molecule. When :mdp:`nstlist` is larger than one,
:mdp:`nstlist` insertions are performed in a sphere with radius
:mdp:`rtpi` around a the same random location using the same
- neighborlist. Since neighborlist construction is expensive,
+ pair list. Since pair list construction is expensive,
one can perform several extra insertions with the same list
almost for free. The random seed is set with
:mdp:`ld-seed`. The temperature for the Boltzmann weighting is
Generate a pair list for groups of atoms. These groups
correspond to the charge groups in the topology. This was the
only cut-off treatment scheme before version 4.6, and is
- **deprecated in |gmx-version|**. There is no explicit buffering of
+ **deprecated since 5.1**. There is no explicit buffering of
the pair list. This enables efficient force calculations for
water, but energy is only conserved when a buffer is explicitly
added.
Frequency to update the neighbor list. When this is 0, the
neighbor list is made only once. With energy minimization the
- neighborlist will be updated for every energy evaluation when
+ pair list will be updated for every energy evaluation when
:mdp:`nstlist` is greater than 0. With :mdp-value:`cutoff-scheme=Verlet` and
:mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
a minimum value and :ref:`gmx mdrun` might increase it, unless
.. mdp-value:: Cut-off
- Plain cut-off with neighborlist radius :mdp:`rlist` and
+ Plain cut-off with pair list radius :mdp:`rlist` and
Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
:mdp:`rcoulomb`.
Use an unmodified Coulomb potential. With the group scheme this
means no exact cut-off is used, energies and forces are
- calculated for all pairs in the neighborlist.
+ calculated for all pairs in the pair list.
.. mdp:: rcoulomb-switch
.. mdp-value:: Cut-off
- Twin range cut-offs with neighbor list cut-off :mdp:`rlist` and
- VdW cut-off :mdp:`rvdw`, where :mdp:`rvdw` >= :mdp:`rlist`.
+ Plain cut-off with pair list radius :mdp:`rlist` and VdW
+ cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
.. mdp-value:: PME
Use an unmodified Van der Waals potential. With the group scheme
this means no exact cut-off is used, energies and forces are
- calculated for all pairs in the neighborlist.
+ calculated for all pairs in the pair list.
.. mdp-value:: Force-switch
.. mdp:: constraints
+ Controls which bonds in the topology will be converted to rigid
+ holonomic constraints. Note that typical rigid water models do not
+ have bonds, but rather a specialized ``[settles]`` directive, so
+ are not affected by this keyword.
+
.. mdp-value:: none
- No constraints except for those defined explicitly in the
- topology, *i.e.* bonds are represented by a harmonic (or other)
- potential or a Morse potential (depending on the setting of
- :mdp:`morse`) and angles by a harmonic (or other) potential.
+ No bonds converted to constraints.
.. mdp-value:: h-bonds
.. mdp-value:: h-angles
- Convert all bonds and additionally the angles that involve
- H-atoms to bond-constraints.
+ Convert all bonds to constraints and convert the angles that
+ involve H-atoms to bond-constraints.
.. mdp-value:: all-angles
- Convert all bonds and angles to bond-constraints.
+ Convert all bonds to constraints and all angles to bond-constraints.
.. mdp:: constraint-algorithm
+ Chooses which solver satisfies any non-SETTLE holonomic
+ constraints.
+
.. mdp-value:: LINCS
LINear Constraint Solver. With domain decomposition the parallel
.. mdp:: continuation
- This option was formerly known as unconstrained-start.
+ This option was formerly known as ``unconstrained-start``.
.. mdp-value:: no
distance restraints over an ensemble of molecules in one
simulation box. Normally, one would perform ensemble averaging
- over multiple subsystems, each in a separate box, using ``mdrun
- -multi``. Supply ``topol0.tpr``, ``topol1.tpr``, ... with
- different coordinates and/or velocities. The environment
+ over multiple simulations, using ``mdrun
+ -multidir``. The environment
variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
- within each ensemble (usually equal to the ``mdrun -multi``
- value).
+ within each ensemble (usually equal to the number of directories
+ supplied to ``mdrun -multidir``).
.. mdp:: disre-weighting
.. mdp-value:: yes
use orientation restraints, ensemble averaging can be performed
- with `mdrun -multi`
+ with ``mdrun -multidir``
.. mdp:: orire-fc
CASSCF method.
-Implicit solvent
-^^^^^^^^^^^^^^^^
-
-.. mdp:: implicit-solvent
-
- .. mdp-value:: no
-
- No implicit solvent
-
- .. mdp-value:: GBSA
-
- Do a simulation with implicit solvent using the Generalized Born
- formalism. Three different methods for calculating the Born
- radii are available, Still, HCT and OBC. These are specified
- with the :mdp:`gb-algorithm` field. The non-polar solvation is
- specified with the :mdp:`sa-algorithm` field.
-
-.. mdp:: gb-algorithm
-
- .. mdp-value:: Still
-
- Use the Still method to calculate the Born radii
-
- .. mdp-value:: HCT
-
- Use the Hawkins-Cramer-Truhlar method to calculate the Born
- radii
-
- .. mdp-value:: OBC
-
- Use the Onufriev-Bashford-Case method to calculate the Born
- radii
-
-.. mdp:: nstgbradii
-
- (1) \[steps\]
- Frequency to (re)-calculate the Born radii. For most practial
- purposes, setting a value larger than 1 violates energy
- conservation and leads to unstable trajectories.
-
-.. mdp:: rgbradii
-
- (1.0) \[nm\]
- Cut-off for the calculation of the Born radii. Currently must be
- equal to rlist
-
-.. mdp:: gb-epsilon-solvent
-
- (80)
- Dielectric constant for the implicit solvent
-
-.. mdp:: gb-saltconc
-
- (0) \[M\]
- Salt concentration for implicit solvent models, currently not used
-
-.. mdp:: gb-obc-alpha
-.. mdp:: gb-obc-beta
-.. mdp:: gb-obc-gamma
-
- Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
- respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
- respectively
-
-.. mdp:: gb-dielectric-offset
-
- (0.009) \[nm\]
- Distance for the di-electric offset when calculating the Born
- radii. This is the offset between the center of each atom the
- center of the polarization energy for the corresponding atom
-
-.. mdp:: sa-algorithm
-
- .. mdp-value:: Ace-approximation
-
- Use an Ace-type approximation
-
- .. mdp-value:: None
-
- No non-polar solvation calculation done. For GBSA only the polar
- part gets calculated
-
-.. mdp:: sa-surface-tension
-
- \[kJ mol-1 nm-2\]
- Default value for surface tension with SA algorithms. The default
- value is -1; Note that if this default value is not changed it will
- be overridden by :ref:`gmx grompp` using values that are specific
- for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
- Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
- while using an sa-algorithm other than None means no non-polar
- calculations are done.
-
-
Computational Electrophysiology
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Use these options to switch on and control ion/water position exchanges in "Computational
Removed features
^^^^^^^^^^^^^^^^
-This feature has been removed from |Gromacs|, but so that old
+These features have been removed from |Gromacs|, but so that old
:ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
fatal error if this is set.
(no)
+.. mdp:: implicit-solvent
+
+ (no)
+
.. _reference manual: gmx-manual-parent-dir_
#include <array>
+#include "gromacs/gpu_utils/gputraits_ocl.h"
#include "gromacs/gpu_utils/oclutils.h"
#include "gpuregiontimer.h"
-template <> struct GpuTraits<GpuFramework::OpenCL>
-{
- using CommandStream = cl_command_queue;
- using CommandEvent = cl_event;
-};
-
-//! Short-hand for external use
-using GpuRegionTimer = GpuRegionTimerWrapper<GpuFramework::OpenCL>;
-
-// cppcheck-suppress noConstructor
/*! \libinternal \brief
- * This is a GPU region timing implementation for OpenCL.
- * It provides methods for measuring the last timespan.
- * Copying/assignment is disabled since the underlying timing events are owned by this.
+ * The OpenCL implementation of the GPU code region timing.
+ * With OpenCL, one has to use cl_event handle for each API call that has to be timed, and
+ * accumulate the timing afterwards. As we would like to avoid overhead on API calls,
+ * we only query and accumulate cl_event timing at the end of time steps, not after the API calls.
+ * Thus, this implementation does not reuse a single cl_event for multiple calls, but instead
+ * maintains an array of cl_events to be used within any single code region.
+ * The array size is fixed at a small but sufficiently large value for the number of cl_events
+ * that might contribute to a timer region, currently 10.
*/
- // cppcheck-suppress noConstructor
-template <> class GpuRegionTimerImpl<GpuFramework::OpenCL>
+class GpuRegionTimerImpl
{
- //! Short-hands
- using CommandStream = typename GpuTraits<GpuFramework::OpenCL>::CommandStream;
- using CommandEvent = typename GpuTraits<GpuFramework::OpenCL>::CommandEvent;
-
/*! \brief The underlying individual timing events array.
* The maximum size is chosen arbitrarily to work with current code, and can be changed.
* There is simply no need for run-time resizing, and it's unlikely we'll ever need more than 10.
public:
- /*! \brief Will be called before the region start. */
+ GpuRegionTimerImpl() = default;
+ ~GpuRegionTimerImpl() = default;
+ //! No copying
+ GpuRegionTimerImpl(const GpuRegionTimerImpl &) = delete;
+ //! No assignment
+ GpuRegionTimerImpl &operator=(GpuRegionTimerImpl &&) = delete;
+ //! Moving is disabled but can be considered in the future if needed
+ GpuRegionTimerImpl(GpuRegionTimerImpl &&) = delete;
+
+ /*! \brief Should be called before the region start. */
inline void openTimingRegion(CommandStream){}
-
- /*! \brief Will be called after the region end. */
+ /*! \brief Should be called after the region end. */
inline void closeTimingRegion(CommandStream){}
-
- /*! \brief Returns the last measured region timespan (in milliseconds) and calls reset() */
+ /*! \brief Returns the last measured region timespan (in milliseconds) and calls reset(). */
inline double getLastRangeTime()
{
double milliseconds = 0.0;
reset();
return milliseconds;
}
-
- /*! \brief Resets internal state */
+ /*! \brief Resets the internal state, releasing the used cl_events. */
inline void reset()
{
for (size_t i = 0; i < currentEvent_; i++)
{
if (events_[i]) // This conditional is ugly, but is required to make some tests (e.g. empty domain) pass
{
- GMX_ASSERT(CL_SUCCESS == clReleaseEvent(events_[i]), "OpenCL event release failure");
+ cl_int gmx_unused cl_error = clReleaseEvent(events_[i]);
+ GMX_ASSERT(CL_SUCCESS == cl_error, "OpenCL event release failure");
}
}
currentEvent_ = 0;
// As long as we're doing nullptr checks, we might want to be extra cautious.
events_.fill(nullptr);
}
-
- /*! \brief Provides next unused cl_event for OpenCL API consumption. */
+ /*! \brief Returns a new raw timing event
+ * for passing into individual GPU API calls
+ * within the region if the API requires it (e.g. on OpenCL).
+ */
inline CommandEvent *fetchNextEvent()
{
GMX_ASSERT(currentEvent_ < events_.size(), "Increase c_maxEventNumber_ if needed");
}
};
+//! Short-hand for external use
+using GpuRegionTimer = GpuRegionTimerWrapper<GpuRegionTimerImpl>;
+
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff