GROMACS

Multidimensional data in canonical layout.

Introduces a multidimensional array that holds its own data and makes it
accessible via the canonical right-aligned layout for indexing the data.

refs: #2282

Change-Id: I883cdb6a41d7277669e100320e230904856d1318

densityfitting - density file format (mrc) header.

Implements mrc/cc4/map format file headers as decribed in
"EMDB Map Distribution Format Description Version 1.01 (c)
emdatabank.org 2014"

Reading and writing is part of a follow-up patch.

refs #2282 and #1877

Change-Id: Ifd43cedb137c0beeb320e1299df8bae9916c8ea8

densityfitting - MDModule declaration

Declaring the infrastructure for running molecular dynamics simulations with
addional forces that are derived from densities.

Adds a IForceProvider for density fitting simulation that is set up with
its DensityFittingParameters that are in turn built from DensityFittingOptions.

refs #2282 #2901

Change-Id: I0732a78747582a6e23bba1e141d73c4cda421011

One dimensional Gaussian function on lattice.

Evaluate a Gaussian of width sigma in one dimension on lattice points with unit spacing.

refs #2282

Change-Id: I57a513f05af44323e7109c4560438dc023793c4c

Three dimensional gauss transform

Added class that adds gaussians functions with specified
amplitudes and coordinates onto a three-dimensional scalar field.

Change-Id: I07ea2cdd219b34afc402975a0b0e8a52eb71acaf
refs: #2282

density fitting forces

Evaluate forces on atoms that increase a measure of the goodness of fit to a reference density.

The density fitting forces are evaluated as the gradient of the goodness of fit of a comparison density is generated from atoms by spreading on a grid via a Gaussian kernel to the reference density.

Applying the chain rule for this gradient yields the density fitting force as the inner product of the derivative of the comparison density to reference density goodness-of-fit function at all density values and the gradient of the spreading kernel used to simulate the density.

This patch assumes that the comparison density to reference density goodness of fit derivative density is given, methods that aid the evaluation of this derivative density are part of a child patch.

refs #2282

Change-Id: I4d93fffbdb41753f9a0a4af921011aca02ade69c

mrc density map reading/writing

Add a class that combines header and mrc data handling for float values
to enable reading and writing of mrc files.

refs #2282

Change-Id: Idd84ab2628a52a2fcafb6121ad66f62e88235c74

Density similarity measure and gradient

Adding a class that allows evaluating the similarity of three dimensional
densities and their gradient given a comparison method, along with a
concrete implementation of the inner-product as a comparison method.

refs #2282

Change-Id: Id73f237e123bed14241227b84cbf83970a09ff49

Mrc format header to lattice coordinate transform

Extracts a coordinate transformation into lattice coordinates from the mrc density
header, as well as the three dimensional grid extents.

refs #2282

Change-Id: I8c01a370e3010add29b8810e2f3320b9ab428c02

Allow non-uniform Gaussians

For three-dimensional Gaussian spreading, as well as density guided force
evaluation, allow spreading with different widths along x, y, and z-direction.

This required to account for the common, slightly non-uniform grid
spacing in input densities.

Added some simplifactions for the vector operations based on newly
implemented functions in for BasicVector in a previous patch.

refs #2282

Change-Id: I730897fe672d2444a04ea68fea83e2273b359b27

Add coordinate scaling class and extend TranslateAndScale

- Make TranslateAndScale copyable and movable.
 - Make coordinate transformation application const on the
TranslateAndScale object itself
 - Add a function that returns the scale operation only without translation.
 - Add a coordinate scaling class that also allows to inverse the scaling, ignoring zero input.

refs #2282

Change-Id: I73f9bd892f1f81692e05ac6b2fece2e7be9e8e69

Add class to look up density fitting amplitudes

Adds a look-up for the weight used for spreading atoms on a grid and
calculate forces on them.

refs #2282

Change-Id: Iadd26f04265aa85ad30a827c92f2c5d5fc48ef85

Move densityfitting options and output into seperate file

Exposes density fitting options and output interface for testing.

Added test for density fitting options class.

refs: #2282

Change-Id: I0107217b5af86abf1ed298dd77553c4c24b1d3f2

Index groups for MdModules from grompp

Make index groups available for mdrun modules during preprocessing.
Notify mdrun modules with a DefaultIndexGroupsAndNames class that
translates index group names into atom indices.

refs #2282

Change-Id: Idc1bc3a5840e7b7ec3c82904416887b02417c92c

Add index group option to density fitting

Adds the option to select a specific group for density fitting, stores
the indices in the tpr file and restores them after reading.

Adapted the densityfittingoptions test to test fixture to better reflect
the increased required complexity for testing the storage of indices.

refs #2282

Change-Id: I3e33508bbcadf968b0ddf978a73e7f6cf5753b5b

Access to GaussTransform3D data

Return a non-constant view to the GaussTransform3D to allow
sum reduction of Gauss transformation data via MPI. The alternative
to have the GaussTransform3D take a commrec to perform the
sum reduction itself leads to a cyclic dependency between
math and mdtypes modules.

refs #2282

Change-Id: I8b786965c3562ed84fe4e97fa0f68cf89ea0f03a

Add density fitting parameters

Adds the mdp parameters that are required for running a
density fitting simulation.

refs #2282

Change-Id: Id22ceee0f0036450173522bd5e85af06542a2c39

Implementing the density fitting force provider

refs #2282

Change-Id: Ib65679a82168f18992920f4529596db2494cccc3

Constructing local atom sets for density fitting

Constructs local atom sets for density fitting during simulation
setup.

refs #2282

Change-Id: I0300376a6818f3ad8bb6474b09a9b0f1cbb46eae

Add checkpointing for MdModules

Adds the possiblity to write and read from checkpoint files for MdModules.

refs #2282

Change-Id: Id3ab57d1c9a40b6e1fb0193430e5b66ffa87d787

Add reference density file option to densityfitting

Add option to density fitting to read reference density for
density fitting code.

refs #2282

Change-Id: I598b679a3c1c63b913a104d7ccff8e1643b3946d

Periodic boundary correction for density fitting

Corrects the periodic boundaries for density fittinng
such that always the periodic image closest to the center
of the density is chosen.

ref #2282

Change-Id: I46d9546d7dbb659e03070b4ba6ffd401eb7368c4

Adding energy output field for density fitting

Added a new energy output field for energies that stem from the density
fitting code.

refs #2282

Change-Id: I78c64213f4b958f00a938f0a67c586c2f4e9033e

Adding every N-steps option to densityfitting

Adds an option to the density fitting module to apply forces only every
N steps.

refs #2282

Change-Id: I8d264734e1d9a82ff9717d270552e38a28b34729

Add option to normalize densities prior to density fitting

Adds an mdp option that makes sure that the sum of voxel values
for both input densities is unity.

refs #2282

Change-Id: I9d3c63d7548bca72a083cdafa6818ded4fcdd400

Relative entropy as density similarity measure

Adds a new density similarity measure that uses the relative entropy of
two densities to compare them to one another. Also adds the gradient of
this measure.

refs #2282

Change-Id: I3be18ec3fad3c2551ce7c9fe896dc257d5789cdf

Account for reference density origin shift in pbc correction

When the refernce density is shifted from the origin, this shift has to
be added to the reference density center. This patch fixes incorrect pbc
correction behaviour, due to not taking this shift into account.

refs #2282

Change-Id: I953f717ecf6ab53985a59195eab896d50965039e

Use the current mass instead of massA in density fitting code.

When using masses to determine the weights of the spread amplitudes,
massA instead of the correct massT was used. This commit fixes this
behavior.

refs #2282

Change-Id: I58deb14b4b45c122ab3c9caf3f6b76c89f9ae739

Densityfitting write int64_t indices instead of gmx::index

When serializing atom indices to a key-value-tree that is subsequently
written to file, the type of the indices needs to be independent of
gmx::index (aka ptrdiff_t) type definition.

This patch introduces this behaviour.

refs #2282

Change-Id: I1384158204354e2267674c266f91c133a01bc5f7

End to end test for density fitting

Implement an end to end test for the density fitting module.

refs #2282

Change-Id: Ic94013cae6820ccf6fa7415887b280daff25d83c

Add comments to grompp generated .mdp output for densityfitting

Adds additional explanatory comments to the grompp generated mdout.mdp
file for densityfitting.

refs #2282

Change-Id: I496cccced2cc87cb2434f877c0caf04cb29c1903

Add release note for density fitting.

Adds a release note that density-guided simulations are now available.

refs #2282

Change-Id: I2ae6896ba32cadfb2029a5c923db6fd76ddbf620

Manual entry for density guided simulations

Extends the reference manual with a section for density guided
simulations.

refs #2282

Change-Id: Ie3017fa5e75fcd2c809c20782300f759182486a8

Add mdp option documentation for density fitting.

Documents the .mdp options for the density fitting module.

refs #2282

Change-Id: Ic2cb616ca13627553a36d739d86192b0fcb0e239

Consistently change densityfitting spreading weight to charge

In the mdp options, the density-guided-simulation-atom-spreading weight
has been changed from charges to "charge" but within the code and in an
.mdp file comment the plural charges was still used. Changed now all
over to make this consistent.

refs #2282

Change-Id: I055743c8301e4ad18ceed5670c62be0a93c2d5f1

Add cross-correlation as density simlarity measure

Add the canonical cross-correlation as similarity measure for densities

refs #2282

Change-Id: Idec820f38dab07c5ee8281944855a532a587a2ff

Amendments to density fitting manual section

- Fixed a sign error in the energy and force definition
 - Added performance considerations
 - Fixed whitespace
 - Changed vector notation to mathbf as in the other parts of the manual
 - Added pressure-coupling considerations
 - Added considerations when using multiple-time-stepping

refs #2282

Change-Id: I8421ccf09ac960fa04508234e738967f51a27fab

Adaptive force scaling for densityfitting

Scales the force adaptively for density-guided-simulations

refs #2282

Change-Id: I96310f498cf2fae9f7385a9396f1253b760d135e

Manual entry and .mdp option for adaptive force scaling

Adds a manual entry and extends the mdp option section to describe the
adpative force scaling parameters.

refs #2282

Change-Id: Ifb2e4af256282340f1111262f91e5d73d93c3208

Fix nst in density-fitting module

An error in the nst variable led to forces from density-guided
simulations to be applied every step, because its internal step
counter would stay at 0.

Change-Id: Ib8b33b407bfe9c56bab497f7e2d505843675afca
refs: #2282

Fix cross-correlation calculation instability

Fixes a fail in calculating the cross-correlation for density guided
simulations in cases where the covariance between densities values had
been negative.

refs #2282

Change-Id: Ibd2a88768eba25c4836b8f692fd9d61e8960e073

InMemorySerializer with endianess swap.

Adds an InMemorySerializer that swaps endianess. Required for reading
data that is not handled with XDR serializers and was written with
different endianess, e.g., mrc files for density guided simulations.

refs #2282

Change-Id: Ice96fe8684bb0b920c22dc7d3c2b2087260eb9ad

Read mrc density map format with all endianesses.

Swaps the endianess of reading mrc density maps if header is not sane.

refs: #2282

Change-Id: I417e402b2ab801c22d9963fabb0e60b186288651

Fix check-pointing for density guided simulations

Previously, checkpointing for density-guided simulations did not take
into account that the checkpointing occurs in the middle of the md-loop.

Now, the state is stored before the force-calculations, so that
simulations are restarted correctly.

refs #2282
fixes #3215

Change-Id: Ide4ebf94f2801acbe476a5cd348af66d0a6f28ac