repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Fix integration issues
2019-08-28
Mark Abraham
Fix
i
n
t
e
gration issues
commit
|
commitdiff
|
tree
2019-08-28
Pascal Mer
z
Introduce th
e
main modular sim
u
lator interfaces and
.
.
.
commit
|
commitdiff
|
tree
2019-08-28
P
aul Bauer
Change tolerance for normal mod
e
tests
commit
|
commitdiff
|
tree
2019-08-28
S
zi
l
árd
Páll
Add clang-
t
idy n
i
ghtly test with SIMD + OpenCL
commit
|
commitdiff
|
tree
2019-08-28
S
zilárd Páll
Move nonbonded
G
PU wai
t
timing into the GPU module
commit
|
commitdiff
|
tree
2019-08-27
Mark Abraham
Add integr
a
tion test
s
for exact restarts
commit
|
commitdiff
|
tree
2019-08-27
Christia
n
Blau
Add
d
ensity
f
itting
par
a
meters
commit
|
commitdiff
|
tree
2019-08-27
Christian
Blau
Acces
s
to Gauss
T
rans
f
or
m
3D data
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add inde
x
group optio
n
t
o
d
en
s
it
y
f
itting
commit
|
commitdiff
|
tree
2019-08-26
P
aul Bauer
Remov
e
sectio
n
checking api level
commit
|
commitdiff
|
tree
2019-08-26
Pau
l
Bauer
Remove insta
l
led heade
r
s fr
o
m CMake
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhmurov
A
d
d
t
empe
r
ature coupling
to
CUDA Leap-Fro
g
integrator
commit
|
commitdiff
|
tree
2019-08-26
M
.
Er
i
c
Irr
g
a
n
g
Move gmx
a
picompat TPR tools to libg
m
xapi
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
E
r
ic Irrg
a
ng
Reduce artificial
h
e
ade
r
de
p
en
d
e
n
ci
e
s in restrai
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Christian Bl
a
u
A
c
t
ivati
o
n of den
s
ity fitting and mo
v
e
o
f modul
e
no
t
ifications
commit
|
commitdiff
|
tree
2019-08-25
Szilár
d
Páll
clan
g
-tidy 8 fixes for the GPU host code-path
commit
|
commitdiff
|
tree
2019-08-25
S
z
i
lárd Páll
Further fixes for clang-ti
d
y c
l
a
n
g version 8
commit
|
commitdiff
|
tree
2019-08-23
Pau
l
Baue
r
R
emov
e
s
checker for instal
l
ed
files
commit
|
commitdiff
|
tree
2019-08-23
Szilárd
P
áll
F
ix c
l
ang-tidy warnings
in the OpenCL build
commit
|
commitdiff
|
tree
2019-08-23
Mark
A
braham
U
pdat
e
clang-tidy t
o
clang version
8
commit
|
commitdiff
|
tree
2019-08-22
Mark Abraham
Merge
bran
c
h release-2019
commit
|
commitdiff
|
tree
2019-08-22
Mark Abraham
I
m
pro
v
e
c
lang-anal
y
zer bu
i
ld time
commit
|
commitdiff
|
tree
2019-08-22
M
.
Er
i
c
Irr
g
ang
C++
c
ode
a
nd Python binding
s
for TPR parameter r
e
a
d
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
Berk Hess
Fix perturbed
bonded bug
commit
|
commitdiff
|
tree
2019-08-21
M
.
Eri
c
Irrgang
Ena
b
l
e
GMXAPI by d
e
fau
l
t
.
commit
|
commitdiff
|
tree
2019-08-20
Berk
H
ess
Merge two
d
ihedral functions
commit
|
commitdiff
|
tree
2019-08-20
B
e
rk He
s
s
Us
e
shiftForc
e
s in
ForceO
u
puts
commit
|
commitdiff
|
tree
2019-08-20
Erik L
i
ndahl
Av
o
id using GMX_SIMD m
a
cros to de
t
ect _mm_pause()
commit
|
commitdiff
|
tree
2019-08-20
Mark Abr
a
ham
Fix issues
for clang-a
n
alyzer
-
8
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make bonded virial compu
t
atio
n
con
d
it
i
on
a
l
commit
|
commitdiff
|
tree
2019-08-19
Szilárd Páll
Switch to ARM HPC
t
oolcha
i
n v19
.
2 in p
o
st-submit
commit
|
commitdiff
|
tree
2019-08-19
Mark Abraham
M
od
e
rn
i
ze t_matri
x
,
t_mapping, t
_
r
g
b
commit
|
commitdiff
|
tree
2019-08-19
Mark Abr
a
ham
Mo
d
ernize t
_
p
sdata
commit
|
commitdiff
|
tree
2019-08-19
Szil
á
rd Páll
Work around clan
g
C
U
D
A
device code codegen
bug
commit
|
commitdiff
|
tree
2019-08-16
Szilárd Páll
Fix
sim_util
.
cpp copyright
header
commit
|
commitdiff
|
tree
2019-08-16
M
a
rk Ab
r
aham
Update tes
t
ing
matrice
s
and fix warnings
commit
|
commitdiff
|
tree
2019-08-16
Mark
A
braham
Stop nbnxm/grid
.
h
depending on
S
I
M
D module
commit
|
commitdiff
|
tree
2019-08-15
Szilárd Páll
Fix OpenCL gather reduction
commit
|
commitdiff
|
tree
2019-08-14
Chris
t
ian Blau
I
nfo class to name
a
nd gener
a
te the den
s
i
t
yfitting
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Mark Abraham
Fix vv integrators
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrg
a
ng
Ad
d
initial
.
clang-
f
orma
t
file
.
commit
|
commitdiff
|
tree
2019-08-13
M
ark Abr
a
h
a
m
Fi
x
icc 19 c
o
degen
iss
u
e
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric Irr
g
a
n
g
Introdu
c
e C
o
ntext requirement
.
commit
|
commitdiff
|
tree
2019-08-12
M
a
rk Abraham
Quiet w
a
r
n
ing
commit
|
commitdiff
|
tree
2019-08-12
Mark Abraham
Fix ocl_ker
n
e
l target
commit
|
commitdiff
|
tree
2019-08-12
Pasca
l
Me
r
z
U
s
e new
s
et
e
n
v
fu
n
ction fo
r
e
nergyou
t
p
u
t te
s
t
commit
|
commitdiff
|
tree
2019-08-12
M
.
Er
i
c
I
r
rga
n
g
Separate
o
ut some abstract base classes
.
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmu
r
ov
Prepare
U
pda
t
e
and Constraints for Dom
a
in Decomposition
commit
|
commitdiff
|
tree
2019-08-09
Artem Z
h
muro
v
R
e
factoring of the SETTLE
test
s
commit
|
commitdiff
|
tree
2019-08-09
Berk
Hess
SIMD acceleration for F_FOURDIHS and F
_
PIDIHS
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraham
Fix esti
m
a
te of the size o
f
a j list
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Ir
r
gan
g
Add g
m
xapi_py
t
est
custom ta
r
get to CMake `check` target
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eri
c
Irrgang
Allow gmxapi
Python packa
g
e
test
s
to be r
u
n
from GROMACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
Christian Blau
Har
m
onize mrc density format extents
wi
t
h
re
s
t of code
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric
I
rrgang
Reenable
gtest
_
m
a
in target
.
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraham
St
o
p
testing ICC o
n
Windows
commit
|
commitdiff
|
tree
2019-08-08
Artem
Zhmur
o
v
Refactor Leap-Frog
t
ests and connect them to CP
U
v
e
r
s
ion
commit
|
commitdiff
|
tree
2019-08-07
M
.
Eric Irrg
a
n
g
U
se
g
mock a
n
d g
t
e
st targets fr
o
m
googlet
e
st-rel
e
ase
.
.
.
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Move ownership
o
f kineti
c
ene
r
gy ob
j
ect t
o
ISimu
l
ator
commit
|
commitdiff
|
tree
2019-08-05
Pascal
M
erz
A
dded Simulator
com
p
arison test
commit
|
commitdiff
|
tree
2019-08-05
Ma
r
k
A
b
raha
m
Remove
libgromacs_gener
a
te
d
c
o
ntributio
n
s from FindCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-02
yongw
a
ngCPH
Solv
e
issue with
demux
.
pl
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Rem
o
ve
a
poi
n
ter in t_force
r
ec
commit
|
commitdiff
|
tree
2019-08-01
Be
r
k Hess
F
i
x nbnxm GPU memory reservat
i
on
i
s
s
ue
commit
|
commitdiff
|
tree
2019-08-01
M
a
rk Abraham
Manage compiler
f
l
ags and some include option
s
per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
Impro
v
e use of obje
c
t libraries in libgromacs
commit
|
commitdiff
|
tree
2019-08-01
Mark A
b
r
aham
Merge
"Merge rele
a
s
e
-2019 into
master"
commit
|
commitdiff
|
tree
2019-07-31
Be
r
k Hess
Add grompp wa
r
ning with use of GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Artem
Z
hmur
o
v
Intro
d
uce function tha
t
chec
k
s if the computations
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
S
z
i
lárd
P
áll
Fixes for F buffer ops
change
commit
|
commitdiff
|
tree
2019-07-31
B
erk H
e
ss
Remove need for GROMOS FF in
test
commit
|
commitdiff
|
tree
2019-07-31
Pasc
a
l
Merz
Rename Sim
u
lat
o
r t
o
LegacyS
i
mulator
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Pá
l
l
Move cycle counting into the GPU bonded module
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Report when devel
o
p
m
ent feature fla
g
s are used
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Mov
e
end of step G
P
U
task la
u
nches to a function
commit
|
commitdiff
|
tree
2019-07-30
Paul Bau
e
r
Add w
r
apper for outputadapter methods
commit
|
commitdiff
|
tree
2019-07-28
B
erk He
s
s
C
onve
r
t
Ewald correction
tabl
e
s to C++
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
Add default
initialization to interaction_const
_
t
commit
|
commitdiff
|
tree
2019-07-26
Christ
i
an
B
lau
Fix fai
l
ing check-sou
r
ce
t
arget on py
t
hon3
.
6
commit
|
commitdiff
|
tree
2019-07-25
Berk Hess
Split
canDet
e
c
t
Gpus()
commit
|
commitdiff
|
tree
2019-07-25
Szi
l
á
r
d
P
áll
Only stop the CUDA profile
r
if th
e
re are
d
evice
s
commit
|
commitdiff
|
tree
2019-07-24
Paul Bauer
Fix doxygen in coordiant
e
io files
commit
|
commitdiff
|
tree
2019-07-24
Paul
B
auer
A
d
d outputada
p
ters
(3/3
)
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Ir
r
gang
Fix
g
mxapi notebook image and sample_res
t
raint
do
c
ker
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eri
c
Irrgang
Impro
v
e
g
m
x
api docker testing e
n
v
ironment
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
Eric Irrgang
Don't instal
l
samp
l
e restraint package by default
.
commit
|
commitdiff
|
tree
2019-07-23
Kevi
n
Boyd
Modernize syntax o
f
enable
_
i
f and tra
i
t
s
t
o us
e
_t
.
.
.
commit
|
commitdiff
|
tree
2019-07-09
Davi
d
v
a
n der Spoel
F
ixed
s
mall bug
i
n
g
mx anaeig
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric Irrga
n
g
Incorpora
t
e
s
a
mple_res
t
raint reposi
t
ory
.
commit
|
commitdiff
|
tree
2019-07-09
M
.
E
r
ic Irrgang
B
e
g
in CMake front-end
for Python packaging
machinery
.
commit
|
commitdiff
|
tree
2019-07-08
Szilárd P
á
ll
E
liminate a
u
se
o
f double
p
r
ec
i
s
i
on in the GPU bonded
.
.
.
commit
|
commitdiff
|
tree
2019-07-08
Be
r
k Hess
S
tore nbnxm gridSet d
a
ta in GridSetDa
t
a
commit
|
commitdiff
|
tree
2019-07-05
M
a
rk A
b
r
a
ham
Mode
r
n
ize FindHwlo
c
.
cmake
commit
|
commitdiff
|
tree
2019-07-05
M
.
E
ric Irrgang
P
ytho
n
bindi
n
gs for mdrun
.
commit
|
commitdiff
|
tree
2019-07-04
Mark
A
b
r
a
h
am
F
urther clang-tidy-7 fix
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhm
u
rov
Co
m
bine CUDA Leap-Frog, L
I
NCS and SETTLE
.
I
I
.
commit
|
commitdiff
|
tree
2019-07-03
Kevin Boyd
Updates
to
m
at
h
/vec
.
h
commit
|
commitdiff
|
tree
2019-07-02
M
a
r
k
Abraham
Cla
r
i
f
y wording of
r
elease notes
commit
|
commitdiff
|
tree
2019-07-02
B
erk Hess
R
e-enable affi
n
ity d
i
agon
o
stics with MPI
commit
|
commitdiff
|
tree
2019-07-02
Kevin Boyd
Add
function f
o
r
cal
c
ul
a
ting 3x3
matr
i
x
determinant
commit
|
commitdiff
|
tree
next