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Partial conversion of gmx_domdec_t to C++
2018-06-13
Ber
k
Hess
Part
i
al
conversion of gm
x
_dom
d
ec_t to
C
++
commit
|
commitdiff
|
tree
2018-06-13
Mark Ab
r
aham
Bump lmfit support t
o
ver
s
i
on 7
commit
|
commitdiff
|
tree
2018-06-07
Aleksei Iupinov
Compile
m
ost of PME G
P
U ho
s
t code with OpenCL
commit
|
commitdiff
|
tree
2018-06-06
Berk Hess
C
l
ean up
make_at2con
commit
|
commitdiff
|
tree
2018-06-06
Mark Abra
h
am
Mov
e
IMD initializ
a
tion a
n
d
f
u
se DD setup
commit
|
commitdiff
|
tree
2018-06-05
M
a
rk Abraham
Make proper BoxDefor
m
ation class
commit
|
commitdiff
|
tree
2018-06-05
B
erk He
s
s
Make nbnxn
_
grid_t c
o
un
t
s and siz
e
s
a
r
r
a
ys
commit
|
commitdiff
|
tree
2018-06-05
Mark Ab
r
aham
Make Constr
a
i
nt
s
a
pr
o
p
e
r
class
commit
|
commitdiff
|
tree
2018-06-04
M
ark Abraha
m
U
p
d
a
te Awh initializa
t
io
n
an
d
l
i
f
et
i
me manageme
n
t
commit
|
commitdiff
|
tree
2018-06-04
Szilárd Páll
Fix timing o
f
clFFT
kernels
commit
|
commitdiff
|
tree
2018-06-04
Magn
u
s Lun
d
borg
W
r
i
t
e la
m
bdas
and
box
to
TNG at cor
r
ect interv
a
ls
commit
|
commitdiff
|
tree
2018-06-01
Kevin Boyd
Cosmetic fixes to
mdp documentation
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
ei Iupi
n
o
v
Merge pm
e
.
cu into pme-
g
pu-
i
nternal
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Al
e
ksei Iupinov
Move pme-timings
.
cu to pme-gpu-
t
imings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Prefe
r
l
i
nkin
g
t
o
s
ystem c
l
FFT rather tha
n
bundled one
commit
|
commitdiff
|
tree
2018-05-31
A
l
ekse
i
Iupinov
Move th
e
P
m
e
GpuSpecific structure i
n
to pme-gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
upinov
Added the bund
l
e
d
cl
F
FT into OpenCL bui
l
d
s
commit
|
commitdiff
|
tree
2018-05-31
Aleks
e
i Iupinov
Gather the P
M
E GPU c
o
n
stants/macros in a single head
e
r
commit
|
commitdiff
|
tree
2018-05-28
Aleksei Iupinov
Support persi
s
t
ent device context-derive
d
d
a
t
a
in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
Mark
Abraham
C
l
ean up f
o
rce
.
h and its us
e
commit
|
commitdiff
|
tree
2018-05-24
Mark
A
braha
m
Remove bDomDec
from t_for
c
erec
commit
|
commitdiff
|
tree
2018-05-24
B
e
r
k H
e
ss
Fix gr
o
mpp bug with b
l
ocks of same molecules
commit
|
commitdiff
|
tree
2018-05-24
M
a
rk Abra
h
am
R
eform Ewald-modul
e
cmake
h
andli
n
g
commit
|
commitdiff
|
tree
2018-05-23
Ro
l
a
nd S
c
h
ulz
Rename G
M
X_OCL_C
L
US
T
ER
_
SIZE
to GMX_OCL_N
B
_CLUSTER_
S
IZE
commit
|
commitdiff
|
tree
2018-05-23
Berk
He
s
s
Split off collect
.
cpp f
r
om do
m
dec
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-23
Be
r
k Hess
Co
n
vert nbnxn_sea
r
ch to C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Change nbnxn grid reallocation
commit
|
commitdiff
|
tree
2018-05-22
Be
r
k Hes
s
Use std::vect
o
r in
n
bnxn_search_t
commit
|
commitdiff
|
tree
2018-05-22
Berk
H
es
s
Use std
:
:
vecto
r
in nb
n
x
n
_grid_t
commit
|
commitdiff
|
tree
2018-05-22
Kevin
Boyd
Cos
m
etic documentation cha
n
ges
commit
|
commitdiff
|
tree
2018-05-22
Kevin Boyd
Mi
n
or fixes
t
o mdrun perform
a
n
c
e
docum
e
ntation
commit
|
commitdiff
|
tree
2018-05-18
Aleksei
I
upi
n
ov
prepareGpuKern
e
lArguments() and l
a
unc
h
GpuKernel() a
r
e
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split off domde
c
d
i
stribution and cellsi
z
es
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split
a
tom red
i
stribution
of
f
from
domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Remove
c
o
mmr
e
c fr
o
m
set_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
Roland Schulz
Use same OpenCL kerne
l
for different
Ve
n
dors
commit
|
commitdiff
|
tree
2018-05-10
Ca
r
sten Kutzner
Int
r
oduce
helper
c
lasses for
f
orc
e
pr
o
vid
e
r i
n
p
ut and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul B
a
uer
Fix m
d
-cpi -noappend
commit
|
commitdiff
|
tree
2018-05-04
Ma
r
k Abraham
Merge "Merge branch r
e
lease-2018"
commit
|
commitdiff
|
tree
2018-05-04
Mark Abraham
Mor
e
c
o
ns
t
c
o
rrectness
commit
|
commitdiff
|
tree
2018-05-03
M
a
r
k
A
b
raham
Merge bra
n
ch release
-
2018
commit
|
commitdiff
|
tree
2018-05-02
Rola
n
d S
c
hul
z
E
nable uncrustify for OpenCL
commit
|
commitdiff
|
tree
2018-05-02
R
oland Sc
h
u
lz
Support 4 sized cl
u
ster for GPU NBL search
commit
|
commitdiff
|
tree
2018-04-27
Berk Hess
Remove
p
ull
M
PI c
o
de
d
uplication
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
R
eorganize f
i
les for r
e
f
e
r
ence manual
commit
|
commitdiff
|
tree
2018-04-26
Paul
B
auer
Spli
t
up a
n
alysi
s
chapter in
r
eference man
u
al
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
Split
up special topics s
e
c
t
ion in
manua
l
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Add page breaks in refer
e
n
ce manua
l
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
S
p
lit up I
n
teractio
n
functions ma
n
ual
page
commit
|
commitdiff
|
tree
2018-04-25
Mark Abra
h
am
Refactor SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul
B
auer
Ch
a
nge image conve
r
sio
n
to only be build onc
e
commit
|
commitdiff
|
tree
2018-04-23
Alekse
i
Iupino
v
Device
B
uffe
r
header
s
are added
commit
|
commitdiff
|
tree
2018-04-23
Szi
l
á
rd Pál
l
Fix icc warning in pos
t
-
s
ubmit
commit
|
commitdiff
|
tree
2018-04-21
Szi
l
á
rd Páll
A
dd
pos
t
-
submit
w
ith
ARM HPC T
o
o
lch
a
i
n
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
Tw
e
ak PME
r
un mod
e
checks
commit
|
commitdiff
|
tree
2018-04-21
P
a
ul Bauer
Conver
t
manual from LaTeX to
M
arkup
commit
|
commitdiff
|
tree
2018-04-21
Pau
l
Baue
r
S
econd chan
g
e tracking commit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Intermedi
a
te
c
ommit
t
o track changes
t
o manual
commit
|
commitdiff
|
tree
2018-04-17
Vivec
a
Lindahl
Disallow
-skip values <= 0 for
g
mx
t
r
jc
o
nv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul Ba
u
er
Fix legacy topology memor
y
error
commit
|
commitdiff
|
tree
2018-04-17
M
a
rk Abrah
a
m
Shift per-step control lo
g
ic to do
_
md
commit
|
commitdiff
|
tree
2018-04-17
Mark Abraham
Brea
k
a
part update_constrain
t
s
commit
|
commitdiff
|
tree
2018-04-16
Szilárd Páll
A
d
d post-sub
m
it
t
e
s
t with hwlo
c
o
ff
commit
|
commitdiff
|
tree
2018-04-16
B
erk Hess
Move natoms_mol out of gmx_molblock
_
t
commit
|
commitdiff
|
tree
2018-04-16
Mark A
b
r
aham
Updated mdrun comparison in
f
ra
s
truc
t
ure
commit
|
commitdiff
|
tree
2018-04-13
Mark
Abraham
C
le
a
n up constraints cod
e
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Re
m
o
v
e
u
s
e
of where(), if D
E
BUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Reor
g
a
nize energy
e
valuation for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
P
r
event O
p
enCL timing mem
o
ry leak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert
g
m
x_molblock_t to
C++
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Simp
l
ified h
a
ndling of simulation
r
unners
commit
|
commitdiff
|
tree
2018-04-05
Mark Ab
r
a
h
am
C
r
eat
e
gr
o
macs/md
r
un module and move
c
o
de there
commit
|
commitdiff
|
tree
2018-04-05
Sz
i
lárd Páll
Refacto
r
cj
p
reload
in t
h
e non
b
onded OpenCL kernels
commit
|
commitdiff
|
tree
2018-04-04
Ma
r
k
Abraham
Quiet checkpoint reading
commit
|
commitdiff
|
tree
2018-04-04
Pas
c
al Merz
Mov
e
checkNumbe
r
OfBon
d
edI
n
tera
c
ti
o
ns
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Con
v
ert gmx_mtop_t
to C++
commit
|
commitdiff
|
tree
2018-04-03
M
ark Abrah
a
m
Re
m
ove
l
eft
o
ver
m
e
n
tio
n
of twin-range scheme
commit
|
commitdiff
|
tree
2018-04-03
M
ark Ab
r
aham
Me
r
ge "Merge
br
a
nch re
l
eas
e
-2018"
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move fil
e
opening out of init_pull()
commit
|
commitdiff
|
tree
2018-03-29
S
z
i
lárd Páll
Tweak/e
n
able icc 18 p
o
st-submit tests
commit
|
commitdiff
|
tree
2018-03-29
Mag
n
us Lundborg
I
m
p
roved check o
f
if
only forces are c
o
mpute
d
in do_pairs()
commit
|
commitdiff
|
tree
2018-03-29
P
a
u
l
Ba
u
er
F
i
x cmake
S
ph
i
nx detec
t
ion for
v
ersi
o
ns
>
1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
S
w
itch CUDA 9
.
0/g
c
c
5
t
est to CU
D
A
9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk H
e
ss
Modula
r
i
ze pull_coord_
w
o
r
k
_t
commit
|
commitdiff
|
tree
2018-03-28
Mark
A
b
r
aham
Fr
e
e
more memory in grompp a
n
d
m
drun
commit
|
commitdiff
|
tree
2018-03-28
Berk H
e
ss
Remove mo
l
s
f
rom gm
x
_mtop
_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abrah
a
m
Merg
e
branch release-2018
commit
|
commitdiff
|
tree
2018-03-27
Mark
Abraham
C
larified mdp options relatin
g
t
o
bonds
commit
|
commitdiff
|
tree
2018-03-27
M
ark Abraham
M
o
re gc
c
-
8 fixes fo
r
POWER
commit
|
commitdiff
|
tree
2018-03-21
David va
n
der Spoel
Renamed
e
nt
r
opy
.
* to thermochemistr
y
.
*
commit
|
commitdiff
|
tree
2018-03-21
M
a
r
k
Abra
h
am
Version 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
M
e
rge "Mer
g
e
b
ranch
r
elease-2
0
16
into release-201
8
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abrah
a
m
U
p
date r
e
l
ease notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Ma
r
k Abraham
M
e
rge br
a
nc
h
r
e
lease-2016 into r
e
leas
e
-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
braha
m
U
pdate use of gpu_i
d
in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
B
e
rk Hess
Dis
a
llow
s
i
ngle s
i
m
u
la
t
ion w
i
th
multisim
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
brah
a
m
Update use of gpu_
i
d
in Jenk
i
n
s
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
Abrah
a
m
Update use of gpu_id in
J
enkins
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
braham
Add helper functi
o
n
t
o make a vector from
a
n ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraham
F
i
x VSX
S
IMD wi
t
h
g
c
c 8
commit
|
commitdiff
|
tree
next