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Quiet warning
2019-08-12
Mark Ab
r
aham
Quiet
warning
commit
|
commitdiff
|
tree
2019-08-12
Mark Ab
r
a
h
a
m
F
ix ocl_kerne
l
tar
g
et
commit
|
commitdiff
|
tree
2019-08-12
Pascal Mer
z
Us
e
new
setenv function for
energy
o
u
tput test
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric I
r
r
gang
S
e
parate out s
o
me ab
s
trac
t
base cla
s
ses
.
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmurov
Prepare Update
an
d
Constraint
s
for
D
om
a
in D
e
compositio
n
commit
|
commitdiff
|
tree
2019-08-09
Artem
Z
h
mur
o
v
Refactor
i
ng of th
e
SETTLE tests
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
SIMD acceleration f
o
r F_FO
U
RD
I
HS and F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraham
Fix e
s
timate
of
t
he
size
o
f a j
l
ist
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eri
c
Irrgang
A
d
d gmxap
i
_pyte
s
t custom target
t
o
CMake `check
`
target
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
ric Irrgang
Allow
gmxapi Python pa
c
kage tests to be r
u
n
f
rom GROMACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
Christian Blau
Harmonize mrc
d
ens
i
ty fo
r
mat extents with rest of code
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Reenable gtest_main
t
arget
.
commit
|
commitdiff
|
tree
2019-08-08
Mark A
b
ra
h
a
m
S
t
op testi
n
g ICC
on Windows
commit
|
commitdiff
|
tree
2019-08-08
Artem Zhmurov
R
e
factor Leap-Frog tests and co
n
nect them to
CP
U
version
commit
|
commitdiff
|
tree
2019-08-07
M
.
Eric
I
r
rg
a
n
g
Use gm
o
c
k a
n
d g
t
e
st targe
t
s fr
o
m goo
g
letest-r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2019-08-05
P
a
scal Mer
z
Move ownership o
f
kinetic energ
y
o
b
j
ect to ISimulato
r
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Added Simulator com
p
arison test
commit
|
commitdiff
|
tree
2019-08-05
Mark Ab
r
aham
Remove libgro
m
acs_generated
contrib
u
t
ions from FindCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Be
r
k H
e
ss
Rem
o
ve a pointer in
t_for
c
e
r
ec
commit
|
commitdiff
|
tree
2019-08-01
Berk
Hess
Fix nb
n
xm G
P
U
m
e
mor
y
reservatio
n
iss
u
e
commit
|
commitdiff
|
tree
2019-08-01
M
ark
A
braham
Manag
e
compiler flags
and some include
o
ptions
p
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark
A
braham
Improve use of object l
i
brar
i
e
s
in li
b
gromacs
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
Merge "Merge release-201
9
into master"
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Add
grompp war
n
i
n
g wi
t
h
u
se of G
R
OMOS F
F
commit
|
commitdiff
|
tree
2019-07-31
A
r
t
em Zhmurov
In
t
roduce functio
n
that c
h
ecks if the comput
a
t
i
ons
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Fixes for F
b
u
ff
e
r
o
ps change
commit
|
commitdiff
|
tree
2019-07-31
Berk Hes
s
Remove need for GRO
M
OS FF in test
commit
|
commitdiff
|
tree
2019-07-31
Pascal Merz
R
e
nam
e
S
i
mulato
r
t
o LegacyS
i
mula
t
or
commit
|
commitdiff
|
tree
2019-07-31
Szilá
r
d
P
áll
Move cycle counting into
t
he GP
U
b
o
nd
e
d module
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Re
p
ort when dev
e
lop
m
e
n
t feature fl
a
gs are u
s
ed
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Move
end of step G
P
U
t
ask la
u
n
ches to a func
t
ion
commit
|
commitdiff
|
tree
2019-07-30
Pau
l
Ba
u
er
Add wrapper for out
p
ut
a
d
apter
m
ethods
commit
|
commitdiff
|
tree
2019-07-28
Berk Hess
Convert Ew
a
ld correc
t
ion table
s
t
o
C++
commit
|
commitdiff
|
tree
2019-07-26
B
erk Hess
A
d
d default in
i
tializatio
n
t
o int
e
raction_const_t
commit
|
commitdiff
|
tree
2019-07-26
C
h
ristia
n
Blau
Fi
x
failing che
c
k
-source target
on pyth
o
n3
.
6
commit
|
commitdiff
|
tree
2019-07-25
Berk H
e
ss
Spli
t
can
D
etectGp
u
s()
commit
|
commitdiff
|
tree
2019-07-25
Szilárd Pál
l
O
n
ly stop the CUD
A
p
r
of
i
le
r
if the
r
e
a
r
e
d
evices
commit
|
commitdiff
|
tree
2019-07-24
Paul B
a
uer
Fix d
o
xygen i
n
coordi
a
nteio
f
i
les
commit
|
commitdiff
|
tree
2019-07-24
P
a
ul B
a
uer
Add outputadapters (3/3)
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
F
i
x gmxap
i
n
o
t
e
book ima
g
e
and sample_restr
a
i
n
t docker
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric
Ir
r
gang
Improv
e
gmxapi docker te
s
ti
n
g environment
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
Eric Irrg
a
n
g
Don't install s
a
mpl
e
re
s
t
raint package by def
a
ult
.
commit
|
commitdiff
|
tree
2019-07-23
Kevin Boyd
Moderniz
e
syntax of
e
nable_if
a
nd tr
a
its
t
o use _t
.
.
.
commit
|
commitdiff
|
tree
2019-07-09
David van der S
p
oel
Fixed small bug in gmx
a
naeig
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric
I
r
r
ga
n
g
Incorp
o
r
ate sample_restraint repo
s
itory
.
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric Irrgang
Begin CMak
e
front-end f
o
r Python pac
k
aging
machi
n
ery
.
commit
|
commitdiff
|
tree
2019-07-08
Szilárd
P
ál
l
Eliminate a use of
do
u
b
le p
r
ecision in
t
he GPU bonded
.
.
.
commit
|
commitdiff
|
tree
2019-07-08
Berk H
e
ss
St
o
re nbnxm
gridSet data in GridSetData
commit
|
commitdiff
|
tree
2019-07-05
Mar
k
Abr
a
ham
Modernize FindHwloc
.
cmake
commit
|
commitdiff
|
tree
2019-07-05
M
.
Er
i
c
Irrgang
Py
t
hon
binding
s
for mdrun
.
commit
|
commitdiff
|
tree
2019-07-04
Mar
k
A
braham
Furth
e
r clang-ti
d
y
-
7 f
i
x
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Co
m
bi
n
e CUDA
L
e
ap-Fro
g
, LI
N
C
S
and SETTLE
.
II
.
commit
|
commitdiff
|
tree
2019-07-03
K
e
vin Boyd
Updates to math/vec
.
h
commit
|
commitdiff
|
tree
2019-07-02
Mark
Abraham
Clarify
wording of release notes
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Re
-
e
n
able af
f
init
y
diagonostics with
MPI
commit
|
commitdiff
|
tree
2019-07-02
Kev
i
n Boyd
Add
f
u
n
ction for calcul
a
t
ing 3x3 ma
t
rix dete
r
m
i
n
a
nt
commit
|
commitdiff
|
tree
2019-07-02
K
e
vin Bo
y
d
Remove referen
c
es to ecu
t
sGROU
P
commit
|
commitdiff
|
tree
2019-07-01
Pascal Merz
Fix
mod
u
le
detection for
physical validation
commit
|
commitdiff
|
tree
2019-07-01
Szilár
d
Pá
l
l
Re
f
act
o
r
tracking of
G
PU shor
t
-
r
ange work/skipping
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Fi
x
MPI deadlo
c
k in affinity setting
commit
|
commitdiff
|
tree
2019-07-01
M
.
E
r
ic Irrgang
gmxapi Pyt
h
on package documentation infras
t
ructure
.
commit
|
commitdiff
|
tree
2019-06-30
Szilárd Pál
l
C
r
eate dedic
a
ted su
b
c
ounter for nonbonded FEP
commit
|
commitdiff
|
tree
2019-06-30
Kevi
n
B
oyd
Re
m
ove group
s
cheme checks from
r
unner
commit
|
commitdiff
|
tree
2019-06-30
Magnus Lu
n
d
b
org
C
l
eaning up the GP
U
bonded kernel
commit
|
commitdiff
|
tree
2019-06-20
Paul B
a
u
e
r
Use
ISerializer for TPR f
i
le IO
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Template free-en
e
r
gy kernel on
soft-c
o
re
commit
|
commitdiff
|
tree
2019-06-20
Christia
n
Bla
u
Ad
d
Basic
V
ector scal
i
n
g, max, mi
n
a
n
d toIvec
commit
|
commitdiff
|
tree
2019-06-19
Szilárd Páll
D
i
s
a
bl
e
P
ME GPU
o
n Apple O
p
enCL
commit
|
commitdiff
|
tree
2019-06-19
B
e
rk
H
es
s
R
e
f
actor PME atom
handling
commit
|
commitdiff
|
tree
2019-06-19
Paul Bauer
Split tpr head
e
r
r
e
a
d
ing reading from tpr body
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Removed unused code paths in
t
he NB FE kernel
commit
|
commitdiff
|
tree
2019-06-18
Paul Bauer
Fix
g
mx dump
commit
|
commitdiff
|
tree
2019-06-18
Mark
Abr
a
ham
Move
c
o
d
e h
a
ndling mdrun
-g
p
u
_id
t
o taskassignmen
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-18
Berk Hess
Make for
c
erec
c
o
nst i
n
dis
p
atchNo
n
b
onded
K
ernel()
commit
|
commitdiff
|
tree
2019-06-18
C
h
ristian
B
l
au
Mrc form
a
t
header
t
o lattice coor
d
in
a
te transf
o
rm
commit
|
commitdiff
|
tree
2019-06-18
Christian Blau
Density similarity measur
e
and
g
radient
commit
|
commitdiff
|
tree
2019-06-18
M
.
Eric
Irrga
n
g
Reduc
e
doc
k
er image
size for gmxapi CI
.
commit
|
commitdiff
|
tree
2019-06-18
Ar
t
e
m
Zhmurov
Bug
fix: Con
s
traints tests are not instantiated with
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark Ab
r
aham
Fix
pygments
d
etection fo
r
sphinx for doc
s
b
uild
commit
|
commitdiff
|
tree
2019-06-11
Mark Abr
a
ham
Use
R
AII
a
p
proaches for ha
r
dw
a
re
i
nfo
r
mati
o
n
d
etection
commit
|
commitdiff
|
tree
2019-06-11
Mark Abr
a
ham
Cle
a
n up
m
ultisim, com
m
u
nication, and
RE
M
D
c
ode
commit
|
commitdiff
|
tree
2019-06-11
M
a
rk Abrah
a
m
Initialize all of gmx_do
m
de
c
_com
m
_t
commit
|
commitdiff
|
tree
2019-06-11
Paul Bauer
Fix res
i
du
e
a
nd molec
u
le indexing in sele
c
tions
commit
|
commitdiff
|
tree
2019-06-11
B
erk Hess
Al
l
ow
A
WH g
e
ometry 'direction
'
to be periodic
commit
|
commitdiff
|
tree
2019-06-11
Paul Bauer
Add
check for too many grid poi
n
t
s in h
b
ond
commit
|
commitdiff
|
tree
2019-06-05
Berk
Hess
F
ix refere
n
ce SIMD memory
alignment
commit
|
commitdiff
|
tree
2019-05-29
Berk He
s
s
Fix
m
issing
i
ntermolecular interactions wit
h
DD
commit
|
commitdiff
|
tree
2019-05-29
Szilár
d
Páll
Template x buffer ops call on whether
GPU is
us
e
d
commit
|
commitdiff
|
tree
2019-05-27
Pascal Merz
C
l
e
an
u
p
ren
a
med
s
im
u
l
ator
.
h file
commit
|
commitdiff
|
tree
2019-05-25
Pasc
a
l
Merz
Remov
e
dep
e
n
d
e
n
c
e of md
o
utf_write_to_traj
e
c
t
ory
_
f
il
e
s
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pascal Me
r
z
Rename
Integra
t
or
c
las
s
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmuro
v
C
larify the En
e
rgyOu
t
put III
commit
|
commitdiff
|
tree
2019-05-24
Arte
m
Zhmur
o
v
Clarif
y
the En
e
rgy
O
utp
u
t I
I
commit
|
commitdiff
|
tree
2019-05-24
Mark
Abraham
Reorder code b
e
fore thread-MPI spawns th
r
eads
commit
|
commitdiff
|
tree
2019-05-23
Szi
l
árd Páll
Fix mulitple link
refs
in
dev
-
ma
n
u
a
l
commit
|
commitdiff
|
tree
2019-05-23
Mark A
b
raham
T
each ArrayR
e
fWithPadding to make a
c
onst
f
lavour
commit
|
commitdiff
|
tree
2019-05-23
Be
r
k Hess
Fix SH
A
KE dH/
d
l
a
mb
d
a
c
ontributions
commit
|
commitdiff
|
tree
2019-05-22
Mark Abra
h
am
Rewr
i
te starti
n
g behavior
commit
|
commitdiff
|
tree
2019-05-22
M
a
rk Ab
r
aham
Introduce t
r
i-s
t
ate enums f
o
r
re
s
ta
r
ts
commit
|
commitdiff
|
tree
2019-05-22
Alan Gray
Pin X bu
f
fer with DD and use pr
o
per abstraction in
.
.
.
commit
|
commitdiff
|
tree
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