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GROMACS 2020 release candidate
2019-12-20
Paul
B
auer
GROMACS 2020 re
l
ease candidate
commit
|
commitdiff
|
tree
2019-12-19
Al
a
n Gray
Fix PME tuning issue when PME-
P
P
c
o
m
muni
c
ations are
.
.
.
commit
|
commitdiff
|
tree
2019-12-19
Szilárd
P
áll
PP-PME lo
a
d balancing
improvements
commit
|
commitdiff
|
tree
2019-12-18
S
z
ilá
r
d Páll
Allow
x
D2H to overla
p
with
GPU forc
e
compute
commit
|
commitdiff
|
tree
2019-12-18
Berk
H
ess
Change grompp d
e
coupl
i
ng
SD warni
n
g t
o
not
e
commit
|
commitdiff
|
tree
2019-12-18
Paul Ba
u
er
Add
ability to
set OMP and tMPI th
r
ead for
c
test
commit
|
commitdiff
|
tree
2019-12-11
Artem Zh
m
uro
v
Clarify what s
e
tting zero
to
some output m
d
p options
.
.
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Er
i
c Irr
g
ang
gmxapi lan
d
ing page update
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
Eric I
r
r
g
ang
Fin
a
l
ize gmxapi 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
Mark
A
br
a
h
a
m
Avoid 386 O3 c
o
d
e
gen bug
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgang
A
dd no
t
es on MPI
with gmxa
p
i
P
ython
package
.
commit
|
commitdiff
|
tree
2019-12-06
A
r
te
m
Zhmurov
Pass
array ref i
n
stea
d
of casting to basic array
in
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Mark
Abraham
Provide more fee
d
b
a
ck whe
n
list
e
d
f
orces tests fail
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric I
r
rgang
gmxapi Python pack
a
ge usage prose
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eri
c
Irrgang
Impr
o
v
e
pytest fixtures for directory management
.
commit
|
commitdiff
|
tree
2019-12-05
Chr
i
sti
a
n Bl
a
u
Relax cros
s
-
correl
a
tion test pre
c
ision
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
Third beta r
e
lease of GROMACS 2020
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
Reve
r
t "Enable GPU update with DD when GPU
comm f
e
atures
.
.
.
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
F
i
x nightly bui
l
d
by
correct
l
y d
e
fining
s
e
veral
commit
|
commitdiff
|
tree
2019-12-03
Alan
G
r
ay
Ena
b
le GPU
u
pdate with
DD when
GPU comm featur
e
s are
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
Berk
Hess
Ad
d
che
c
k for co
u
pled constraints
for CUDA up
d
ate
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
E
xtrac
t
LINCS CUD
A
helper functions
commit
|
commitdiff
|
tree
2019-12-01
Paul Bauer
Use
D
OI for
citing in reference manual s
e
ction
commit
|
commitdiff
|
tree
2019-12-01
Mar
k
Abraham
Further i
m
prove ta
s
kassig
n
m
e
n
t
e
xcep
t
ion handling
commit
|
commitdiff
|
tree
2019-11-29
Paul Bauer
Fix unaligned access with AVX512
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmurov
Print OpenCL error info i
n
ca
s
e
of failed
assertio
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
P
a
u
l Bauer
Fix postsubmit
commit
|
commitdiff
|
tree
2019-11-28
Chr
i
stian Blau
Fi
x
check-po
i
nting for dens
i
ty guided simu
l
ations
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraham
Rel
a
x to
l
erance for
bd tests
commit
|
commitdiff
|
tree
2019-11-26
Paul Bauer
F
ix unused var
i
able warni
n
g in ewald c
o
de
commit
|
commitdiff
|
tree
2019-11-26
Berk Hess
Fix
i
ssues
with AWH with periodi
c
p
u
lling
commit
|
commitdiff
|
tree
2019-11-25
C
h
r
i
stian Blau
Fix
duplicate
C
O
N
NECT record
s
in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Use same
matr
i
x f
o
r
Parrinello-Rahma
n
and Ber
e
nds
e
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
C
hristian Blau
Read
mrc densi
t
y map
format with all endianesses
.
commit
|
commitdiff
|
tree
2019-11-25
C
h
r
i
stian Blau
Check
mrc header for sanity
commit
|
commitdiff
|
tree
2019-11-25
Ar
t
em Z
h
murov
Fix index
mapping
issue with LI
N
C
S
on GPU
commit
|
commitdiff
|
tree
2019-11-20
Paul Ba
u
e
r
Merg
e
'origin/release-2019' int
o
release-2020
commit
|
commitdiff
|
tree
2019-11-20
Mark Abr
a
ham
Quiet uninitia
l
ized variable warnin
g
w
ith clang 9
commit
|
commitdiff
|
tree
2019-11-17
Szi
l
árd Pál
l
Trigger ocl_nbnxm_kernels ta
r
g
et
w
ith cl
a
ng-tid
y
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric I
r
rgang
Remove extr
a
neous
file
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irr
g
ang
Add transiti
o
nal li
n
ks for
online g
m
xapi
Python packa
g
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric
I
r
rga
n
g
Im
p
rove
gmxapi Do
c
kerfiles
.
commit
|
commitdiff
|
tree
2019-11-17
Sz
i
l
árd
P
á
ll
Fix clang-tidy 8 wa
r
n
in
g
s in OpenCL nbnxm kernels
commit
|
commitdiff
|
tree
2019-11-16
Mark Abraham
Stop testing that h
w
l
oc cache-size
detection works
.
.
.
commit
|
commitdiff
|
tree
2019-11-14
Paul Ba
u
er
F
ix formatt
i
ng
error
commit
|
commitdiff
|
tree
2019-11-13
Erik L
i
ndahl
Updated physica
l
c
onstants
t
o CODATA
2018
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgan
g
Ac
h
ieve gmxapi fr15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrg
a
ng
Up
d
ates to gmxapi
FR1
5
a
cceptanc
e
t
e
st
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgan
g
Update notes and
t
ests regarding gmxapi acceptance
.
.
.
commit
|
commitdiff
|
tree
2019-11-09
Alan G
r
ay
Modern
i
ze
n
am
i
ng
i
n
GPU buffer ops kernels
commit
|
commitdiff
|
tree
2019-11-09
ejjordan
Fix
mdp parameter handl
i
ng in m
d
run
tests
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eric Irrgan
g
Fix
b
u
g introduced
b
y clang-format reformat
.
commit
|
commitdiff
|
tree
2019-11-07
Paul
B
auer
App
l
y clang-fo
r
mat
t
o
sourc
e
tree
commit
|
commitdiff
|
tree
2019-11-06
Erik Lindahl
Work ar
o
u
n
d broken Apple compilers in Mac OS 10
.
15
commit
|
commitdiff
|
tree
2019-11-04
M
.
E
ric Irrgang
Update gmxapi Pyt
h
on documentation instructions
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eri
c
Irrgang
Update Sphinx li
n
k
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Irrg
a
ng
F
i
x t
y
pos
.
commit
|
commitdiff
|
tree
2019-11-01
Paul Bauer
Second beta rel
e
a
s
e of GROMACS
2
020
commit
|
commitdiff
|
tree
2019-11-01
Chr
i
stia
n
Blau
Fix
cr
o
ss-correlation calcul
a
tion i
n
stabil
i
ty
commit
|
commitdiff
|
tree
2019-11-01
Sz
i
lárd
Pá
l
l
Rename referen
c
e checksum
g
enerat
i
ng target
commit
|
commitdiff
|
tree
2019-11-01
S
zilárd P
á
ll
U
se "-" in checksum-rel
a
ted ver
s
ion suffix
commit
|
commitdiff
|
tree
2019-11-01
S
zilárd Páll
Improve wo
r
k
l
o
ad data structures'
docs
commit
|
commitdiff
|
tree
2019-11-01
Alan Gray
Remove energy step dependen
c
e on
G
P
U
force buffer
ops
commit
|
commitdiff
|
tree
2019-11-01
Berk Hess
A
d
d haveEwaldSurfaceContribution t
o
SimulationWorklo
a
d
commit
|
commitdiff
|
tree
2019-11-01
M
.
Eric
I
rrgang
Normalize sample_restrai
n
t target
n
a
mes
.
commit
|
commitdiff
|
tree
2019-11-01
Pa
u
l Ba
u
er
Prepare for 2020 beta 2
commit
|
commitdiff
|
tree
2019-11-01
P
a
ul Bauer
Add validation of tarbal
l
bu
i
lds
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
Allow validation of t
h
e generated CMake toolchain file
.
commit
|
commitdiff
|
tree
2019-10-31
Paul Ba
u
er
Use type of
e
xplicit size
i
n
inmemoryserializer
commit
|
commitdiff
|
tree
2019-10-29
Pascal Merz
Fix compatibility
check
of modular simulator
commit
|
commitdiff
|
tree
2019-10-29
Be
r
k Hess
A
d
d mdrun GPU up
d
ate doc
u
mentation
commit
|
commitdiff
|
tree
2019-10-29
B
e
r
k
H
ess
Fix
Ewald d
i
p
o
le correction with GPU upda
t
e
commit
|
commitdiff
|
tree
2019-10-29
Paul Ba
u
er
M
e
rge "Merge
b
ranch 're
l
ease-2019' into mas
t
e
r
"
commit
|
commitdiff
|
tree
2019-10-29
P
a
u
l Ba
u
er
Mer
g
e branch 'rele
a
s
e
-2019' into mast
e
r
commit
|
commitdiff
|
tree
2019-10-29
Alan Gray
E
xp
l
icit
l
y de
s
troy PME-PP GPU co
m
munic
a
tion object
commit
|
commitdiff
|
tree
2019-10-28
M
.
Eric Irrgang
Update bu
n
d
l
ed
pybind
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
E
ri
c
Irrgang
Fix CMake mess
a
ge typo
.
commit
|
commitdiff
|
tree
2019-10-27
Pascal Merz
Enab
l
e for
c
ed rota
t
ion for modular simulator
commit
|
commitdiff
|
tree
2019-10-23
M
.
Eric Irr
g
a
ng
Suppr
e
ss
s
ome
o
utput when sample
_
r
e
s
t
rain
t
is
b
uilt
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal
Me
r
z
A
d
apt e
n
um to style c
o
nve
n
tio
n
(mod
u
lar simulator)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Sm
a
ll improvement to
E
n
e
rgyElement (modular si
m
ulator)
commit
|
commitdiff
|
tree
2019-10-22
Pasc
a
l Me
r
z
Fi
x
D
omDec
s
tep (modular simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix
P
me
L
oadBalanceHelper
initialization (mod
u
lar simulator)
commit
|
commitdiff
|
tree
2019-10-21
M
.
Eric Irrgang
A
d
d trajectory
ou
t
pu
t
to m
d
r
u
n
o
pera
t
i
o
n
.
commit
|
commitdiff
|
tree
2019-10-18
Berk Hes
s
Update
grompp cutoff-sche
m
e warnings
commit
|
commitdiff
|
tree
2019-10-16
S
zilá
r
d Páll
Mak
e
t
h
e wait on nonbonded GPU results cond
i
tional
commit
|
commitdiff
|
tree
2019-10-15
M
.
E
ric I
r
rgang
Add
g
eneric check for gmxapi s
u
ppor
t
library to
Pytho
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-09
Be
r
k Hes
s
I
ncr
e
ase spc minimization te
s
t toleranc
e
commit
|
commitdiff
|
tree
2019-10-09
B
erk H
e
ss
Fix random ene
r
gy and vi
r
ial with PME on GPU on a P
M
E
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
M
.
Er
i
c Irrgang
Build gmxapi documenta
t
ion in main GROMACS document
a
tion
.
commit
|
commitdiff
|
tree
2019-10-02
Paul Bauer
Fix failures
in clan
g
-8 n
i
ghtly
build
commit
|
commitdiff
|
tree
2019-10-02
P
a
ul Bauer
Prepare for 2019
.
5
commit
|
commitdiff
|
tree
2019-10-02
P
aul B
a
uer
GROMACS
v
e
r
si
o
n 2019
.
4
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Alway
s
output
corre
c
t kinetic at last step
commit
|
commitdiff
|
tree
2019-10-01
Pascal Merz
Output
corre
c
t kine
t
ic at last step (modula
r
simulator)
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Fix location of angle in vsite figure
commit
|
commitdiff
|
tree
2019-09-27
Mark
A
br
a
ham
Add tests for
e
ditconf file conversion with indexing
commit
|
commitdiff
|
tree
2019-09-26
Paul Baue
r
Revert "
R
e
m
ove up
d
a
t
e
f
lag again"
commit
|
commitdiff
|
tree
2019-09-25
Paul
B
au
e
r
GROMACS 2020 f
i
r
st beta r
e
lease
commit
|
commitdiff
|
tree
2019-09-25
Mark Abraham
F
ix l
o
g
file flag output
commit
|
commitdiff
|
tree
next