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GROMACS 2020 release candidate
2019-09-24
Magnus Lundb
o
rg
A
d
d
.
part0001
.
to
fil
e
s
from t
h
e first run with -noap
p
end
.
commit
|
commitdiff
|
tree
2019-09-24
Paul Bauer
Me
r
ge b
r
a
nch release-201
9
into
mas
t
e
r
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Grom
p
p
error for mism
a
tching nst fo
r
en
e
rgy cal
u
latio
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Christia
n
Blau
Amendment
s
to dens
i
ty fitting manual section
commit
|
commitdiff
|
tree
2019-09-23
Mark
Abraham
Fixe
s
to
broken C
U
DA
compiler flags
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al Mer
z
Make CheckpointHe
l
p
er saf
e
r and easier to use
commit
|
commitdiff
|
tree
2019-09-18
C
hristian Blau
A
d
d md
p
option d
o
c
umentation for de
n
sity fitting
.
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Fix todos for update groups
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix
m
odular
si
m
ula
t
o
r MP
I
bugs
commit
|
commitdiff
|
tree
2019-09-17
Pascal M
e
rz
Make modul
a
r simulator the default co
d
e
p
ath for md
.
.
.
commit
|
commitdiff
|
tree
2019-09-17
Pa
s
cal Mer
z
Fix for
c
e e
l
ement
commit
|
commitdiff
|
tree
2019-09-17
P
a
scal
Merz
Enable checkpointing for modular simulat
o
r
commit
|
commitdiff
|
tree
2019-09-15
M
.
Eri
c
Irrg
a
ng
Import gmxapi do
c
s
t
o main GROMACS do
c
s
dir
e
ctory
.
commit
|
commitdiff
|
tree
2019-09-13
P
aul Bauer
A
dd
l
ist of unsupported functions in
2020
commit
|
commitdiff
|
tree
2019-09-13
Berk Hes
s
Add
n
bnxm kernel benc
h
mark
t
ool
commit
|
commitdiff
|
tree
2019-09-12
Berk
Hess
Updated mdp documentation f
o
r group
schem
e
removal
commit
|
commitdiff
|
tree
2019-09-12
Christian Blau
Manual entry for density
gui
d
ed
simulations
commit
|
commitdiff
|
tree
2019-09-12
Erik Linda
h
l
Ad
d
ed S
I
MD c
b
rt and invcbrt
f
unctions
commit
|
commitdiff
|
tree
2019-09-11
P
aul Ba
u
er
D
isable false posi
t
i
v
e
warning
in I
C
C and MSVC
commit
|
commitdiff
|
tree
2019-09-10
M
agn
u
s Lundborg
More t
e
mpla
t
i
ng
o
f
g
mx_nb_free_energy_ker
n
el()
commit
|
commitdiff
|
tree
2019-09-10
Szilárd Pá
l
l
El
i
m
inate ra
w
force f
l
ags in do_force_lowle
v
el()
commit
|
commitdiff
|
tree
2019-09-10
Ma
r
k Abraha
m
Use more RAI
I
s
emantics with
t
_commrec
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Ext
r
act Cartesian data from DDRankSetup
commit
|
commitdiff
|
tree
2019-09-09
Christian Bl
a
u
A
dding every N-s
t
ep
s
option to densityfit
t
ing
commit
|
commitdiff
|
tree
2019-09-04
Szilárd P
á
ll
Centralize more M
D
/force shedule flags
commit
|
commitdiff
|
tree
2019-09-02
Berk
H
ess
Fix inc
o
rrect rvdw on
G
PU wi
t
h rvd
w
<rcoul
o
m
b
commit
|
commitdiff
|
tree
2019-08-30
C
h
r
i
stian Bl
a
u
Const
r
u
c
t
i
ng local atom sets for density fitting
commit
|
commitdiff
|
tree
2019-08-30
Mar
k
A
braham
Fix build matri
c
es
commit
|
commitdiff
|
tree
2019-08-29
Eri
k
Lindahl
Som
e
quotes I bumped
i
nt
o
last week
commit
|
commitdiff
|
tree
2019-08-28
Pa
u
l Bauer
Hav
e
s
elections availab
l
e f
o
r m
d
run only
commit
|
commitdiff
|
tree
2019-08-28
Mark
A
braham
Im
p
r
oved usability of grompp by rejecting mor
e
inva
l
id
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Mark
Abraha
m
M
ake FEP
rerun tests cover the int
e
nded
lambda s
p
ace
commit
|
commitdiff
|
tree
2019-08-26
M
a
rk Ab
r
aham
Fix pairlist bug
commit
|
commitdiff
|
tree
2019-08-23
Eri
k
L
i
ndahl
Default to AVX2_2
5
6 SIMD f
o
r
Zen2
commit
|
commitdiff
|
tree
2019-08-22
Mark
Abraham
F
ix relea
s
e matrix
commit
|
commitdiff
|
tree
2019-08-06
M
.
E
r
i
c Irrg
a
ng
Conv
e
rt test infrastru
c
t
u
re ta
r
ge
t
s to
static library
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric I
r
rgang
A
dd libg
r
omacs depe
n
den
c
y to
g
pu_ut
i
lstest_cu
d
a target
.
commit
|
commitdiff
|
tree
2019-08-06
Mark
Abraham
Fix for MSVC+CUDA
commit
|
commitdiff
|
tree
2019-08-02
Berk Hess
Made gmx dis
r
e work with non
-
c
onsecutively labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-02
Pascal
Merz
Introduce Simulato
r
b
ase cl
a
s
s
commit
|
commitdiff
|
tree
2019-08-02
M
.
Eric Irrgang
R
e
duce co
n
fl
i
cts with extern
a
l googlet
e
st files
.
commit
|
commitdiff
|
tree
2019-07-23
Mark Abraham
Update developer
g
uide
commit
|
commitdiff
|
tree
2019-07-11
Mark Abraham
Fi
x
pre-submit
build
m
atrix and descript
i
on
commit
|
commitdiff
|
tree
2019-07-11
Ke
v
i
n Boy
d
Use const vi
e
ws
i
n
m
a
tri
x
determin
a
nt calcula
t
ion
commit
|
commitdiff
|
tree
2019-07-11
Kevin Boyd
Add trace functiona
l
ity to 3
x
3 matrices
commit
|
commitdiff
|
tree
2019-07-11
Pascal M
e
r
z
Ge
t
r
i
d of cla
n
g-tidy
w
arning i
n
do_md/rerun/mimic
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
Remove dependence of compute_globals on t_stat
e
commit
|
commitdiff
|
tree
2019-07-11
P
a
scal Merz
Make r
e
lax_shell_flexcon independent of t_state
commit
|
commitdiff
|
tree
2019-07-11
Kevin
B
oyd
Clea
n
up gm
x
solvate
commit
|
commitdiff
|
tree
2019-07-10
Kevin B
o
yd
Add implicit con
v
ersion of mdspan-conta
i
ning types
.
.
.
commit
|
commitdiff
|
tree
2019-07-10
M
.
Eric I
r
rgang
g
m
xapi P
y
thon package documentat
i
on layout
.
commit
|
commitdiff
|
tree
2019-07-09
Paul
Bauer
Fix li
n
k to acpype repository
commit
|
commitdiff
|
tree
2019-07-09
Paul Bauer
Fix postsubmit
commit
|
commitdiff
|
tree
2019-07-08
Pa
u
l Bau
e
r
F
ix
issues
found by
c
l
ang-tidy 7
commit
|
commitdiff
|
tree
2019-07-08
M
a
r
k Ab
r
aham
Fix
hwloc and
s
phi
n
x
detection
commit
|
commitdiff
|
tree
2019-07-08
Mark Abraham
Test spe
c
ific hwloc
versi
o
ns
commit
|
commitdiff
|
tree
2019-07-05
Mark Abraham
I
mpro
v
e
t
ests
o
f
index
b
lock construction
commit
|
commitdiff
|
tree
2019-07-04
Mark Abraham
Fix clang-tidy-7 issue
s
commit
|
commitdiff
|
tree
2019-07-02
Kevin Boyd
Add mdspan basic
e
lem
e
nt
w
ise math
commit
|
commitdiff
|
tree
2019-07-02
M
.
E
r
ic Irrg
a
ng
Updat
e
gmxapi test fixtures
.
commit
|
commitdiff
|
tree
2019-07-02
P
aul Bauer
Fix bug in gmx xpm2ps
commit
|
commitdiff
|
tree
2019-06-27
Sz
i
lárd Páll
Remove a
l
ready resolved
post-submit matri
x
TO
D
O
commit
|
commitdiff
|
tree
2019-06-24
Szi
l
árd Páll
Only use AVX512 in
o
wn-FFTW if GROMACS also us
e
s it
commit
|
commitdiff
|
tree
2019-06-24
P
a
s
c
al Me
r
z
Mak
e
globa
l
topology constant in trajectory
w
riting
commit
|
commitdiff
|
tree
2019-06-14
Paul Bauer
Prepare
f
o
r
2019
.
4
commit
|
commitdiff
|
tree
2019-06-14
Paul Bauer
Vers
i
on 2019
.
