From: M. Eric Irrgang Date: Sat, 2 Nov 2019 11:28:55 +0000 (+0300) Subject: Fix typos. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=2d0907b178d4de0c2f10b13b1f5fa47a09e30ff4;p=alexxy%2Fgromacs.git Fix typos. A search for "the the" revealed a lot of easy-to-fix typos. Change-Id: I42ed8f6bd7a5cf2f3d15117c8045cf3af4313b18 --- diff --git a/docs/gmxapi/userguide/install.rst b/docs/gmxapi/userguide/install.rst index 1af1ce1d0f..1d3b3f1bd4 100644 --- a/docs/gmxapi/userguide/install.rst +++ b/docs/gmxapi/userguide/install.rst @@ -421,7 +421,7 @@ determined by the local environment or by additional arguments to ``setup.py``. `creating a source distribution `_ -Package maintainers may update the the online respository by uploading a freshly +Package maintainers may update the online respository by uploading a freshly built ``sdist`` with ``python -m twine upload dist/*`` .. _gmxapi_package_documentation: diff --git a/docs/reference-manual/algorithms/molecular-dynamics.rst b/docs/reference-manual/algorithms/molecular-dynamics.rst index ab865fffd1..04ef9295ee 100644 --- a/docs/reference-manual/algorithms/molecular-dynamics.rst +++ b/docs/reference-manual/algorithms/molecular-dynamics.rst @@ -760,7 +760,7 @@ energies using the half-step-averaged kinetic energies ( of small step size than will the full-step kinetic energy (using :mdp-value:`integrator=md-vv`). For NVE simulations, this difference is usually not significant, since the positions and velocities of the particles are -still identical; it makes a difference in the way the the temperature of +still identical; it makes a difference in the way the temperature of the simulations are **interpreted**, but **not** in the trajectories that are produced. Although the kinetic energy is more accurate with the half-step-averaged method, meaning that it changes less as the timestep @@ -1523,7 +1523,7 @@ Using the Trotter decomposition, we get :label: eqnMTTKthermandbarTrotterdecomp The action of :math:`\exp\left(iL_1 {\Delta t}\right)` comes from the -solution of the the differential equation +solution of the differential equation :math:`\dot{{{\mathbf{r}}}}_i = {{\mathbf{v}}}_i + {v_{\epsilon}}{{\mathbf{r}}}_i` with :math:`{{\mathbf{v}}}_i = {{\mathbf{p}}}_i/m_i` diff --git a/docs/reference-manual/functions/bonded-interactions.rst b/docs/reference-manual/functions/bonded-interactions.rst index fcffc66e78..e8b9cffd1e 100644 --- a/docs/reference-manual/functions/bonded-interactions.rst +++ b/docs/reference-manual/functions/bonded-interactions.rst @@ -597,7 +597,7 @@ torsion angle at only one minimum value. In this case, the factor cannot have maxima both at :math:`-\phi_0` and :math:`+\phi_0` maxima, but only one of them. For this reason, all the dihedral angles of the starting configuration should have their values in the desired angles -interval and the the equilibrium :math:`\phi_0` value should not be too +interval and the equilibrium :math:`\phi_0` value should not be too close to the interval limits (as for the restricted bending potential, described in :ref:`ReB`, at least :math:`10^{\circ}` difference is recommended). diff --git a/docs/reference-manual/functions/free-energy-interactions.rst b/docs/reference-manual/functions/free-energy-interactions.rst index 1d48ce7c0d..2f29ceac05 100644 --- a/docs/reference-manual/functions/free-energy-interactions.rst +++ b/docs/reference-manual/functions/free-energy-interactions.rst @@ -210,7 +210,7 @@ Soft-core interactions :math:`C_6^A=C_{12}^A=C_6^B=C_{12}^B=1`. In a free-energy calculation where particles grow out of nothing, or -particles disappear, using the the simple linear interpolation of the +particles disappear, using the simple linear interpolation of the Lennard-Jones and Coulomb potentials as described in :eq:`Equations %s ` and :eq:`%s ` may lead to poor convergence. When the particles have nearly disappeared, or are close to diff --git a/docs/reference-manual/functions/interaction-methods.rst b/docs/reference-manual/functions/interaction-methods.rst index 2f60cbbc01..c6b219b4e5 100644 --- a/docs/reference-manual/functions/interaction-methods.rst +++ b/docs/reference-manual/functions/interaction-methods.rst @@ -213,7 +213,7 @@ can be constructed from “particles” that are simpler virtual sites. { | \mathbf{r}_{ij} | } :label: eqnvsite2fdatom -- In this case the virtual site is on the line through the the other two +- In this case the virtual site is on the line through the other two particles at a distance of :math:`|a|` from :math:`i`. The force on particles :math:`i` and :math:`j` due to the force on the virtual site can be computed as: diff --git a/docs/reference-manual/special/awh.rst b/docs/reference-manual/special/awh.rst index fb17a1d606..1a76aa321b 100644 --- a/docs/reference-manual/special/awh.rst +++ b/docs/reference-manual/special/awh.rst @@ -219,7 +219,7 @@ samples as prescribed by :eq:`Eq. %s `, entails a too rapid decay of the free energy update size. This motivates splitting the simulation into an *initial stage* where the weight histogram grows according to a more restrictive and robust protocol, and -a *final stage* where the the weight histogram grows linearly at the +a *final stage* where the weight histogram grows linearly at the sampling rate (:eq:`Eq. %s `). The AWH initial stage takes inspiration from the well-known Wang-Landau algorithm \ :ref:`138 `, although there are differences in the details. diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst index 38f47562d5..673d0a528e 100644 --- a/docs/user-guide/mdp-options.rst +++ b/docs/user-guide/mdp-options.rst @@ -64,7 +64,7 @@ Run control of motion. For constant NVE simulations started from corresponding points in the same trajectory, the trajectories are analytically, but not binary, identical to the - :mdp-value:`integrator=md` leap-frog integrator. The the kinetic + :mdp-value:`integrator=md` leap-frog integrator. The kinetic energy, which is determined from the whole step velocities and is therefore slightly too high. The advantage of this integrator is more accurate, reversible Nose-Hoover and Parrinello-Rahman diff --git a/python_packaging/src/external/pybind/include/pybind11/detail/common.h b/python_packaging/src/external/pybind/include/pybind11/detail/common.h index 6da5470608..579e2a5fa3 100644 --- a/python_packaging/src/external/pybind/include/pybind11/detail/common.h +++ b/python_packaging/src/external/pybind/include/pybind11/detail/common.h @@ -341,7 +341,7 @@ enum class return_value_policy : uint8_t { object without taking ownership similar to the above return_value_policy::reference policy. In contrast to that policy, the function or property’s implicit this argument (called the parent) is - considered to be the the owner of the return value (the child). + considered to be the owner of the return value (the child). pybind11 then couples the lifetime of the parent to the child via a reference relationship that ensures that the parent cannot be garbage collected while Python is still using the child. More advanced diff --git a/python_packaging/src/gmxapi/operation.py b/python_packaging/src/gmxapi/operation.py index f4f41974e6..9468136e20 100644 --- a/python_packaging/src/gmxapi/operation.py +++ b/python_packaging/src/gmxapi/operation.py @@ -3019,7 +3019,7 @@ class SubgraphNodeBuilder(NodeBuilder): In the SubgraphContext, these handles cannot represent uniquely identifiable results. They are placeholders for relative positions in graphs that are - not defined until the the subgraph is being executed. + not defined until the subgraph is being executed. Such references should be tracked and invalidated when exiting the subgraph context. Within the subgraph context, they are used to establish diff --git a/src/gromacs/awh/bias.h b/src/gromacs/awh/bias.h index 27ce32699e..43ab69aec5 100644 --- a/src/gromacs/awh/bias.h +++ b/src/gromacs/awh/bias.h @@ -98,7 +98,7 @@ class PointState; * collected at a constant bias potential, between updates. * * The bias keeps a grid with coordinate points that organizes spatial - * information about the coordinate. The grid has the the same geometry + * information about the coordinate. The grid has the same geometry * as the coordinate, i.e. they have the same dimensionality and periodicity * (if any). The number of points in the grid sets the resolution of * the collected data and its extent defines the sampling region of interest. diff --git a/src/gromacs/awh/biasparams.h b/src/gromacs/awh/biasparams.h index d8eb69c317..e3b4bd137b 100644 --- a/src/gromacs/awh/biasparams.h +++ b/src/gromacs/awh/biasparams.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2015,2016,2017,2018,2019, 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. @@ -104,7 +104,7 @@ class BiasParams } /*! \brief - * Returns the the radius that needs to be sampled around a point before it is considered covered. + * Returns the radius that needs to be sampled around a point before it is considered covered. */ inline const awh_ivec &coverRadius() const { diff --git a/src/gromacs/awh/biaswriter.cpp b/src/gromacs/awh/biaswriter.cpp index e6e605ea4e..4dcea0f7b8 100644 --- a/src/gromacs/awh/biaswriter.cpp +++ b/src/gromacs/awh/biaswriter.cpp @@ -362,7 +362,7 @@ void BiasWriter::prepareBiasOutput(const Bias &bias) gmx::ArrayRef pmf = block_[getVarStartBlock(AwhOutputEntryType::Pmf)].data(); bias.state().getPmf(pmf); - /* Pack the the data point by point. + /* Pack the data point by point. * Unfortunately we can not loop over a class enum, so we cast to int. * \todo Use strings instead of enum when we port the output to TNG. */ diff --git a/src/gromacs/awh/grid.h b/src/gromacs/awh/grid.h index 5db855f33f..b212b866cd 100644 --- a/src/gromacs/awh/grid.h +++ b/src/gromacs/awh/grid.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by + * Copyright (c) 2015,2016,2017,2019, 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. @@ -171,7 +171,7 @@ class GridAxis * \brief A point in the grid. * * A grid point has a coordinate value and a coordinate index of the same dimensionality as the grid. - * It knows the the linear indices of its neighboring point (which are useful only when handed up to + * It knows the linear indices of its neighboring point (which are useful only when handed up to * the grid). */ struct GridPoint diff --git a/src/gromacs/awh/histogramsize.cpp b/src/gromacs/awh/histogramsize.cpp index 2810229ee1..d732dd86e2 100644 --- a/src/gromacs/awh/histogramsize.cpp +++ b/src/gromacs/awh/histogramsize.cpp @@ -82,7 +82,7 @@ double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms, FILE *fplog) { /* The histogram size is kept constant until the sampling region has been covered - and the the current sample weight is large enough and the histogram is ready. */ + and the current sample weight is large enough and the histogram is ready. */ if (!detectedCovering || (logScaledSampleWeight_ < maxLogScaledSampleWeight_) || equilibrateHistogram_) diff --git a/src/gromacs/awh/tests/biasstate.cpp b/src/gromacs/awh/tests/biasstate.cpp index 1dae643d0f..85750cb543 100644 --- a/src/gromacs/awh/tests/biasstate.cpp +++ b/src/gromacs/awh/tests/biasstate.cpp @@ -169,7 +169,7 @@ TEST_P(BiasStateTest, InitializesFromFile) } // Test that Bias initialization open and reads the correct initialization -// files and the the correct PMF and target distribution is set. +// files and the correct PMF and target distribution is set. INSTANTIATE_TEST_CASE_P(WithParameters, BiasStateTest, ::testing::Values("pmf_target_format0.xvg", "pmf_target_format1.xvg")); diff --git a/src/gromacs/domdec/gpuhaloexchange_impl.cu b/src/gromacs/domdec/gpuhaloexchange_impl.cu index 1e5038d0e4..73b2dbb341 100644 --- a/src/gromacs/domdec/gpuhaloexchange_impl.cu +++ b/src/gromacs/domdec/gpuhaloexchange_impl.cu @@ -218,7 +218,7 @@ void GpuHaloExchange::Impl::communicateHaloCoordinates(const matrix box const int size = xSendSize_; // The coordinateShift changes between steps when we have // performed a DD partition, or have updated the box e.g. when - // performing pressure coupling. So, for simplicity, the the box + // performing pressure coupling. So, for simplicity, the box // is used every step to pass the shift vector as an argument of // the packing kernel. // diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp index 92c0a0fd20..69e0fc7943 100644 --- a/src/gromacs/gmxana/gmx_wham.cpp +++ b/src/gromacs/gmxana/gmx_wham.cpp @@ -3223,7 +3223,7 @@ int gmx_wham(int argc, char *argv[]) " the pullx [TT]mdrun[tt] output files. The [REF].tpr[ref] and pullx files must", " be in corresponding order, i.e. the first [REF].tpr[ref] created the", " first pullx, etc.", - "* Same as the previous input mode, except that the the user", + "* Same as the previous input mode, except that the user", " provides the pull force output file names ([TT]pullf.xvg[tt]) with option [TT]-if[tt].", " From the pull force the position in the umbrella potential is", " computed. This does not work with tabulated umbrella potentials.", diff --git a/src/gromacs/gpu_utils/gpuregiontimer.h b/src/gromacs/gpu_utils/gpuregiontimer.h index 64c2a7918b..d33cc9baec 100644 --- a/src/gromacs/gpu_utils/gpuregiontimer.h +++ b/src/gromacs/gpu_utils/gpuregiontimer.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by + * Copyright (c) 2016,2017,2018,2019, 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. @@ -113,7 +113,7 @@ template class GpuRegionTimerWrapper impl_.closeTimingRegion(s); } /*! \brief - * Accumulates the last timespan of all the events used into the the total duration, + * 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). diff --git a/src/gromacs/listed_forces/listed_forces.h b/src/gromacs/listed_forces/listed_forces.h index 84faefc9e4..2cb13d65cd 100644 --- a/src/gromacs/listed_forces/listed_forces.h +++ b/src/gromacs/listed_forces/listed_forces.h @@ -38,7 +38,7 @@ * \brief Handles computing energies and forces for listed * interactions. * - * Located here is the the code for + * Located here is the code for * - computing energies and forces for interactions between a small number of particles, e.g bonds, position restraints and listed non-bonded interactions (e.g. 1-4). diff --git a/src/gromacs/nbnxm/opencl/nbnxm_ocl_jit_support.cpp b/src/gromacs/nbnxm/opencl/nbnxm_ocl_jit_support.cpp index 7354275d20..fdafcad3ea 100644 --- a/src/gromacs/nbnxm/opencl/nbnxm_ocl_jit_support.cpp +++ b/src/gromacs/nbnxm/opencl/nbnxm_ocl_jit_support.cpp @@ -108,7 +108,7 @@ static const char * kernel_VdW_family_definitions[] = * -DLJ_EWALD_COMB_GEOM (The evdwOclFSWITCH flavour) * -DVDWNAME=_VdwLJEwCombGeom (The second part of the generated kernel name ) * - * prune/energy are still generated as originally. It is only the the flavour-level that has changed, so that + * prune/energy are still generated as originally. It is only the flavour-level that has changed, so that * only the required flavour for the simulation is compiled. * * If eeltype is single-range Ewald, then we need to add the diff --git a/src/gromacs/selection/nbsearch.cpp b/src/gromacs/selection/nbsearch.cpp index 5a799aa981..4b751ad292 100644 --- a/src/gromacs/selection/nbsearch.cpp +++ b/src/gromacs/selection/nbsearch.cpp @@ -479,7 +479,7 @@ bool AnalysisNeighborhoodSearchImpl::initGridCells( { // Determine the size of cubes where there are on average 10 positions. // The loop takes care of cases where some of the box edges are shorter - // than the the desired cube size; in such cases, a single grid cell is + // than the desired cube size; in such cases, a single grid cell is // used in these dimensions, and the cube size is determined only from the // larger box vectors. Such boxes should be rare, but the bounding box // approach can result in very flat boxes with certain types of selections diff --git a/src/gromacs/selection/selelem.h b/src/gromacs/selection/selelem.h index f2f218744c..91f06b680b 100644 --- a/src/gromacs/selection/selelem.h +++ b/src/gromacs/selection/selelem.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by + * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2019, 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. @@ -442,7 +442,7 @@ class SelectionTreeElement gmx_ana_index_t cgrp; //! Data for \ref SEL_EXPRESSION and \ref SEL_MODIFIER elements. struct { - //! Pointer the the method used in this expression. + //! Pointer the method used in this expression. struct gmx_ana_selmethod_t *method; //! Pointer to the data allocated by the method's \p init_data (see sel_datafunc()). void *mdata; diff --git a/src/gromacs/selection/selhelp.cpp b/src/gromacs/selection/selhelp.cpp index b7d161f80d..7a966f6ef8 100644 --- a/src/gromacs/selection/selhelp.cpp +++ b/src/gromacs/selection/selhelp.cpp @@ -425,7 +425,7 @@ const char *const PositionsHelpText::text[] = { " even if only part of it is selected.", " [TT]part_[tt] prefix calculates the centers for the selected atoms, but", " uses always the same atoms for the same residue/molecule. The used atoms", - " are determined from the the largest group allowed by the selection.", + " are determined from the largest group allowed by the selection.", " [TT]dyn_[tt] calculates the centers strictly only for the selected atoms.", " If no prefix is specified, whole selections default to [TT]part_[tt] and", " other places default to [TT]whole_[tt].", diff --git a/src/gromacs/swap/swapcoords.cpp b/src/gromacs/swap/swapcoords.cpp index 193354b3f0..edc034cd78 100644 --- a/src/gromacs/swap/swapcoords.cpp +++ b/src/gromacs/swap/swapcoords.cpp @@ -1925,7 +1925,7 @@ static void translate_positions( } -/*! \brief Write back the the modified local positions from the collective array to the official positions. */ +/*! \brief Write back the modified local positions from the collective array to the official positions. */ static void apply_modified_positions( swap_group *g, rvec x[])