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Use moltype directly for obtaining residueAtomRanges
2020-03-03
Pa
u
l Bauer
Prepare
for 2020
.
2
commit
|
commitdiff
|
tree
2020-03-03
Pau
l
Ba
u
er
Ve
r
sion 2020
.
1
commit
|
commitdiff
|
tree
2020-03-03
Alan Gray
Allow PME
coordinate se
n
d before H2D coordinate transfer
commit
|
commitdiff
|
tree
2020-03-03
Ma
g
nus Lundborg
S
t
ore dH
d
L for all neighbor lambd
a
s
commit
|
commitdiff
|
tree
2020-03-02
B
e
rk Hess
Fix grompp unbo
u
nd ato
m
check
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix nrdf wit
h
p
a
rtial COMM removal
commit
|
commitdiff
|
tree
2020-03-02
Paul Bau
e
r
Revert "Rem
o
ve frozen
atoms from VCM
g
roups"
commit
|
commitdiff
|
tree
2020-02-28
Paul Bauer
Merge branch release-2019 into r
e
lease-2
0
20
commit
|
commitdiff
|
tree
2020-02-28
P
aul Bauer
De
f
ine all
C
P
U
NB ker
n
els
commit
|
commitdiff
|
tree
2020-02-28
Jonatha
n
Vincent
Moves
c
all to c
h
oose be
s
t performaing kern
e
ls to
p
me_gpu_rei
.
.
.
commit
|
commitdiff
|
tree
2020-02-28
Paul
B
auer
Ve
r
sion 2019
.
6
commit
|
commitdiff
|
tree
2020-02-27
P
a
s
c
a
l
Mer
z
Use legac
y
co
d
e pa
t
h for
t
_gra
p
h (
m
odula
r
simulato
r
)
commit
|
commitdiff
|
tree
2020-02-25
Szil
á
rd P
á
ll
Improve
GPU u
p
date tasks as
s
ignment cons
i
s
t
ency
commit
|
commitdiff
|
tree
2020-02-25
Paul Bau
e
r
Avoi
d
i
n
teger overflow
i
n dispersi
o
n correction
commit
|
commitdiff
|
tree
2020-02-25
Paul Ba
u
er
R
e
v
e
rt "Expose
vs
i
te count
i
n
g
"
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
M
ake
gmxapi
.
version
.
h
as_feat
u
re warnin
g
mo
r
e us
e
ful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Use subprocess
.
run instead of subproces
s
.
check
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Im
p
r
o
ve gmxapi
.
operation error handling
.
commit
|
commitdiff
|
tree
2020-02-24
Pascal Merz
Use Array
R
ef in comput
e
_
globals
commit
|
commitdiff
|
tree
2020-02-21
M
.
Eric Irrga
n
g
Simp
l
ify Git
L
a
b
C
I
Doc
k
erfile
s
.
commit
|
commitdiff
|
tree
2020-02-21
Artem Zhmur
o
v
Refactor and enable RVec to float conver
s
ion test
commit
|
commitdiff
|
tree
2020-02-10
Szilárd P
á
ll
Avoid dev flags in tri
g
gering g
p
uupdate
nigh
t
ly matrix
commit
|
commitdiff
|
tree
2020-02-10
Szilárd Pá
l
l
Avoid
(
re)init
i
alizing GPU upd
a
te
w
ithout
D
D
commit
|
commitdiff
|
tree
2020-02-06
A
rtem
Z
hmu
r
ov
Use
RVec
i
nstead of float for x, v
and f device buffers
commit
|
commitdiff
|
tree
2020-02-06
Szilá
r
d Páll
Remove mu_
t
ot fro
m
compute_
g
lo
b
als()
commit
|
commitdiff
|
tree
2020-02-05
Paul
B
a
u
e
r
U
s
e more MDLo
g
g
e
r in preproces
s
ing
commit
|
commitdiff
|
tree
2020-02-05
Berk Hess
Actually f
i
x
P
M
E
forces with FE w
i
th
o
u
t
pert
u
r
be
d
q/LJ
commit
|
commitdiff
|
tree
2020-02-05
Pa
s
cal
M
erz
Minor improvements t
o
vc
m
.
cp
p
commit
|
commitdiff
|
tree
2020-02-05
Pa
s
c
a
l Merz
Merge VV implementations of ComputeGlobalsElemen
t
commit
|
commitdiff
|
tree
2020-02-03
A
rtem Zhmurov
Enabl
e
GPU
upda
t
e
fo
r
supported cases of FEP
commit
|
commitdiff
|
tree
2020-01-31
Pau
l
Bauer
Use
MDL
o
gg
e
r in grompp
commit
|
commitdiff
|
tree
2020-01-31
Szilárd P
á
ll
E
l
i
m
inate t
h
e legacyFla
g
s
m
anipulation in do_force()
commit
|
commitdiff
|
tree
2020-01-31
Chri
s
tian Blau
Documen
t
ation fix for
l
ocal
a
tom set data
commit
|
commitdiff
|
tree
2020-01-31
P
a
scal
Me
r
z
Sta
t
ePropagatorData:
M
ake con
s
t box
getters
c
onst
fu
n
ctions
commit
|
commitdiff
|
tree
2020-01-30
Ar
t
e
m
Zhmurov
Cl
e
aning bool
e
ans in NBN
X
M in OpenCL bui
l
d
commit
|
commitdiff
|
tree
2020-01-29
Szilárd Páll
Small
i
m
provement in O
p
enCL
e
rror handling
commit
|
commitdiff
|
tree
2020-01-29
A
rtem Z
h
murov
Spli
t
and move
t
he checkDeviceBuffer(
.
.
.
)
f
unc
t
i
o
n
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmu
r
ov
Remov
e
the
r
est of the de
v
i
c
e
coordinates management
.
.
.
commit
|
commitdiff
|
tree
2020-01-28
Paul Bauer
Merg
e
b
r
anch origin/re
l
ease-202
0
into master
commit
|
commitdiff
|
tree
2020-01-27
Mark Abraha
m
Update
s
o
m
e nbnxm
k
ernel c
o
nstants
t
o con
s
texpr
commit
|
commitdiff
|
tree
2020-01-24
Paul Bauer
U
se utf-8 for python
file r
e
ading
commit
|
commitdiff
|
tree
2020-01-23
Berk
H
e
ss
Fix DD rank count
p
rime check
commit
|
commitdiff
|
tree
2020-01-23
Artem Zhm
u
rov
Fi
x
a coupl
e
of
c
ommas in c
o
ol quotes
commit
|
commitdiff
|
tree
2020-01-23
Gau
r
av G
a
rg
F
ix PME
c
h
ecks in GPU update
a
ssi
g
nm
e
n
t decision
commit
|
commitdiff
|
tree
2020-01-21
Paul Bauer
Fix doc
u
mentation error with
do
x
ygen >1
.
8
.
16
commit
|
commitdiff
|
tree
2020-01-20
Berk
H
es
s
Use ArrayRef(WithPadd
i
ng) in const
r
a
int c
o
d
e
commit
|
commitdiff
|
tree
2020-01-17
P
a
ul Bauer
Ac
t
ually fix Gitlab doc b
u
il
d
commit
|
commitdiff
|
tree
2020-01-16
M
a
rk Abraham
M
a
ke nbnx
m
headers more self-co
n
taine
d
commit
|
commitdiff
|
tree
2020-01-16
S
z
ilárd
Pál
l
F
i
x PME
r
u
n mode wit
h
out PM
E
commit
|
commitdiff
|
tree
2020-01-16
Pau
l
Bauer
Fi
x
nightly
bui
l
d f
a
il
u
re o
n
Gitlab
commit
|
commitdiff
|
tree
2020-01-15
Christoph
Junghans
cmake: inst
a
ll pbc
.
h for GMX_I
N
STA
L
L_L
E
G
A
C
Y
_
API
commit
|
commitdiff
|
tree
2020-01-14
P
a
u
l Bauer
Us
e
utf-8 for
p
ython file r
e
ading
commit
|
commitdiff
|
tree
2020-01-08
R
oland
S
chulz
Me
r
g
e rele
a
s
e
-
2
019 into r
e
lease
-
2020
commit
|
commitdiff
|
tree
2020-01-07
Paul B
a
ue
r
Mer
g
e
bran
c
h ori
g
in/releas
e
-2020 into master
commit
|
commitdiff
|
tree
2020-01-07
Erik Lindah
l
Write TPR body as opa
q
ue X
D
R data in b
i
g-
e
ndian format
commit
|
commitdiff
|
tree
2020-01-07
Paul Baue
r
Merge commit
d
30f2cb6 from
release-2020 into
master
commit
|
commitdiff
|
tree
2020-01-01
Paul Bauer
Prep
a
re for 2020
.
1
commit
|
commitdiff
|
tree
2020-01-01
Pa
u
l Baue
r
GR
O
MACS 2020 rele
a
se
commit
|
commitdiff
|
tree
2020-01-01
Paul Bauer
Revert "GROMACS 2020 release"
commit
|
commitdiff
|
tree
2019-12-30
Paul Ba
u
er
Fi
x
b
u
ild error with wrong name from cached cmak
e
fil
e
commit
|
commitdiff
|
tree
2019-12-29
E
ri
k
Lindahl
Write TPR
body as opaque XDR da
t
a in big-endia
n
format
commit
|
commitdiff
|
tree
2019-12-28
M
.
Eric
Irrga
n
g
Re
s
olve CMa
k
e ambi
g
uiti
e
s
for gmxa
p
i Py
t
hon
package
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Paul B
a
uer
Change
rel
e
ng to give information about G
i
tlab
commit
|
commitdiff
|
tree
2019-12-28
Paul
B
auer
Extend
information for GPU update
commit
|
commitdiff
|
tree
2019-12-28
Mark Abraham
Remov
e
GMX_CYCLEC
O
U
N
TERS
commit
|
commitdiff
|
tree
2019-12-28
Paul
Bauer
Exclude
b
uild-system files from
C
Pack
commit
|
commitdiff
|
tree
2019-12-28
Paul Ba
u
er
Deprec
a
te s
u
pport for Armv7
commit
|
commitdiff
|
tree
2019-12-27
Artem
Zhmuro
v
Add a no
t
e to the log file when
-update
gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Paul Bauer
A
d
d
copyright check
a
nd
im
p
rove c
a
che usage
commit
|
commitdiff
|
tree
2019-12-27
Paul Ba
u
er
M
e
r
g
e
origin/re
l
e
a
s
e-2019 int
o
release-2020
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Clean
b
a
d auto-format in deci
d
egpuusage d
o
xyg
e
n comments
commit
|
commitdiff
|
tree
2019-12-23
Paul Ba
u
e
r
Add
files for Gitlab
C
I
commit
|
commitdiff
|
tree
2019-12-23
Paul B
a
u
e
r
Prep
a
re for GROMA
C
S
2019
.
6
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
GRO
M
A
C
S ver
s
io
n
2019
.
5
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
Rever
t
"Fix tha
t
tests
intended
f
or multiple ranks
.
.
.
commit
|
commitdiff
|
tree
2019-12-20
Pa
u
l Bauer
Fur
t
h
e
r updates
t
o Gitl
a
b C
I
commit
|
commitdiff
|
tree
2019-12-20
P
a
ul Bauer
GROMAC
S
2
0
20 release c
a
ndidate
commit
|
commitdiff
|
tree
2019-12-19
Ala
n
Gray
F
i
x PME tuning issue when PME-PP
comm
u
nication
s
a
r
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-19
Szilárd Páll
PP-
P
ME load b
a
lanci
n
g impr
o
vem
e
nt
s
commit
|
commitdiff
|
tree
2019-12-18
Szilárd Páll
A
l
low x D2H to overlap with GP
U
force c
o
mpute
commit
|
commitdiff
|
tree
2019-12-18
Ber
k
Hes
s
Change grompp decoupling SD warning to note
commit
|
commitdiff
|
tree
2019-12-18
Paul Bauer
A
d
d abi
l
it
y
to
s
et OMP an
d
tMPI
t
hr
e
a
d
for ctes
t
commit
|
commitdiff
|
tree
2019-12-18
P
au
l
Bauer
Add abi
l
ity to set
OMP a
n
d tM
P
I
thread
f
o
r
ctes
t
commit
|
commitdiff
|
tree
2019-12-16
B
e
rk He
s
s
F
ix iss
u
es in ListOfLists
commit
|
commitdiff
|
tree
2019-12-15
Paul Bauer
Ignore bu
i
ld h
o
st
for CI buil
d
s
commit
|
commitdiff
|
tree
2019-12-13
Pa
u
l Bauer
Set correc
t
dependency
for doc
buil
d
o
n
g
m
x
a
pi
commit
|
commitdiff
|
tree
2019-12-13
Paul Bauer
Fix c
o
mp
i
ler warni
n
g about extr
a
;
commit
|
commitdiff
|
tree
2019-12-13
Paul Bau
e
r
Che
c
k for
using corr
e
ct
hwloc headers
a
nd runtim
e
commit
|
commitdiff
|
tree
2019-12-11
A
r
tem Zhmurov
C
l
a
r
ify what setting
z
er
o
to some output m
d
p
options
.
.
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eri
c
Irrgang
gmxap
i
landing pa
g
e update
.
commit
|
commitdiff
|
tree
2019-12-11
Paul
B
a
ue
r
Update Gitla
b
CI to latest fixes
commit
|
commitdiff
|
tree
2019-12-09
Paul Bauer
Hopefully final
g
itlab
CI fix
commit
|
commitdiff
|
tree
2019-12-09
P
a
ul Bauer
Mov
e
d
oc b
u
i
l
d in gitlab to post-t
e
st stage
commit
|
commitdiff
|
tree
2019-12-09
P
a
ul
B
a
u
er
Even more gitlab
C
I fixe
s
commit
|
commitdiff
|
tree
2019-12-09
Paul B
a
uer
More fixes
to gitla
b
C
I fi
l
e
s
commit
|
commitdiff
|
tree
2019-12-09
Paul B
a
uer
Fix error
i
n gitlab CI file
commit
|
commitdiff
|
tree
2019-12-07
M
.
E
r
i
c I
r
rgang
Fina
l
i
z
e
g
mxapi 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
Mark Abraha
m
Avo
i
d
3
86 O3
codegen bug
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric I
r
rgang
Add
notes on MPI w
i
th gmxa
p
i Python packa
g
e
.
commit
|
commitdiff
|
tree
2019-12-06
Artem Zh
m
u
rov
Pass array
r
ef
i
ns
t
ead of casting
t
o basi
c
array in
.
.
.
commit
|
commitdiff
|
tree
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