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Fix center of mass motion removal with frozen atoms
2020-03-02
Berk Hess
Fix center
o
f mass motio
n
re
m
oval
with frozen atoms
commit
|
commitdiff
|
tree
2020-03-02
Artem
Zh
m
urov
Update the message on whether update and constraints
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Paul B
a
u
er
Remo
v
e frozen atoms from VCM groups
commit
|
commitdiff
|
tree
2020-02-27
Pasc
a
l Me
r
z
L
oosen g
m
x
a
p
i
stopsignaler
t
est
commit
|
commitdiff
|
tree
2020-02-27
P
ascal
M
erz
Extract
and
e
xpose
function to determi
n
e whether molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
S
zilárd Páll
Remove outd
a
ted PME-GPU limitat
i
on
in
u
ser guide
commit
|
commitdiff
|
tree
2020-02-25
Mag
n
u
s
Lun
d
b
org
Fix out of sync
c
heckpoi
n
t f
i
les i
n
simulations
s
hari
n
g
.
.
.
commit
|
commitdiff
|
tree
2020-02-24
Paul Bauer
Fix clang
-
6
i
mage template
commit
|
commitdiff
|
tree
2020-01-29
Paul Bauer
W
o
rkaro
u
nd for Gitlab a
r
chive size
commit
|
commitdiff
|
tree
2020-01-17
Paul Bauer
Fix bad l
i
nk in developer doc
s
commit
|
commitdiff
|
tree
2020-01-17
B
e
rk
H
ess
A
d
d che
c
k for
she
l
ls and
G
PU update
commit
|
commitdiff
|
tree
2020-01-13
Pau
l
Bauer
R
e
vert "Exclude build-syste
m
files from
CPack"
commit
|
commitdiff
|
tree
2020-01-13
C
h
r
i
stoph J
u
nghans
gmxManageMPI
.
cmake: convert MPI FLAGS to lists
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irrgan
g
Remove tr
a
nsi
t
ional links f
o
r onli
n
e gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-01
Paul Bauer
GROMACS 202
0
relea
s
e
commit
|
commitdiff
|
tree
2020-01-01
Erik Lindahl
Ad
d
l
i
nk to p
a
per explaining GROMOS
t
wi
n
-range issues
.
commit
|
commitdiff
|
tree
2019-12-31
Ma
r
k Abraham
Avoid 386 O3 cod
e
gen bug even more
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmu
r
ov
Inform user why forcing GPU update is not possible
commit
|
commitdiff
|
tree
2019-12-31
A
rtem
Zhmurov
A
d
d description
of GM
X
_FORCE_UPDATE_DEFAULT
_
GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
A
r
tem Zhmurov
Fix gpuup
d
ate matrix
commit
|
commitdiff
|
tree
2019-12-28
A
r
tem Z
h
murov
Change th
e
b
e
h
a
vior of the
GPU upd
a
te UI
commit
|
commitdiff
|
tree
2019-12-28
Ma
r
k Abraha
m
Merge "
M
erge origin/release-2019 i
n
to
r
elease-2020
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Pa
u
l Ba
u
er
R
emove membed from feature
s
commit
|
commitdiff
|
tree
2019-12-20
Szilárd Páll
Enable buffer ops when GMX_
G
PU
_
DD_COM
M
S is se
t
commit
|
commitdiff
|
tree
2019-12-19
Paul Bauer
F
i
x
r
egressiontests failing with
ctest
commit
|
commitdiff
|
tree
2019-12-18
Paul Ba
u
er
Ignore bui
l
d
h
ost for
CI builds
commit
|
commitdiff
|
tree
2019-12-17
Mark Ab
r
a
h
am
Fix t
h
at
tests intended
for multipl
e
ranks ru
n
that w
a
y
commit
|
commitdiff
|
tree
2019-12-16
Szilárd Páll
F
ix the GPU bonded stream with 1
P
P +
1
PME rank
commit
|
commitdiff
|
tree
2019-12-15
Christian Blau
Fix densi
t
yfi
t
t
ing s
t
alling and energies
commit
|
commitdiff
|
tree
2019-12-14
Mark Ab
r
aham
Simp
l
ify gmxapi RPATH h
a
nd
l
ing
commit
|
commitdiff
|
tree
2019-12-12
Arte
m
Zhmurov
Allow
using
GPU upd
a
te with
DD
and update groups
commit
|
commitdiff
|
tree
2019-12-11
Mark
A
b
raham
D
ocum
e
nt DOMAINDECO
M
P(cr) correctly
commit
|
commitdiff
|
tree
2019-12-04
Mark Abraham
Ad
d
e
d
OpenCL build
t
o
r
elease
m
at
r
i
x
commit
|
commitdiff
|
tree
2019-12-04
Mar
k
Ab
r
aham
Removed unnecessary link_
d
i
re
c
tories comman
d
for gtest
commit
|
commitdiff
|
tree
2019-11-29
Paul B
a
ue
r
Fix build error witho
u
t thre
a
d or regular mpi
commit
|
commitdiff
|
tree
2019-11-29
Ma
r
k Abrah
a
m
Merge br
a
nch relea
s
e
-20
1
9 in
t
o release-202
0
commit
|
commitdiff
|
tree
2019-11-29
Artem Z
h
mur
o
v
Rename some variables
i
n G
P
U Upda
t
e
commit
|
commitdiff
|
tree
2019-11-28
Paul
B
auer
Check
f
or using corr
e
ct hwl
o
c head
e
r
s
a
nd
runti
m
e
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmuro
v
C
lear devi
c
e force buffer if it was realloc
a
t
ed
commit
|
commitdiff
|
tree
2019-11-27
A
r
tem Zhm
u
rov
Add method for c
o
ordinates
s
c
aling i
n
to GPU updat
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irrgang
Add gmxapi_extension
t
ests
t
o 'test
s
'
target
.
commit
|
commitdiff
|
tree
2019-11-27
A
l
a
n G
r
ay
Event
-
bas
e
d D
e
pende
n
c
y
for GPU
F
o
rce H
a
lo Excha
n
ge
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraham
Improve handling
o
f task-assig
n
men
t
e
xceptions
commit
|
commitdiff
|
tree
2019-11-25
Alan G
r
ay
Fix race condi
t
ion in GPU X halo exchange with GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Christ
i
a
n
Blau
InMemorySeria
l
izer wit
h
endianess swap
.
commit
|
commitdiff
|
tree
2019-11-21
Mark A
b
raham
New cool
q
uote
commit
|
commitdiff
|
tree
2019-11-20
Artem Z
h
m
u
r
ov
A
dd
D2H copies fo
r
t
he checkpoi
n
tin
g
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m Zhmurov
M
ove the
c
opy
o
f
the v
e
loci
t
ies for the output clo
s
er
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
Berk Hes
s
Quiet p
d
b2gmx and u
s
e
g
m
x_fata
l
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric
I
rrg
a
ng
Remove stub con
t
en
t
fro
m
gmxapi d
o
cs
.
commit
|
commitdiff
|
tree
2019-11-16
Mark Abraham
Re
l
axed listed forces test tole
r
ances
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
Dep
r
ecated s
c
-r-
p
o
w
er=48
commit
|
commitdiff
|
tree
2019-11-04
Pa
u
l
B
a
uer
A
dd
build for cla
n
g-format
commit
|
commitdiff
|
tree
2019-11-04
Paul
Bauer
Split up source code
f
orm
a
tting sc
r
ipts
commit
|
commitdiff
|
tree
2019-11-04
Te
e
mu Murtola
Upd
a
te clang-
f
or
m
at
c
onfig
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric
Irrgang
Improv
e
uniformity
o
f OS X CMake c
o
nfigurat
i
o
n
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irr
g
ang
Restore CMake convenience targets for
s
am
p
le_restraint
.
commit
|
commitdiff
|
tree
2019-10-31
Alan Gra
y
Remove dead
c
ode f
o
r nbnxm H2D c
o
o
r
dinate copy ev
e
nt
commit
|
commitdiff
|
tree
2019-10-31
A
lan
G
ray
Bug
f
ix for event passe
d
t
o
GPU c
o
mm f
e
at
u
res
commit
|
commitdiff
|
tree
2019-10-31
Pasca
l
M
er
z
Check for
c
ont
r
adicting envir
o
nment variables (modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
M
a
rk Abr
a
h
a
m
T
e
sts for v
a
l
i
d periodic a
c
tions
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
Disable its tests
when sample_restraint
i
s not th
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
D
e
cr
e
ase the maximum allow
e
d Python vers
i
o
n for gmxapi
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhm
u
rov
Disable GPU upda
t
e whe
n
co
o
rdinates s
w
apping is enabled
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add bool useDomain
D
ecomposition in mdru
n
ner
commit
|
commitdiff
|
tree
2019-10-24
Berk He
s
s
Add gmx_mtop_interac
t
i
o
n_coun
t
()
commit
|
commitdiff
|
tree
2019-10-23
ejjordan
Make t_nextnb an implementati
o
n deta
i
l
commit
|
commitdiff
|
tree
2019-10-23
Pa
s
cal M
e
r
z
Correct fo
r
sk
e
wed box
before
dom
a
in decompo
s
ition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Alan Gray
Enable
G
P
U Peer A
c
cess in GPU Utilities
commit
|
commitdiff
|
tree
2019-10-22
ejjordan
R
e
move unused fu
n
c
tions from
g
mxpreprocess
commit
|
commitdiff
|
tree
2019-10-22
Be
r
k Hess
Require -ei for essential
d
ynamics
commit
|
commitdiff
|
tree
2019-10-22
e
jjordan
R
emove
unused fu
n
cti
o
n
generate_excls and make cl
e
a
n
_
e
x
c
l
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Berk Hess
Const corr
e
c
t
ness for genhydro
commit
|
commitdiff
|
tree
2019-10-15
Paul Bau
e
r
F
i
x bug in
p
reprocess
i
ng
commit
|
commitdiff
|
tree
2019-10-14
M
.
Er
i
c Ir
r
gang
Fix l
o
gic error
i
n gmxapi
.
version
.
api_i
s
_at_least()
.
commit
|
commitdiff
|
tree
2019-10-13
M
a
rk Ab
r
aham
E
nsure
environment var
i
abl
e
use does not give warnings
commit
|
commitdiff
|
tree
2019-10-12
Berk Hess
Add class FixedCapacityV
e
c
t
o
r
commit
|
commitdiff
|
tree
2019-10-12
Artem Zh
m
urov
Centralize management of coordinate
s
ready on GPU event
commit
|
commitdiff
|
tree
2019-10-08
Prash
a
nth Kanduri
Fused two if branches wit
h
the same conditional
commit
|
commitdiff
|
tree
2019-10-02
Ca
r
ste
n
Ku
t
zner
Upda
t
e the www link to the Doxygen doc
u
mentation in
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
Berk Hess
Fix h
a
r
mless
Open
M
P wr
i
te r
a
ce
commit
|
commitdiff
|
tree
2019-10-02
Ma
r
k Abraham
Impr
o
v
e
P
M
E t
e
s
ting
commit
|
commitdiff
|
tree
2019-10-01
Be
r
k H
e
ss
Use gmx::Range in domdec
commit
|
commitdiff
|
tree
2019-10-01
Artem
Z
h
m
urov
State
P
ropagatorDataG
p
u objec
t
to manage GPU fo
r
ces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
M
a
rk Abraham
Fix i
c
c
w
arnings
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Completely remove charge groups
commit
|
commitdiff
|
tree
2019-10-01
Paul Bauer
Fi
x
chain ID
handlin
g
in make_ndx
commit
|
commitdiff
|
tree
2019-10-01
Christoph
J
u
nghans
cmake: add mis
s
ing header to leg
a
cy api
commit
|
commitdiff
|
tree
2019-10-01
Mark
A
braha
m
Removed dependency on commre
c
of m
d
ru
n
setup
commit
|
commitdiff
|
tree
2019-09-30
Carsten Kutz
n
e
r
M
o
ve F
o
rceProvi
d
ers
c
lass int
o
t
he
gmx names
p
ace
commit
|
commitdiff
|
tree
2019-09-30
Mark Abra
h
am
M
a
ke
a
builder for DD
commit
|
commitdiff
|
tree
2019-09-30
Be
r
k
H
e
ss
Remove
charge
g
roup c
o
de from fo
r
c
erec
commit
|
commitdiff
|
tree
2019-09-30
S
zilárd Pál
l
Make the wait
on P
M
E G
P
U
results conditional
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Improve MiMiC test impl
e
me
n
tation
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Fix gro file
o
utput
w
it
h
inde
x
gr
o
ups
commit
|
commitdiff
|
tree
2019-09-27
M
a
r
k
A
braha
m
Fix gro file output
w
ith index grou
p
s
commit
|
commitdiff
|
tree
2019-09-27
Mar
k
A
b
r
a
ha
m
R
emove left
o
ver s
u
pport
for pre
-
9
.
0
CUDA
commit
|
commitdiff
|
tree
2019-09-24
P
aul Bauer
Add te
s
t for noap
p
end
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
Fix no
-
MPI CUDA build
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraha
m
Merge "Merge branch release-
2
019 into master"
commit
|
commitdiff
|
tree
next