@ -1,7 +1,8 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019,2020 by the GROMACS development team.
+ * 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.
@@ -120,7 +121,8 @@ public:
      * Accumulates the last timespan of all the events used into the total duration,
      * and resets the internal timer state.
      * To be called after closeTimingRegion() and the command stream of the event having been
-     * synchronized. \returns The last timespan (in milliseconds).
+     * synchronized.
+     * \returns The last timespan (in milliseconds).
      */
     double getLastRangeTime()
     {

diff --git a/src/gromacs/gpu_utils/ocl_compiler.cpp b/src/gromacs/gpu_utils/ocl_compiler.cpp
index 98b02df93a4163a12d27d855c219e0627e7c6dc3..5f826e5e0ab334dffe87b54d5a26e7ddb4b2ca96 100644 (file)
--- a/src/gromacs/gpu_utils/ocl_compiler.cpp
+++ b/src/gromacs/gpu_utils/ocl_compiler.cpp
@@ -80,7 +80,7 @@ static bool useBuildCache = getenv("GMX_OCL_GENCACHE") != nullptr;
 
 /*! \brief Handles writing the OpenCL JIT compilation log to \c fplog.
  *
- * If \c fplog is non-null and either the GMX_OCL_DUMP_LOG environment
+ * If \c fplog is non-null and either the \c GMX_OCL_DUMP_LOG environment
  * variable is set or the compilation failed, then the OpenCL
  * compilation log is written.
  *
@@ -89,7 +89,8 @@ static bool useBuildCache = getenv("GMX_OCL_GENCACHE") != nullptr;
  * \param deviceId            Id of the device for which compilation took place
  * \param kernelFilename      File name containing the kernel
  * \param preprocessorOptions String containing the preprocessor command-line options used for the
- * build \param buildFailed         Whether the OpenCL build succeeded
+ *                            build
+ * \param buildFailed         Whether the OpenCL build succeeded
  *
  * \throws std::bad_alloc if out of memory */
 static void writeOclBuildLog(FILE*              fplog,

diff --git a/src/gromacs/mdlib/calc_verletbuf.h b/src/gromacs/mdlib/calc_verletbuf.h
index a013cf2bf9aef0bf49cd541145ebf763b9d23331..59b6be9ef338dde3f84421c3fe1fd3eb2d96ca1e 100644 (file)
--- a/src/gromacs/mdlib/calc_verletbuf.h
+++ b/src/gromacs/mdlib/calc_verletbuf.h
@@ -2,7 +2,7 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, 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.
@@ -112,7 +112,8 @@ VerletbufListSetup verletbufGetSafeListSetup(ListSetupType listType);
  * \param[in] inputrec      The input record
  * \param[in] nstlist       The pair list update frequency in steps (is not taken from \p inputrec)
  * \param[in] listLifetime  The lifetime of the pair-list, usually nstlist-1, but could be different
- * for dynamic pruning \param[in] referenceTemperature  The reference temperature for the ensemble
+ *                          for dynamic pruning
+ * \param[in] referenceTemperature  The reference temperature for the ensemble
  * \param[in] listSetup     The pair-list setup
  * \returns The computed pair-list radius including buffer
  */

diff --git a/src/gromacs/mdlib/coupling.h b/src/gromacs/mdlib/coupling.h
index 4e8857c3b0310cdd6f16637b12532e7622b49484..65b5fe74ff88e7c27051f720e29e02ba9a8015a3 100644 (file)
--- a/src/gromacs/mdlib/coupling.h
+++ b/src/gromacs/mdlib/coupling.h
@@ -266,11 +266,15 @@ void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir);
  *       the default code path.
  *
  * \param[in] kk     present value of the kinetic energy of the atoms to be thermalized (in
- * arbitrary units) \param[in] sigma  target average value of the kinetic energy (ndeg k_b T/2)  (in
- * the same units as kk) \param[in] ndeg   number of degrees of freedom of the atoms to be
- * thermalized \param[in] taut   relaxation time of the thermostat, in units of 'how often this
- * routine is called' \param[in] step   the time step this routine is called on \param[in] seed the
- * random number generator seed \return  the new kinetic energy
+ *                   arbitrary units)
+ * \param[in] sigma  target average value of the kinetic energy (ndeg k_b T/2)  (in
+ *                   the same units as kk)
+ * \param[in] ndeg   number of degrees of freedom of the atoms to be thermalized
+ * \param[in] taut   relaxation time of the thermostat, in units of 'how often this
+ *                   routine is called'
+ * \param[in] step   the time step this routine is called on
+ * \param[in] seed   the random number generator seed
+ * \return  the new kinetic energy
  */
 real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut, int64_t step, int64_t seed);
 

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index 54915133af947b5c076914feaba052877b960c28..5fad2c1d3f4ba3440734bc9a44dd752d69dbb042 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -527,7 +527,8 @@ static real averageKineticEnergyEstimate(const t_grpopts& groupOptions)
  *
  * \param[in] step      The step number, used for checking and printing
  * \param[in] enerd     The energy data; the non-bonded group energies need to be added to
- * enerd.term[F_EPOT] before calling this routine \param[in] inputrec  The input record
+ *                      \c enerd.term[F_EPOT] before calling this routine
+ * \param[in] inputrec  The input record
  */
 static void checkPotentialEnergyValidity(int64_t step, const gmx_enerdata_t& enerd, const t_inputrec& inputrec)
 {

diff --git a/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp b/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp
index 84f26a198c85dadc1f9dfb1f72112eb132652516..c45ec35cc545e570579743940cd625fb040638a2 100644 (file)
--- a/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp
+++ b/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp
@@ -206,7 +206,7 @@ std::tuple<int, int> StatePropagatorDataGpu::Impl::getAtomRangesFromAtomLocality
                                "be All, Local or NonLocal.");
     }
     GMX_ASSERT(atomsStartAt >= 0,
-               "The first elemtnt to copy has negative index. Probably, the GPU propagator state "
+               "The first element to copy has negative index. Probably, the GPU propagator state "
                "was not initialized.");
     GMX_ASSERT(numAtomsToCopy >= 0,
                "Number of atoms to copy is negative. Probably, the GPU propagator state was not "

diff --git a/src/gromacs/nbnxm/nbnxm.h b/src/gromacs/nbnxm/nbnxm.h
index b438c9bc332babd3581949d1b6909c35c042a18f..51b7a4a853043828eff01431fdbf5373dbd7c14f 100644 (file)
--- a/src/gromacs/nbnxm/nbnxm.h
+++ b/src/gromacs/nbnxm/nbnxm.h
@@ -326,7 +326,8 @@ public:
      * The API function for the transformation of the coordinates from one layout to another.
      *
      * \param[in] locality     Whether coordinates for local or non-local atoms should be
-     * transformed. \param[in] coordinates  Coordinates in plain rvec format to be transformed.
+     *                         transformed.
+     * \param[in] coordinates  Coordinates in plain rvec format to be transformed.
      */
     void convertCoordinates(gmx::AtomLocality locality, gmx::ArrayRef<const gmx::RVec> coordinates);
 
@@ -373,23 +374,23 @@ public:
 
     //! Executes the non-bonded free-energy kernels, local + non-local, always runs on the CPU
     void dispatchFreeEnergyKernels(const gmx::ArrayRefWithPadding<const gmx::RVec>& coords,
-                                   gmx::ForceWithShiftForces*                forceWithShiftForces,
-                                   bool                                      useSimd,
-                                   int                                       ntype,
-                                   real                                      rlist,
-                                   const interaction_const_t&                ic,
-                                   gmx::ArrayRef<const gmx::RVec>            shiftvec,
-                                   gmx::ArrayRef<const real>                 nbfp,
-                                   gmx::ArrayRef<const real>                 nbfp_grid,
-                                   gmx::ArrayRef<const real>                 chargeA,
-                                   gmx::ArrayRef<const real>                 chargeB,
-                                   gmx::ArrayRef<const int>                  typeA,
-                                   gmx::ArrayRef<const int>                  typeB,
-                                   t_lambda*                                 fepvals,
-                                   gmx::ArrayRef<const real>                 lambda,
-                                   gmx_enerdata_t*                           enerd,
-                                   const gmx::StepWorkload&                  stepWork,
-                                   t_nrnb*                                   nrnb);
+                                   gmx::ForceWithShiftForces*     forceWithShiftForces,
+                                   bool                           useSimd,
+                                   int                            ntype,
+                                   real                           rlist,
+                                   const interaction_const_t&     ic,
+                                   gmx::ArrayRef<const gmx::RVec> shiftvec,
+                                   gmx::ArrayRef<const real>      nbfp,
+                                   gmx::ArrayRef<const real>      nbfp_grid,
+                                   gmx::ArrayRef<const real>      chargeA,
+                                   gmx::ArrayRef<const real>      chargeB,
+                                   gmx::ArrayRef<const int>       typeA,
+                                   gmx::ArrayRef<const int>       typeB,
+                                   t_lambda*                      fepvals,
+                                   gmx::ArrayRef<const real>      lambda,
+                                   gmx_enerdata_t*                enerd,
+                                   const gmx::StepWorkload&       stepWork,
+                                   t_nrnb*                        nrnb);
 
     /*! \brief Add the forces stored in nbat to f, zeros the forces in nbat
      * \param [in] locality         Local or non-local

diff --git a/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp b/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp
index 3bde29600811dddcd8e7ad6ef88b37553bac18b5..b4b28c06526441dbc7f2b5e162a4a1d56bd4bb13 100644 (file)
--- a/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp
+++ b/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp
@@ -654,7 +654,8 @@ void gpu_launch_kernel(NbnxmGpu* nb, const gmx::StepWorkload& stepWork, const Nb
  *  for OpenCL local memory.
  *
  * \param[in] num_threads_z cj4 concurrency equal to the number of threads/work items in the 3-rd
- * dimension. \returns   the amount of local memory in bytes required by the pruning kernel
+ * dimension.
+ * \returns   the amount of local memory in bytes required by the pruning kernel
  */
 static inline int calc_shmem_required_prune(const int num_threads_z)
 {

diff --git a/src/gromacs/nbnxm/pairlist.cpp b/src/gromacs/nbnxm/pairlist.cpp
index 09338ad44e4f63231e40893a282ef2d9f318ea45..cd44bc180a691aa563781b218f622d569814150a 100644 (file)
--- a/src/gromacs/nbnxm/pairlist.cpp
+++ b/src/gromacs/nbnxm/pairlist.cpp
@@ -121,7 +121,8 @@ static constexpr int jClusterSize()
  *
  * \tparam    jClusterSize      The number of atoms in a j-cluster
  * \tparam    jSubClusterIndex  The j-sub-cluster index (0/1), used when size(j-cluster) <
- * size(i-cluster) \param[in] ci                The i-cluster index
+ *                              size(i-cluster)
+ * \param[in] ci                The i-cluster index
  */
 template<int jClusterSize, int jSubClusterIndex>
 static inline int cjFromCi(int ci)
@@ -158,7 +159,8 @@ static inline int cjFromCi(int ci)
  *
  * \tparam    layout            The pair-list layout
  * \tparam    jSubClusterIndex  The j-sub-cluster index (0/1), used when size(j-cluster) <
- * size(i-cluster) \param[in] ci                The i-cluster index
+ *                              size(i-cluster)
+ * \param[in] ci                The i-cluster index
  */
 template<NbnxnLayout layout, int jSubClusterIndex>
 static inline int cjFromCi(int ci)

diff --git a/src/gromacs/pulling/transformationcoordinate.h b/src/gromacs/pulling/transformationcoordinate.h
index c9b6c50119b569ac20a44231cdbc8059dd79d815..b8caf90cb86d6697c5fb25d1499f82aa3507e3bb 100644 (file)
--- a/src/gromacs/pulling/transformationcoordinate.h
+++ b/src/gromacs/pulling/transformationcoordinate.h
@@ -59,7 +59,8 @@ class ArrayRef;
  * This requires the values of the pull coordinates of lower indices to be set
  * \param[in] coord  The (transformation) coordinate to compute the value for
  * \param[in] variableCoords  Pull coordinates used as variables, entries 0 to coord->coordIndex
- * will be used \returns Transformation value for pull coordinate.
+ *                            will be used
+ * \returns Transformation value for pull coordinate.
  */
 double getTransformationPullCoordinateValue(pull_coord_work_t*                coord,
                                             ArrayRef<const pull_coord_work_t> variableCoords);

diff --git a/src/gromacs/taskassignment/decidegpuusage.h b/src/gromacs/taskassignment/decidegpuusage.h
index 76b6f40042a0fec1ecd7bcec55482aec9d3ac72d..693804efd1c3fb1d79c98a1b1817af3df109aca6 100644 (file)
--- a/src/gromacs/taskassignment/decidegpuusage.h
+++ b/src/gromacs/taskassignment/decidegpuusage.h
@@ -243,7 +243,8 @@ bool decideWhetherToUseGpusForPme(bool                    useGpuForNonbonded,
  *
  * \param[in]  useGpuForPme              PME task assignment, true if PME task is mapped to the GPU.
  * \param[in]  pmeFftTarget              The user's choice for -pmefft for where to assign the FFT
- * work of the PME task. \param[in]  inputrec                  The user input record
+ *                                       work of the PME task.
+ * \param[in]  inputrec                  The user input record
  * */
 PmeRunMode determinePmeRunMode(bool useGpuForPme, const TaskTarget& pmeFftTarget, const t_inputrec& inputrec);