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Add integration tests for exact restarts
2019-08-27
Ma
r
k Abraha
m
Add integrati
o
n tests
f
o
r exa
c
t
r
estarts
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add d
e
n
s
ity fitting parame
t
e
rs
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Access to GaussTran
s
form3D
data
commit
|
commitdiff
|
tree
2019-08-27
C
h
ristian Bla
u
Add
i
ndex
g
roup optio
n
to den
s
ity fitting
commit
|
commitdiff
|
tree
2019-08-26
Pa
u
l Bauer
Remove sectio
n
che
c
king api l
e
vel
commit
|
commitdiff
|
tree
2019-08-26
Paul Bauer
R
e
move inst
a
l
led head
e
rs from CMake
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhmurov
Add temperature couplin
g
to CU
D
A Lea
p
-Fr
o
g in
t
egrat
o
r
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric I
r
rgang
Move
gmxa
p
icompat TP
R
tools to l
i
bgmx
a
pi
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Irrgang
Reduce artificial header dependencies in restr
a
int
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Ch
r
istian B
l
au
Activation of den
s
ity fittin
g
and move o
f
module notifications
commit
|
commitdiff
|
tree
2019-08-25
S
z
i
lárd Páll
clang-tidy
8
fixes for the GPU hos
t
code
-
p
a
t
h
commit
|
commitdiff
|
tree
2019-08-25
Szilárd Páll
F
ur
t
her fixes for clang-
t
idy clang version 8
commit
|
commitdiff
|
tree
2019-08-23
Paul Ba
u
e
r
Removes
c
h
e
cker for
in
s
t
a
lled
f
iles
commit
|
commitdiff
|
tree
2019-08-23
Szil
á
rd
P
áll
Fi
x
clan
g
-ti
d
y warnin
g
s in the OpenCL bu
i
l
d
commit
|
commitdiff
|
tree
2019-08-23
Mark Abraham
Updat
e
cla
n
g-tidy to clang ve
r
s
ion 8
commit
|
commitdiff
|
tree
2019-08-22
Mark Abraham
Merge b
r
a
nch release-
2
01
9
commit
|
commitdiff
|
tree
2019-08-22
Mark Abraham
Improve clang-
a
nalyzer bui
l
d
t
i
m
e
commit
|
commitdiff
|
tree
2019-08-22
M
.
E
r
ic
I
rr
g
ang
C++ code
a
n
d
Python b
i
n
d
ing
s
for TPR parameter
r
ead
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
Be
r
k Hess
Fix
p
e
rturbed bonded
b
ug
commit
|
commitdiff
|
tree
2019-08-21
M
.
Er
i
c I
r
rgang
Enable
G
MXAPI by def
a
u
lt
.
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Mer
g
e two dih
e
dral functions
commit
|
commitdiff
|
tree
2019-08-20
Berk
H
ess
Use sh
i
ftForces
i
n
ForceO
u
puts
commit
|
commitdiff
|
tree
2019-08-20
Erik Lin
d
ahl
A
v
o
i
d u
s
ing G
M
X_SIMD mac
r
os
to detect _
m
m_pause()
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Fix issues for clan
g
-anal
y
zer-8
commit
|
commitdiff
|
tree
2019-08-20
Be
r
k Hess
Make bo
n
ded vi
r
ial computation c
o
nditional
commit
|
commitdiff
|
tree
2019-08-19
Szilárd Páll
S
w
itch to ARM HPC to
o
lchain v19
.
2 in po
s
t-s
u
bmit
commit
|
commitdiff
|
tree
2019-08-19
Mark Abraham
Modernize t_ma
t
rix, t_
m
appin
g
, t_rgb
commit
|
commitdiff
|
tree
2019-08-19
M
ark Abraham
M
o
dernize t_
p
sdata
commit
|
commitdiff
|
tree
2019-08-19
Szilárd Páll
Work
around clang
C
UDA
d
evice c
o
de codege
n
bug
commit
|
commitdiff
|
tree
2019-08-16
Szilárd Páll
Fix sim
_
util
.
cpp copyright heade
r
commit
|
commitdiff
|
tree
2019-08-16
M
ark Abrah
a
m
Up
d
a
te
t
estin
g
matrices and fix warnings
commit
|
commitdiff
|
tree
2019-08-16
Mark A
b
raham
Stop nbnxm/grid
.
h depending on SIMD module
commit
|
commitdiff
|
tree
2019-08-15
Szilárd Páll
F
i
x OpenCL gather reduction
commit
|
commitdiff
|
tree
2019-08-14
Chri
s
tian Bl
a
u
In
f
o
class to nam
e
a
nd gen
e
rate the
d
ensityfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Mark
Abraham
Fix vv integrators
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric I
r
rga
n
g
Add initial
.
clang-forma
t
file
.
commit
|
commitdiff
|
tree
2019-08-13
M
a
rk
A
braham
Fix icc 19 codegen
i
ssue
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric
Irrgan
g
Introduce Cont
e
xt r
e
q
u
irement
.
commit
|
commitdiff
|
tree
2019-08-12
Mark Abraham
Quiet
w
a
rning
commit
|
commitdiff
|
tree
2019-08-12
M
ar
k
Abra
h
am
F
i
x o
c
l_
k
ernel target
commit
|
commitdiff
|
tree
2019-08-12
Pascal Merz
Use
new setenv function
f
o
r energyoutput test
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric Irrgang
Sep
a
rate out some
a
bstract base
c
lass
e
s
.
commit
|
commitdiff
|
tree
2019-08-09
Art
e
m
Zhmu
r
ov
Prepa
r
e Updat
e
a
nd Constrain
t
s
for
D
o
m
a
i
n Dec
o
mpo
s
it
i
o
n
commit
|
commitdiff
|
tree
2019-08-09
Artem
Zhmu
r
ov
Refactoring
o
f
the SETTLE tests
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
SIMD acceler
a
tion for
F
_FOURDIHS
a
nd F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-08
M
a
rk Abraham
Fix estimate of the size
of a
j
l
i
st
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
r
ic Irrgang
Add g
m
xa
p
i_
p
ytest custom target to CMake `chec
k
` tar
g
et
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eri
c
Irrgan
g
Allow gmxapi Python packag
e
tests
to be
r
un from GROMACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
Christi
a
n
B
lau
Harmonize mrc density fo
r
mat extents with rest of code
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
r
ic Irrg
a
n
g
Reenable
g
test_ma
i
n
target
.
commit
|
commitdiff
|
tree
2019-08-08
M
ark
Abraham
Stop testing ICC on Windows
commit
|
commitdiff
|
tree
2019-08-08
Arte
m
Zhmu
r
ov
Refactor Leap-Frog
tests and co
n
nect
t
h
e
m to CPU
v
ersion
commit
|
commitdiff
|
tree
2019-08-07
M
.
Eric
I
rr
g
an
g
Use gmock and gtest target
s
fro
m
google
t
est-release
.
.
.
commit
|
commitdiff
|
tree
2019-08-05
Pas
c
al Me
r
z
Move ownership of kin
e
tic energy object to ISimulator
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Added Simulator comparison test
commit
|
commitdiff
|
tree
2019-08-05
Mark
A
braham
Rem
o
ve lib
g
r
o
macs_genera
t
ed cont
r
ibutio
n
s
from FindCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-02
yongwang
C
P
H
Solve issu
e
with de
m
u
x
.
p
l
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Re
m
ove a pointer in t_f
o
rcerec
commit
|
commitdiff
|
tree
2019-08-01
Berk Hes
s
Fix n
b
nxm
G
PU memory reservation issue
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
Mana
g
e
compile
r
flags and some inclu
d
e
option
s
per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark
A
bra
h
am
Improve use of object
lib
r
aries in li
b
groma
c
s
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
Merge "M
e
rge re
l
ease
-
201
9
into master"
commit
|
commitdiff
|
tree
2019-07-31
Berk
H
ess
Add grompp warning wit
h
use of GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Artem Zh
m
urov
Int
r
oduc
e
f
unction that checks if the com
p
uta
t
ions
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Szil
á
rd
Páll
F
i
xes for F buffer
o
p
s cha
n
ge
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Remove need
f
or GR
O
MO
S
FF in test
commit
|
commitdiff
|
tree
2019-07-31
Pascal Merz
Rename Simulat
o
r to LegacyS
i
mulator
commit
|
commitdiff
|
tree
2019-07-31
Szilár
d
P
áll
Move c
y
cle
co
u
n
ting
into
t
he
G
PU b
o
nd
e
d mo
d
ule
commit
|
commitdiff
|
tree
2019-07-31
Szilárd
P
á
ll
Report whe
n
development
f
eature flags ar
e
u
s
ed
commit
|
commitdiff
|
tree
2019-07-31
Szil
á
r
d
P
á
l
l
Move end of st
e
p
G
PU t
a
sk
launc
h
es to a function
commit
|
commitdiff
|
tree
2019-07-30
Paul B
a
uer
Add w
r
apper fo
r
o
utputada
p
ter method
s
commit
|
commitdiff
|
tree
2019-07-28
B
e
rk He
s
s
Co
n
vert
E
wald correction tables to C++
commit
|
commitdiff
|
tree
2019-07-26
Berk H
e
ss
Add de
f
a
ult
i
nitia
l
izat
i
on to inter
a
ction_const_t
commit
|
commitdiff
|
tree
2019-07-26
Christian Blau
Fix failing che
c
k-source t
a
rget on python3
.
6
commit
|
commitdiff
|
tree
2019-07-25
B
e
rk Hess
Spli
t
canDetectGpus(
)
commit
|
commitdiff
|
tree
2019-07-25
Szilárd Páll
O
n
ly stop the CUDA profiler
if there are
d
evice
s
commit
|
commitdiff
|
tree
2019-07-24
Paul B
a
uer
F
ix doxygen in coordianteio files
commit
|
commitdiff
|
tree
2019-07-24
Paul Bauer
Add o
u
tp
u
tadapt
e
rs (
3
/
3
)
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
F
i
x
g
mxapi notebo
o
k im
a
ge and sa
m
ple_re
s
tra
i
nt dock
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irr
g
a
n
g
Im
p
rove
gmxapi d
o
cker testing
envi
r
o
nment
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
Eri
c
Irr
g
ang
Don't install sampl
e
restrai
n
t pa
c
kage
b
y defaul
t
.
commit
|
commitdiff
|
tree
2019-07-23
K
e
vin Boyd
Mo
d
ernize syntax of enabl
e
_i
f
and trait
s
t
o
use _t
.
.
.
commit
|
commitdiff
|
tree
2019-07-09
David van der
S
po
e
l
Fixed s
m
al
l
bug in gmx anaeig
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric
I
rrgang
Incorporate
s
ampl
e
_restraint repository
.
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric Irrgang
Begin
CMake front-end f
o
r Python packaging machinery
.
commit
|
commitdiff
|
tree
2019-07-08
Szilárd P
á
l
l
E
liminate a us
e
of
d
ou
b
le
p
recision i
n
the GPU bonded
.
.
.
commit
|
commitdiff
|
tree
2019-07-08
Berk Hess
Sto
r
e nbnxm
g
ri
d
S
et
d
ata in GridSetData
commit
|
commitdiff
|
tree
2019-07-05
Mark Abraha
m
M
o
de
r
niz
e
FindHwl
o
c
.
cmake
commit
|
commitdiff
|
tree
2019-07-05
M
.
Er
i
c
I
rr
g
ang
P
y
thon bi
n
dings for mdr
u
n
.
commit
|
commitdiff
|
tree
2019-07-04
Mark
Abra
h
am
Furth
e
r
c
l
ang-tidy-7 fix
commit
|
commitdiff
|
tree
2019-07-03
Ar
t
em Zhmurov
Combine
CUDA
Leap-
F
rog, L
I
NCS and SETT
L
E
.
II
.
commit
|
commitdiff
|
tree
2019-07-03
Kevin Boyd
Updates
t
o
math/
v
ec
.
h
commit
|
commitdiff
|
tree
2019-07-02
Mark A
b
r
a
ham
Clarify w
o
r
ding of release
notes
commit
|
commitdiff
|
tree
2019-07-02
Berk H
e
ss
R
e
-en
a
ble af
f
inity dia
g
onostics wit
h
MPI
commit
|
commitdiff
|
tree
2019-07-02
K
e
v
i
n Bo
y
d
Add f
u
nction for
c
a
l
c
ulating 3x3 matrix deter
m
in
a
nt
commit
|
commitdiff
|
tree
2019-07-02
Kevi
n
Boyd
R
e
m
o
v
e references to
ecutsGR
O
U
P
commit
|
commitdiff
|
tree
2019-07-01
P
ascal Merz
Fix
m
o
dule det
e
ction for physical val
i
dation
commit
|
commitdiff
|
tree
2019-07-01
Szilárd Páll
Refactor tracking of GPU
s
h
ort-r
a
nge
w
o
r
k/skippin
g
commit
|
commitdiff
|
tree
2019-07-01
Berk Hes
s
F
ix
MPI dea
d
lock in a
f
finity s
e
tting
commit
|
commitdiff
|
tree
2019-07-01
M
.
Eri
c
I
r
rgang
gmxapi P
y
th
o
n package
d
o
c
umentation infrastr
u
cture
.
commit
|
commitdiff
|
tree
next