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Merge branch release-2019
2019-08-22
Ma
r
k Ab
r
aha
m
Merge b
r
anch release-
2
0
1
9
commit
|
commitdiff
|
tree
2019-08-22
Mark Abraham
Improve
c
lang-
a
nalyzer
b
uild time
commit
|
commitdiff
|
tree
2019-08-22
M
.
Eric
I
r
r
gang
C++ c
o
de and P
y
thon bindings for
T
PR parameter
read
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
Berk
H
ess
F
ix perturbed bon
d
ed bug
commit
|
commitdiff
|
tree
2019-08-21
M
.
Eri
c
Irrgan
g
E
n
ab
l
e GMXAPI by
defaul
t
.
commit
|
commitdiff
|
tree
2019-08-20
B
e
rk Hess
Merge two dihedral functi
o
ns
commit
|
commitdiff
|
tree
2019-08-20
Ber
k
Hess
Use shift
F
orces in ForceO
u
puts
commit
|
commitdiff
|
tree
2019-08-20
Erik Lindahl
Avoid
using GMX_SIMD
macros to de
t
ect
_
mm
_
pause()
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Fix issues
f
o
r cla
n
g-an
a
lyzer-8
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make bonded virial computa
t
i
o
n
conditional
commit
|
commitdiff
|
tree
2019-08-19
Szilárd Páll
Switch to ARM H
P
C to
o
l
chain
v
1
9
.
2 in post-submit
commit
|
commitdiff
|
tree
2019-08-19
M
ark A
b
ra
h
am
Modernize t
_
m
a
trix, t_mapping,
t
_rgb
commit
|
commitdiff
|
tree
2019-08-19
M
ark
A
braham
Modernize t_ps
d
at
a
commit
|
commitdiff
|
tree
2019-08-19
Szilárd
Páll
Work around clang
CU
D
A devi
c
e code codege
n
b
u
g
commit
|
commitdiff
|
tree
2019-08-16
Szilárd Páll
Fix sim_util
.
cpp copy
r
ight header
commit
|
commitdiff
|
tree
2019-08-16
M
ark Abraham
Update test
i
n
g
matrice
s
and fix warnings
commit
|
commitdiff
|
tree
2019-08-16
Mark Abraham
Stop nbnxm/grid
.
h depending on SI
M
D module
commit
|
commitdiff
|
tree
2019-08-15
Szilárd Páll
Fix
OpenCL g
a
ther reduction
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
Info class to name and
generate the densityfitti
n
g
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Mark Abrah
a
m
Fix vv integrat
o
rs
commit
|
commitdiff
|
tree
2019-08-14
M
.
E
r
ic Irrgang
A
dd initial
.
c
l
ang-format file
.
commit
|
commitdiff
|
tree
2019-08-13
Mark
A
braham
F
i
x
icc 19 c
o
de
g
en
issue
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric
Irrgang
Intro
d
uce Conte
x
t requirement
.
commit
|
commitdiff
|
tree
2019-08-12
Mark
Abraham
Qu
i
et warni
n
g
commit
|
commitdiff
|
tree
2019-08-12
Mark Abraham
Fix o
c
l
_kernel t
a
rget
commit
|
commitdiff
|
tree
2019-08-12
Pascal Mer
z
Use new
s
e
tenv function for ene
r
gyoutp
u
t test
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric Irrgang
Separate out some abstract base classes
.
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmurov
Prepare Update and C
o
nstraints for Domain Decomposition
commit
|
commitdiff
|
tree
2019-08-09
Artem
Z
hmurov
Refac
t
oring of the SETTLE t
e
st
s
commit
|
commitdiff
|
tree
2019-08-09
B
erk Hess
SI
M
D a
c
ce
l
eration for F_F
O
URDIHS and
F
_PIDI
H
S
commit
|
commitdiff
|
tree
2019-08-08
Ma
r
k Ab
r
ah
a
m
Fix estimate of t
h
e s
i
ze
o
f a j l
i
st
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Add gmxapi_py
t
e
st custom target to
C
M
a
k
e `check` target
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrga
n
g
Allow gmxapi
Python package t
e
sts to be run f
r
om G
R
O
M
ACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
Christ
i
an Blau
Ha
r
monize mrc density format extent
s
w
i
th rest of code
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
r
ic
I
rrgang
Reenable
g
t
est_main targe
t
.
commit
|
commitdiff
|
tree
2019-08-08
Mark Abrah
a
m
Stop testing ICC on
Windows
commit
|
commitdiff
|
tree
2019-08-08
Ar
t
e
m Zhmuro
v
Re
f
a
c
tor Leap-Frog tes
t
s
a
nd
c
onnec
t
them to
C
PU version
commit
|
commitdiff
|
tree
2019-08-07
M
.
Eric Irrgang
U
se gmock
a
nd gtest targets from googletest-relea
s
e
.
.
.
commit
|
commitdiff
|
tree
2019-08-05
P
a
s
c
al Merz
M
ove own
e
r
ship of kinetic ene
r
g
y
obj
e
c
t
t
o ISimulat
o
r
commit
|
commitdiff
|
tree
2019-08-05
P
a
scal M
e
rz
Adde
d
Si
m
ulator
comparison t
e
st
commit
|
commitdiff
|
tree
2019-08-05
Mark Abraham
Re
m
ove libgromacs_generated contributi
o
ns from FindCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-02
yongwang
C
PH
Solve issue with dem
u
x
.
pl
commit
|
commitdiff
|
tree
2019-08-01
Be
r
k Hess
Remove a pointer
i
n t_forcerec
commit
|
commitdiff
|
tree
2019-08-01
Be
r
k Hess
Fix nbnxm GP
U
memory re
s
ervation
issue
commit
|
commitdiff
|
tree
2019-08-01
M
a
rk Abrah
a
m
Manage com
p
iler flags and some in
c
lu
d
e o
p
tion
s
per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Ma
r
k Ab
r
ah
a
m
Im
p
r
o
v
e
use of object libraries in
l
ibgr
o
macs
commit
|
commitdiff
|
tree
2019-08-01
Mark
A
brah
a
m
Merg
e
"
M
erg
e
r
e
l
ea
s
e-2019 into master"
commit
|
commitdiff
|
tree
2019-07-31
Ber
k
Hess
Add
g
rompp
war
n
ing with
us
e
of
G
ROMO
S
FF
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhm
u
rov
Int
r
oduce fu
n
c
t
ion
t
hat checks if
t
he
compu
t
atio
n
s
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Szilárd
P
ál
l
Fixes for F
b
uffer ops chang
e
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Remove need for GROMOS
F
F
in t
e
st
commit
|
commitdiff
|
tree
2019-07-31
Pasca
l
Mer
z
Renam
e
Si
m
ulator t
o
L
egacySimulator
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Mo
v
e cyc
l
e counting into the GPU bonded modul
e
commit
|
commitdiff
|
tree
2019-07-31
Sz
i
lárd Páll
Report when development feat
u
re flags a
r
e used
commit
|
commitdiff
|
tree
2019-07-31
Szilár
d
Páll
M
o
ve end of step GPU task launches to
a functio
n
commit
|
commitdiff
|
tree
2019-07-30
Paul Baue
r
Add wrapper
fo
r
o
u
tputadapter
me
t
hods
commit
|
commitdiff
|
tree
2019-07-28
B
e
rk Hess
C
o
nver
t
Ewald co
r
rection tables to
C++
commit
|
commitdiff
|
tree
2019-07-26
B
er
k
Hess
Add default initializa
t
ion
t
o
inte
r
action_const_t
commit
|
commitdiff
|
tree
2019-07-26
Christian Bla
u
Fix
f
ailing c
h
eck-source
t
arget on python3
.
6
commit
|
commitdiff
|
tree
2019-07-25
Berk Hes
s
Split canDet
e
ctGpus()
commit
|
commitdiff
|
tree
2019-07-25
Szi
l
árd Páll
O
nly stop
t
h
e CU
D
A profi
l
er if t
h
ere
a
re devices
commit
|
commitdiff
|
tree
2019-07-24
Paul Bauer
Fix doxyge
n
in coor
d
ianteio files
commit
|
commitdiff
|
tree
2019-07-24
Pau
l
Ba
u
er
Add
outputadapters (3/3)
commit
|
commitdiff
|
tree
2019-07-24
M
.
E
r
i
c
Irrgang
Fix gmxapi n
o
t
e
book image an
d
sample_re
s
trai
n
t docke
r
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
E
r
ic Irr
g
an
g
I
m
prove gmxap
i
dock
e
r
t
e
sting environ
m
ent
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
E
r
i
c
Ir
r
gang
D
o
n
't
ins
t
all sa
m
p
l
e
restraint pac
k
age by def
a
ul
t
.
commit
|
commitdiff
|
tree
2019-07-23
K
evin Bo
y
d
Modernize syntax of e
n
able_if and trait
s
to u
s
e _t
.
.
.
commit
|
commitdiff
|
tree
2019-07-09
David van der Sp
o
el
Fix
e
d
small bug in gmx anaeig
commit
|
commitdiff
|
tree
2019-07-09
M
.
E
ric Irrga
n
g
In
c
or
p
ora
t
e
s
ampl
e
_
restraint
r
eposit
o
ry
.
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric Irrgang
B
e
gin CMake front-end
f
or
P
ytho
n
pac
k
a
g
ing m
a
chinery
.
commit
|
commitdiff
|
tree
2019-07-08
Szilárd Pál
l
Elimin
a
te
a
use of double
precision in the GPU bon
d
ed
.
.
.
commit
|
commitdiff
|
tree
2019-07-08
Berk Hess
Store nbnxm g
r
idSe
t
data in
G
ridSe
t
D
a
ta
commit
|
commitdiff
|
tree
2019-07-05
Mark Abraha
m
Modern
i
ze FindHwl
o
c
.
cmake
commit
|
commitdiff
|
tree
2019-07-05
M
.
E
r
ic Irrgan
g
Python
b
inding
s
for mdrun
.
commit
|
commitdiff
|
tree
2019-07-04
Mark Abraham
Fur
t
her
clang-tidy-
7
fix
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmu
r
o
v
Combine CUDA
L
eap
-
F
r
o
g,
L
INCS and
S
ETTLE
.
II
.
commit
|
commitdiff
|
tree
2019-07-03
Kevin Boyd
Updates to
m
a
th/vec
.
h
commit
|
commitdiff
|
tree
2019-07-02
Mark Abrah
a
m
Clarify wording
of
r
elease note
s
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Re-ena
b
le affinity
d
iagonostics
wi
t
h MPI
commit
|
commitdiff
|
tree
2019-07-02
Kevin B
o
yd
Add
function for calcu
l
ating 3x3 matri
x
det
e
rminant
commit
|
commitdiff
|
tree
2019-07-02
Kevin
B
o
y
d
Remove r
e
ferences to e
c
uts
G
ROUP
commit
|
commitdiff
|
tree
2019-07-01
P
ascal
Merz
Fix
modul
e
detection for
p
hys
i
cal v
a
lidatio
n
commit
|
commitdiff
|
tree
2019-07-01
Szilá
r
d Páll
Refa
c
tor tracking of GPU
shor
t
-range
work/sk
i
pping
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
F
i
x MP
I
deadlock in affinity setting
commit
|
commitdiff
|
tree
2019-07-01
M
.
Eric Irrg
a
ng
gmxapi
Py
t
h
o
n
package
docume
n
tation inf
r
astruc
t
ure
.
commit
|
commitdiff
|
tree
2019-06-30
Szilárd
P
áll
C
re
a
te dedicated subcoun
t
er
for nonbonded FEP
commit
|
commitdiff
|
tree
2019-06-30
Kevin
B
oyd
R
e
mo
v
e grou
p
scheme ch
e
cks fr
o
m runner
commit
|
commitdiff
|
tree
2019-06-30
M
agnus
L
undbo
r
g
Cle
a
ning up the GPU bonded
kerne
l
commit
|
commitdiff
|
tree
2019-06-20
Paul
B
auer
Us
e
ISerializer
fo
r
TPR f
i
le IO
commit
|
commitdiff
|
tree
2019-06-20
Berk He
s
s
Template free-en
e
rgy
k
ernel on soft
-
cor
e
commit
|
commitdiff
|
tree
2019-06-20
Chri
s
tian Blau
Add BasicVector scaling, m
a
x, min and toIv
e
c
commit
|
commitdiff
|
tree
2019-06-19
Szilár
d
Pál
l
Disable PME GPU on Apple OpenCL
commit
|
commitdiff
|
tree
2019-06-19
B
e
rk He
s
s
Refactor PME atom handli
n
g
commit
|
commitdiff
|
tree
2019-06-19
Pau
l
Ba
u
e
r
Split tpr h
e
ader readi
n
g
r
e
a
ding f
r
om tpr body
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
R
e
m
ove
d
unused
c
ode paths
in the
NB FE kernel
commit
|
commitdiff
|
tree
2019-06-18
P
aul Bauer
Fix gmx
d
ump
commit
|
commitdiff
|
tree
2019-06-18
M
ark A
b
raham
Move code hand
l
i
n
g mdrun -g
p
u_i
d
t
o taskassig
n
ment
.
.
.
commit
|
commitdiff
|
tree
2019-06-18
Berk Hess
Make force
r
ec const in d
i
spatchNon
b
onde
d
Kernel()
commit
|
commitdiff
|
tree
2019-06-18
Christian
Blau
Mrc forma
t
header to latti
c
e coordinat
e
transf
o
rm
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Density similari
t
y
measure and gradient
commit
|
commitdiff
|
tree
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