#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2021, 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.
exit 1
fi
-# We cannot detect wether it is a C++ or C header. Should be fine to always use C++
+# We cannot detect whether it is a C++ or C header. Should be fine to always use C++
if [ "${filename##*.}" == "h" ]; then
cmd="$cmd -x c++"
fi
/*
* These routines handle reading and writing of preprocessed
* topology files in any of the following formats:
- * TPR : topology in XDR format, portable accross platforms
+ * TPR : topology in XDR format, portable across platforms
*
* Files are written in the precision with which the source are compiled,
* but double and single precision can be read by either.
Any ``CMAKE_BUILD_TYPE`` which enables asserts (e.g. ASAN) works. Such a configured build will
run both the compiler as well as clang-tidy when building. The name of the clang-tidy executable is set with
``-DCLANG_TIDY=...``, and the full path to it can be set with ``-DCLANG_TIDY_EXE=...``.
- To apply the automatic fixes to the issue identified clang-tidy should be run seperately (running clang-tidy
+ To apply the automatic fixes to the issue identified clang-tidy should be run separately (running clang-tidy
with ``-fix-errors`` as part of the build can corrupt header files). To fix a specific file run
``clang-tidy -fix-errors -header-filter '.*' {file}``, to fix all files in parallel
``run-clang-tidy.py -fix -header-filter '.*' '(?<!/selection/parser\.cpp|selection/scanner\.cpp)$'``,
Currently unsupported.
When user tables are used for electrostatics and/or VdW, here one
- can give pairs of energy groups for which seperate user tables
+ can give pairs of energy groups for which separate user tables
should be used. The two energy groups will be appended to the table
file name, in order of their definition in :mdp:`energygrps`,
- seperated by underscores. For example, if ``energygrps = Na Cl
+ separated by underscores. For example, if ``energygrps = Na Cl
Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
normal ``table.xvg`` which will be used for all other energy group
clLengths[1] = fftPlan->length[1];
//NON_SQUARE_KERNEL_ORDER currKernelOrder;
- // controling the transpose and swap kernel order
+ // controlling the transpose and swap kernel order
// if leading dim is larger than the other dim it makes sense to swap and transpose
if (clLengths[0] > clLengths[1])
{
int memory; /**< amount of memory used in Mbyte. XXX:? */
int runtype; /**< flag indicating the calculation method. */
int scftype; /**< SCF type: RHF, UHF, ROHF, GVB or MCSCF wfn. */
- int status; /**< indicates wether SCF and geometry optimization
+ int status; /**< indicates whether SCF and geometry optimization
* have converged properly. */
int num_electrons; /**< number of electrons. XXX: can be fractional in some DFT codes */
int totalcharge; /**< total charge of system. XXX: can be fractional in some DFT codes */
* \tparam[in] atomsPerBlock Number of atoms processed by a block - should be accounted for
* in the sizes of the shared memory arrays.
* \tparam[in] atomsPerWarp Number of atoms processed by a warp
- * \tparam[in] writeSmDtheta Bool controling if the theta derivative should be written to shared memory. Enables calculation of dtheta if set.
+ * \tparam[in] writeSmDtheta Bool controlling if the theta derivative should be written to shared memory. Enables calculation of dtheta if set.
* \tparam[in] writeGlobal A boolean which tells if the theta values and gridlines should be written to global memory. Enables calculation of dtheta if set.
* \param[in] kernelParams Input PME CUDA data in constant memory.
* \param[in] atomIndexOffset Starting atom index for the execution block w.r.t. global memory.
std::vector<t_atom> atom;
//! Chargegroup number.
int cgnr = NOTSET;
- //! Type of attachement.
+ //! Type of attachment.
int tp = 0;
//! Number of control atoms.
int nctl = 0;
IncompatibleClusterSize = 3,
//! There are known issues with OpenCL on NVIDIA Volta and newer.
IncompatibleNvidiaVolta = 4,
- /* \brief The device originates from non-recommended SYCL backend.
+ /*! \brief The device originates from non-recommended SYCL backend.
* The device might work by itself, but to simplify device allocation, it is marked as incompatible.
* */
NotPreferredBackend = 5,
int numAtomsForce = 0;
/* There are two different ways to distribute the bonded force calculation
- * over the threads. We dedice which to use based on the number of threads.
+ * over the threads. We decide which to use based on the number of threads.
*/
//! Maximum thread count for uniform distribution of bondeds over threads
int max_nthread_uniform = 0;
}
}
-/*! \brief Combines MTS level0 and level1 force buffes into a full and MTS-combined force buffer.
+/*! \brief Combines MTS level0 and level1 force buffers into a full and MTS-combined force buffer.
*
* \param[in] numAtoms The number of atoms to combine forces for
* \param[in,out] forceMtsLevel0 Input: F_level0, output: F_level0 + F_level1
// TODO Argument parsing can't handle std::string. We should
// fix that by changing the parsing, once more of the roles of
// handling, validating and implementing defaults for user
- // command-line options have been seperated.
+ // command-line options have been separated.
hw_opt.devicesSelectedByUser = devicesSelectedByUser;
hw_opt.userGpuTaskAssignment = userGpuTaskAssignment;
}
// The GPU update is decided here because we need to know whether the constraints or
- // SETTLEs can span accross the domain borders (i.e. whether or not update groups are
+ // SETTLEs can span across the domain borders (i.e. whether or not update groups are
// defined). This is only known after DD is initialized, hence decision on using GPU
// update is done so late.
try
// while clang requires it to avoid -Wunused
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wattributes"
- //! Wether we use forceMtsCombined_
+ //! Whether we use forceMtsCombined_
gmx_used_in_debug bool useForceMtsCombined_;
#pragma GCC diagnostic pop
};
PaddedHostVector<RVec> forceMtsCombined_;
//! The view to the force buffer
ForceBuffersView view_;
- //! Wether we use forceMtsCombined_
+ //! Whether we use forceMtsCombined_
bool useForceMtsCombined_;
};
public:
//! Whether to compute nonbonded pair interactions
bool computeNonbonded = false;
- //! Wether nonbonded pair forces are to be computed at slow MTS steps only
+ //! Whether nonbonded pair forces are to be computed at slow MTS steps only
bool computeNonbondedAtMtsLevel1 = false;
//! Whether total dipole needs to be computed
bool computeMuTot = false;
const DeviceStream* localStream_;
//! GPU NBNXM non-local stream.
const DeviceStream* nonLocalStream_;
- //! GPU Update-constreaints stream.
+ //! GPU Update-constraints stream.
const DeviceStream* updateStream_;
// Streams to use for coordinates H2D and D2H copies (one event for each atom locality)
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 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.
#
# Many C kernel files, each defining a single kernel function. These
# functions can take a noticeable time to compile, and should tend
-# to be in seperate files to take advantage of make-time
+# to be in separate files to take advantage of make-time
# parallelism.
#
# This script should be run from the directory in which it is
double x_r0;
/* This function is called using either v_ewald_lr or v_lj_ewald_lr as a function argument
- * depending on wether we should create electrostatic or Lennard-Jones Ewald tables.
+ * depending on whether we should create electrostatic or Lennard-Jones Ewald tables.
*/
if (numPoints < 2)
// is busy, for which we currently only check PME or Ewald.
// (It would be better to dynamically assign bondeds based on timings)
// Note that here we assume that the auto setting of PME ranks will not
- // choose seperate PME ranks when nonBonded are assigned to the GPU.
+ // choose separate PME ranks when nonBonded are assigned to the GPU.
bool usingOurCpuForPmeOrEwald =
(EVDW_PME(inputrec.vdwtype)
|| (EEL_PME_EWALD(inputrec.coulombtype) && !useGpuForPme && numPmeRanksPerSimulation <= 0));
FILE* test = fopen(fname.c_str(), "r");
if (test == nullptr)
{
-/*Windows doesn't allow fopen of directory - so we need to check this seperately */
+/*Windows doesn't allow fopen of directory - so we need to check this separately */
#if GMX_NATIVE_WINDOWS
DWORD attr = GetFileAttributes(fname.c_str());
return (attr != INVALID_FILE_ATTRIBUTES) && (attr & FILE_ATTRIBUTE_DIRECTORY);
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, 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.
* \p input, each match of \p from is replaced with \p to, and the search for
* the next match begins after the end of the previous match.
*
- * Compexity is O(N), where N is length of output.
+ * Complexity is O(N), where N is length of output.
*
* \see replaceAllWords()
*/
return std::forward<Function>(f)();
}
-/** \internal \brief Helper function to select appropriate template based on runtime values.
+/*! \internal \brief
+ * Helper function to select appropriate template based on runtime values.
*
* Can use enums or booleans for template parameters.
* These enums must have a member \c Count indicating the total number of valid values.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff