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Interaction Energy calculation on GPU for GIST #787

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Merged
drroe merged 5 commits into from
Jan 9, 2020
Merged

Interaction Energy calculation on GPU for GIST #787

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b79a765
Added GPU Compatibility to GIST
jokr91 Nov 19, 2019
86ba3b6
Added skipS flag
jokr91 Dec 16, 2019
c80f1c1
Updated Documentation, Change Version
jokr91 Dec 17, 2019
12a6f53
Changes to comply with reviews by @drroe
jokr91 Jan 8, 2020
912393b
Merge branch 'master' into GPUgistInteraction
drroe Jan 9, 2020
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31 changes: 30 additions & 1 deletion doc/cpptraj.lyx
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Original file line number Diff line number Diff line change
Expand Up @@ -1174,6 +1174,10 @@ closest
watershell
\end_layout

\begin_layout LyX-Code
gist
\end_layout

\begin_layout Section
General Concepts
\end_layout
Expand Down Expand Up @@ -22490,7 +22494,7 @@ gist

\end_inset

[doorder] [doeij] [skipE] [refdens <rdval>] [temp <tval>]
[doorder] [doeij] [skipS] [skipE] [refdens <rdval>] [temp <tval>]
\end_layout

\begin_layout LyX-Code
Expand Down Expand Up @@ -22543,6 +22547,10 @@ literal "true"
).
\end_layout

\begin_layout Description
[skipS] Skip all entropy calculations.
\end_layout

\begin_layout Description

\series bold
Expand Down Expand Up @@ -22922,6 +22930,27 @@ refdens
keyword, instead of allowing GIST to supply the default value.
\end_layout

\begin_layout Standard
For GIST, a GPU accelerated version is available, in which the interaction
energy is calculated using CUDA.
When using the GPU accelerated version of GIST, the
\series bold
doeij
\series default
keyword is not available.
It is recommended to use a grid covering the entire box, when using the
GPU implementation.
You may also choose a smaller grid, but all interaction energies, i.e., each
atom with each atom, will always be calculated independent of the chosen
grid.
This ensures optimum performance when calculating the interaction energies.
Thus, the additional time required to calculate the order parameters (
\series bold
doorder
\series default
) is negligible.
\end_layout

\begin_layout Subsubsection*
\paragraph_spacing other 3
\noindent
Expand Down
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