A search for "the the" revealed a lot of easy-to-fix typos.
Change-Id: I42ed8f6bd7a5cf2f3d15117c8045cf3af4313b18
`creating a source distribution
<https://docs.python.org/3/distutils/sourcedist.html#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:
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
: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`
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).
: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 <eqdVljdlambda>` and :eq:`%s <eqdVcoulombdlambda>` may lead to poor
convergence. When the particles have nearly disappeared, or are close to
{ | \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:
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 <eqawhwupdate>`). The AWH initial
stage takes inspiration from the well-known Wang-Landau algorithm \ :ref:`138 <refwang2001efficient>`,
although there are differences in the details.
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
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
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
* 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.
/*
* 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.
}
/*! \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
{
gmx::ArrayRef<float> 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.
*/
/*
* 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.
* \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
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_)
}
// 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"));
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.
//
" 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.",
/*
* 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.
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).
* \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).
* -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
{
// 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
/*
* 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.
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;
" 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].",
}
-/*! \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[])
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff