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Convert nbnxn_search to C++
2018-05-23
Berk He
s
s
Convert nbn
x
n_search
t
o C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
C
h
ange
n
bnxn grid real
l
oc
a
t
i
on
commit
|
commitdiff
|
tree
2018-05-22
B
erk Hess
Use st
d
::vect
o
r in nbn
x
n_sear
c
h_t
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
H
e
s
s
Use std::vector in nbnxn_grid_t
commit
|
commitdiff
|
tree
2018-05-22
K
evin
B
oyd
C
o
s
m
eti
c
documen
t
at
i
on changes
commit
|
commitdiff
|
tree
2018-05-22
Kevin
B
oyd
Minor fi
x
es
t
o mdrun perfor
m
ance documentation
commit
|
commitdiff
|
tree
2018-05-18
Al
e
k
s
ei Iupinov
prepareGpuK
e
rnelArg
u
ments() and launchG
p
uKer
n
el
(
)
a
re
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Ber
k
Hess
S
plit
off
d
o
mdec
distr
i
bution and
c
ellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Spl
i
t atom redistribution
off from domdec
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-17
B
e
rk H
e
ss
Remove comm
r
e
c
fr
o
m se
t
_ddbo
x
()
commit
|
commitdiff
|
tree
2018-05-15
Roland Schulz
Use same
O
p
enCL kernel for
different Ve
n
dors
commit
|
commitdiff
|
tree
2018-05-10
Carsten Kutzner
Introduce hel
p
er
c
lasses for force provider input and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul Bauer
Fi
x
md -c
p
i
-noappe
n
d
commit
|
commitdiff
|
tree
2018-05-04
Mark
Abraham
Merge "Merge branch
relea
s
e-2018"
commit
|
commitdiff
|
tree
2018-05-04
Mark Abraham
More cons
t
corre
c
t
ness
commit
|
commitdiff
|
tree
2018-05-03
M
ark Abraham
Merge branch releas
e
-2018
commit
|
commitdiff
|
tree
2018-05-02
Roland
Schulz
Enable uncrustify f
o
r OpenCL
commit
|
commitdiff
|
tree
2018-05-02
R
olan
d
Schulz
Suppo
r
t
4
sized cluster fo
r
GPU NB
L
sear
c
h
commit
|
commitdiff
|
tree
2018-04-27
B
erk H
e
s
s
Remove pull MPI code duplica
t
i
o
n
commit
|
commitdiff
|
tree
2018-04-26
Paul
Bauer
Reor
g
aniz
e
files for r
e
ference manual
commit
|
commitdiff
|
tree
2018-04-26
P
a
u
l Ba
u
er
Split up ana
l
ysis chapter in reference
manual
commit
|
commitdiff
|
tree
2018-04-26
Pau
l
Bauer
Split
u
p speci
a
l top
i
cs s
e
ction in manual
commit
|
commitdiff
|
tree
2018-04-25
Pa
u
l
B
a
u
er
A
d
d
page breaks
i
n referen
c
e manual
commit
|
commitdiff
|
tree
2018-04-25
P
aul
B
auer
Split
up Inte
r
actio
n
functions manu
a
l page
commit
|
commitdiff
|
tree
2018-04-25
Mar
k
A
braham
R
efactor SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul Ba
u
er
Chan
g
e image
c
o
nversio
n
to only be bu
i
ld on
c
e
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
De
v
i
c
eBuffer headers are a
d
ded
commit
|
commitdiff
|
tree
2018-04-23
Szilárd Páll
Fix
i
cc
w
arning
i
n
p
ost
-
submit
commit
|
commitdiff
|
tree
2018-04-21
Sz
i
lárd Páll
Add p
o
st
-
submit
w
it
h
A
R
M HPC T
o
olchain
commit
|
commitdiff
|
tree
2018-04-21
Szi
l
árd Páll
T
weak PME run mode che
c
ks
commit
|
commitdiff
|
tree
2018-04-21
P
a
ul Bau
e
r
Convert
m
a
n
ual from LaTeX to M
a
rkup
commit
|
commitdiff
|
tree
2018-04-21
Pau
l
Bauer
S
econd change tr
a
ck
i
n
g
commit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Int
e
rme
d
iate
c
o
mmit to track chan
g
es to manual
commit
|
commitdiff
|
tree
2018-04-17
V
i
veca
Lindahl
D
isallow -
s
kip
values
<
= 0 for gmx tr
j
conv
.
commit
|
commitdiff
|
tree
2018-04-17
Pau
l
Bauer
Fix legacy topol
o
gy m
e
mory err
o
r
commit
|
commitdiff
|
tree
2018-04-17
Mark
Abr
a
ham
Shift per-step control logic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark Ab
r
a
ham
Break
apart
update_constrain
t
s
commit
|
commitdiff
|
tree
2018-04-16
Szilár
d
Pál
l
Ad
d
post
-
submit
test with hwloc off
commit
|
commitdiff
|
tree
2018-04-16
B
er
k
Hess
Move n
a
toms_mo
l
out of gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-16
Mark Abraham
U
p
dated mdrun co
m
parison infrastruc
t
ure
commit
|
commitdiff
|
tree
2018-04-13
Mark Abra
h
a
m
C
l
ean
u
p c
o
nstr
a
ints code
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Remove
use of wh
e
re(),
i
f DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Reorganize ene
r
gy evalua
t
ion for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
Prevent OpenCL timing memory leak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert gmx_molblock
_
t to C
+
+
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Simplified handling of sim
u
lati
o
n ru
n
ners
commit
|
commitdiff
|
tree
2018-04-05
Mark
A
braham
Create gro
m
acs/mdrun module a
n
d move cod
e
there
commit
|
commitdiff
|
tree
2018-04-05
Szilárd Páll
Refacto
r
cj pr
e
load in
the nonbonded OpenCL kernels
commit
|
commitdiff
|
tree
2018-04-04
Mark Abraha
m
Quie
t
checkpoint reading
commit
|
commitdiff
|
tree
2018-04-04
Pascal Merz
Move checkNumber
O
fBonde
d
Inte
r
actions
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Conve
r
t gm
x
_mtop_t t
o
C++
commit
|
commitdiff
|
tree
2018-04-03
Ma
r
k Ab
r
a
h
a
m
Remove
left
o
ver ment
i
on of
twin-range
sc
h
eme
commit
|
commitdiff
|
tree
2018-04-03
Mar
k
Abraham
Me
r
ge "
M
erge branc
h
rele
a
se-2018"
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
ess
Move file opening out o
f
init_pull(
)
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
T
we
a
k
/enable icc
1
8 post-submit tests
commit
|
commitdiff
|
tree
2018-03-29
M
a
gnus
L
u
ndborg
Improved check of if only forces are computed in do_pa
i
rs()
commit
|
commitdiff
|
tree
2018-03-29
Paul B
a
uer
Fix c
m
ake Sphinx dete
c
t
ion f
o
r
v
ersion
s
>1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
S
zilárd Páll
Switc
h
CUDA 9
.
0/gcc 5 test t
o
CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modular
i
ze p
u
ll_coo
r
d
_
work_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abr
a
ham
Fre
e
more memory
in grompp and mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remove mols from gmx_mto
p
_t
commit
|
commitdiff
|
tree
2018-03-28
Mark
A
b
raham
Merge b
r
anch release-
2
0
18
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
Clarified mdp opt
i
ons relating to bon
d
s
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
Mo
r
e
gcc-8 fix
e
s for POW
E
R
commit
|
commitdiff
|
tree
2018-03-21
Da
v
id
v
a
n der Spoel
Renamed entropy
.
*
to ther
m
ochem
i
stry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Versio
n
2
0
18
.
1
commit
|
commitdiff
|
tree
2018-03-21
Ma
r
k Abrah
a
m
Merge "M
e
r
ge b
r
anch rele
a
se-2016 into releas
e
-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
U
pdate relea
s
e notes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Ab
r
aham
Me
r
ge branch rel
e
ase
-
2016 into release
-
2018
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
Ab
r
aham
Update use of g
p
u_id in Jen
k
ins
commit
|
commitdiff
|
tree
2018-03-20
Berk
H
ess
Disallo
w
single s
i
mul
a
tion
with multisim
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abraham
Upd
a
te use of
g
pu
_
id in Jen
k
ins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Updat
e
u
se of
g
pu
_
id
i
n
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
M
a
r
k Ab
r
aham
A
d
d
h
e
lp
e
r func
t
ion to make a
vector from an A
r
r
ayRef
commit
|
commitdiff
|
tree
2018-03-19
M
a
r
k
A
braham
Fix VSX
S
I
MD with gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bau
e
r
Only free topol
o
gy
when allocated
commit
|
commitdiff
|
tree
2018-03-16
B
e
rk Hess
Correct
P
M
F
s
ig
n
error in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
B
erk He
s
s
Improve
i
nter-simulation signa
l
ing
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Make a persistent phys
i
cal
n
ode communicator
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
ess
Fix mdrun signalling with
A
WH bias
s
h
a
r
ing
commit
|
commitdiff
|
tree
2018-03-13
B
erk Hess
Add AWH fixes to rel
e
ase
notes
commit
|
commitdiff
|
tree
2018-03-13
Sz
i
lárd
P
áll
Requir
e
OpenCL
1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
F
i
x
AWH ensem
b
l
e
c
heckpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH de
c
onvolut
i
o
n
when shari
n
g a bias
commit
|
commitdiff
|
tree
2018-03-13
Mar
k
Abrah
a
m
Int
r
o
d
uce constrain_shake
commit
|
commitdiff
|
tree
2018-03-13
Szilárd P
á
l
l
Fix cla
n
g 6
.
0
wit
h
CUDA 9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark Abraham
M
e
rge
"
Merge branch
r
e
lease-2018"
commit
|
commitdiff
|
tree
2018-03-09
Berk
H
ess
Corre
c
t pdb2gmx -m
i
s
s
ing option
commit
|
commitdiff
|
tree
2018-03-06
Berk
Hess
Conv
e
rt t_filenm t
o
C++
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Merg
e
branch rele
a
se-2018
commit
|
commitdiff
|
tree
2018-03-06
Mark
A
braham
Fixed dvdl
a
mbd
a
for SHAK
E
+ FE
commit
|
commitdiff
|
tree
2018-03-05
Szilárd Páll
Add to the contr
i
butor secti
o
n
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect AM
D
SMT topolog
y
commit
|
commitdiff
|
tree
2018-02-28
M
ark Abraham
Moved a
n
d r
e
moved constraint code
commit
|
commitdiff
|
tree
2018-02-28
Mark A
b
raham
Reorga
n
iz
e
d
c
onstraint code
commit
|
commitdiff
|
tree
2018-02-27
Mark
A
b
raham
F
ix GPU utils te
s
t
commit
|
commitdiff
|
tree
2018-02-26
Paul Bauer
C
h
ange
TNG file opening
commit
|
commitdiff
|
tree
2018-02-26
M
ark Abraham
Pe
r
mit
d
efine
.
mdp field to ass
i
g
n
values
commit
|
commitdiff
|
tree
2018-02-26
Al
e
ksei
Iu
p
inov
Advi
c
e users on inf
i
nite output of
T
PI
commit
|
commitdiff
|
tree
2018-02-26
Mar
k
A
brah
a
m
Organize for reco
r
ding 2016-er
a
release notes and add
.
.
.
commit
|
commitdiff
|
tree
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