3
commit
|
commitdiff
|
tree
2019-06-14
P
a
ul
Bauer
Merge b
r
anch
r
ele
a
se
-
2018 into release-201
9
commit
|
commitdiff
|
tree
2019-06-12
Paul
B
a
uer
F
i
x qsort
n
ot being defi
n
ed on Apple
Clang
commit
|
commitdiff
|
tree
2019-06-11
Paul Baue
r
Ext
e
nd
i
nformation for gmxcpp syntax
e
r
ror
.
commit
|
commitdiff
|
tree
2019-05-29
Pau
l
Bauer
Versio
n
20
1
8
.
7
commit
|
commitdiff
|
tree
2019-05-27
Berk Hes
s
Work around gcc 7 avx512 bug
commit
|
commitdiff
|
tree
2019-05-27
Paul Bauer
Add mo
r
e info for wrong line
e
ndings
commit
|
commitdiff
|
tree
2019-05-24
Paul Ba
u
er
Fix
membran
e
embedd
i
ng
commit
|
commitdiff
|
tree
2019-05-23
Mark Abrah
a
m
Revert "Fixed dvdl
a
mbda for SHAKE +
F
E"
commit
|
commitdiff
|
tree
2019-05-23
Paul Bauer
A
d
d chec
k
for a
l
locatin
g
too many interaction
s
commit
|
commitdiff
|
tree
2019-05-13
Artem Zhmur
o
v
Clarify t
h
e Ener
g
y
Output
I
commit
|
commitdiff
|
tree
2019-05-13
Paul Bauer
Prepar
e
for 201
8
.
7
commit
|
commitdiff
|
tree
2019-05-07
Mark Ab
r
a
h
a
m
Provide bett
e
r help for usi
n
g
lib
c
+
+
commit
|
commitdiff
|
tree
2019-05-06
Artem Z
h
murov
F
ixing
mi
n
or memory issues in MD
L
i
b
commit
|
commitdiff
|
tree
2019-05-03
Paul Bauer
Replace t_grp
s
with std::vect
o
r
commit
|
commitdiff
|
tree
2019-05-02
Paul Bauer
Fix FPE i
n
do_
s
teep
commit
|
commitdiff
|
tree
2019-04-25
Szil
á
rd Páll
Fix c
l
ang warning about
NUL
L
use
commit
|
commitdiff
|
tree
2019-04-25
Szil
á
r
d
Páll
Avoid
u
si
n
g AtomLocalit
y
:
:
C
o
unt as a valid
v
al
u
e
commit
|
commitdiff
|
tree
2019-04-25
A
rtem Zhmurov
Improvemen
t
s
f
o
r energy outp
u
t test
.
commit
|
commitdiff
|
tree
2019-04-23
Mark Abrah
a
m
Updated clang -Weverythi
n
g c
h
e
c
k
s
t
o clang-7
commit
|
commitdiff
|
tree
2019-04-18
Paul
B
auer
Update clang-tidy to check
for
d
angling
references
commit
|
commitdiff
|
tree
2019-04-18
Berk Hes
s
Fix pdb-rel
a
ted issues
commit
|
commitdiff
|
tree
2019-04-17
Paul
B
aue
r
C
reate gmx::compat::string_view
commit
|
commitdiff
|
tree
2019-04-16
Paul Bauer
P
r
e
p
are
f
or version 2019
.
3
commit
|
commitdiff
|
tree
2019-04-16
ejjordan
D
ie wi
t
h
helpful note in case of
i
ncorre
c
t
input to
.
.
.
commit
|
commitdiff
|
tree
2019-04-16
Berk
H
e
s
s
Make
m
drun -nsteps work again
.
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
Update 2019
r
e
l
ease notes for i
s
s
u
e
2845
commit
|
commitdiff
|
tree
2019-04-15
S
zilárd Pál
l
Add user guide
n
o
te on A
V
X512 throttle in GP
U
r
u
ns
commit
|
commitdiff
|
tree
2019-04-15
B
erk Hess
Disallow pull geometry direc
t
ion-periodic with
A
W
H
commit
|
commitdiff
|
tree
2019-04-10
M
.
Eri
c
I
rrgang
Us
e
pybind
1
1 to make a minim
a
l C++ Python e
x
tension
.
commit
|
commitdiff
|
tree
2019-04-09
Mark Abr
a
ham
F
i
x
t
ypo in AVX512 detection code
commit
|
commitdiff
|
tree
2019-04-03
P
a
ul Ba
u
er
Fix post subm
i
t
commit
|
commitdiff
|
tree
2019-03-28
Roland Sc
h
u
l
z
Fix UB vector
usage
commit
|
commitdiff
|
tree
2019-03-25
Mark
A
b
raham
Convert g
m
x
dump to module
commit
|
commitdiff
|
tree
2019-03-22
C
h
r
i
stian Blau
d
ensityf
i
tting - serializ
e
r fo
r
m
r
c
h
eader dat
a
.
commit
|
commitdiff
|
tree
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