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Fix ocl_kernel target
2019-08-12
Mark A
b
raham
Fix ocl_kern
e
l ta
r
get
commit
|
commitdiff
|
tree
2019-08-12
Pascal
M
e
rz
Use ne
w
setenv
fun
c
tion for energyoutput test
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric
I
rrgang
Separate
o
ut
some a
b
s
tract bas
e
c
l
as
s
es
.
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmuro
v
Prepare Up
d
a
t
e
a
nd
C
o
n
strain
t
s
for Domain Decompositi
o
n
commit
|
commitdiff
|
tree
2019-08-09
A
r
tem Zhmurov
Refactoring of the
S
E
TTLE tests
commit
|
commitdiff
|
tree
2019-08-09
Berk Hes
s
S
IMD
a
cceleration for F_FOURDIHS
and F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-08
Mark Ab
r
aham
Fix estimat
e
o
f
the si
z
e of a j list
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Ir
r
gang
Add
gmxapi_pytest
c
us
t
om
target to
CMake `c
h
eck` target
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
r
i
c Irrga
n
g
Allow gmxapi Python package tes
t
s
to be run from
G
ROM
A
CS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
Chr
i
stian
B
l
a
u
H
armonize mrc densit
y
fo
r
mat
e
xtents with
r
e
st of code
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Reenab
l
e
gtest_main tar
g
et
.
commit
|
commitdiff
|
tree
2019-08-08
Mar
k
Abraham
Stop te
s
ti
n
g ICC
o
n
Windows
commit
|
commitdiff
|
tree
2019-08-08
A
rt
e
m
Z
h
muro
v
Refacto
r
Le
a
p-Frog
t
e
st
s
and connect them to
CPU ve
r
sion
commit
|
commitdiff
|
tree
2019-08-07
M
.
Eri
c
Irrgang
U
s
e gmock
a
nd gtest targ
e
t
s
f
r
om googletest-rele
a
se
.
.
.
commit
|
commitdiff
|
tree
2019-08-05
Pasc
a
l
Me
r
z
Move ownersh
i
p of
kinetic energy object to
I
Si
m
ulator
commit
|
commitdiff
|
tree
2019-08-05
Pasca
l
Merz
Added
Simulator
c
omparison test
commit
|
commitdiff
|
tree
2019-08-05
Mark Abrah
a
m
R
emove libgromac
s
_gene
r
ated c
o
ntribu
t
ion
s
from
FindCU
D
A
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Remov
e
a pointer in t_forcerec
commit
|
commitdiff
|
tree
2019-08-01
Berk Hes
s
Fix n
b
nxm G
P
U
memory re
s
erv
a
tion issue
commit
|
commitdiff
|
tree
2019-08-01
M
ark
A
braham
Manage compiler fla
g
s and some includ
e
options per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
Improve use of obj
e
c
t
lib
r
aries in libgromacs
commit
|
commitdiff
|
tree
2019-08-01
Mark
A
b
raham
M
er
g
e "Merge
release-2019 into ma
s
ter"
commit
|
commitdiff
|
tree
2019-07-31
B
e
rk Hess
Add grompp warning with u
s
e of GROMOS
F
F
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
Intro
d
u
ce functi
o
n
that checks i
f
the computations
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Fixes
f
or F buffer ops c
h
an
g
e
commit
|
commitdiff
|
tree
2019-07-31
Ber
k
Hes
s
Remove n
e
ed for
G
ROMOS FF in test
commit
|
commitdiff
|
tree
2019-07-31
P
a
scal
Merz
Rename Simulator
t
o
L
e
g
acySimul
a
tor
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Move cycle
c
ounting into
the GPU bonded modul
e
commit
|
commitdiff
|
tree
2019-07-31
Sz
i
lárd Pál
l
Re
p
ort
w
hen
development feature flags are u
s
ed
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
M
o
ve end
o
f
s
tep GPU task launches to a fu
n
ctio
n
commit
|
commitdiff
|
tree
2019-07-30
Paul
B
auer
A
d
d
wrapper for outputada
p
ter method
s
commit
|
commitdiff
|
tree
2019-07-28
B
e
rk Hess
Convert
E
wald
c
orrection tabl
e
s to C+
+
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
Add
d
e
faul
t
initialization to interaction_const_t
commit
|
commitdiff
|
tree
2019-07-26
Ch
r
i
stian Blau
Fix failing check-sourc
e
t
a
rget on pytho
n
3
.
6
commit
|
commitdiff
|
tree
2019-07-25
Berk Hess
Spli
t
canDetect
G
pus()
commit
|
commitdiff
|
tree
2019-07-25
Szilárd
P
á
ll
O
nly stop
the CUDA
pro
f
iler if t
h
ere are d
e
vices
commit
|
commitdiff
|
tree
2019-07-24
Paul B
a
uer
F
ix doxyge
n
i
n coordiant
e
io files
commit
|
commitdiff
|
tree
2019-07-24
Paul Bauer
A
dd output
a
d
apters
(3/3)
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric
Irrgang
Fix
g
mxapi n
o
te
b
ook image and sa
m
p
l
e
_
re
s
traint docker
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
E
r
ic Irrgang
Im
p
ro
v
e gmxapi doc
k
er testin
g
environment
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
Eric Irrgang
Don't install sample
r
estraint
pack
a
ge
by d
e
fa
u
lt
.
commit
|
commitdiff
|
tree
2019-07-23
Kevin
B
oyd
Modern
i
ze syntax
of enable_i
f
and trai
t
s to
u
s
e
_t
.
.
.
commit
|
commitdiff
|
tree
2019-07-09
Dav
i
d van der Spoel
F
ix
e
d s
m
all
b
ug in gmx a
n
a
e
i
g
commit
|
commitdiff
|
tree
2019-07-09
M
.
E
ric Irrg
a
ng
In
c
o
r
porate sa
m
ple_rest
r
ai
n
t repository
.
commit
|
commitdiff
|
tree
2019-07-09
M
.
Eric Ir
r
gang
Begin CMak
e
front-en
d
for Python packaging machinery
.
commit
|
commitdiff
|
tree
2019-07-08
Szilá
r
d
Páll
Eliminate a use of doub
l
e prec
i
sion in
t
he GPU
b
onded
.
.
.
commit
|
commitdiff
|
tree
2019-07-08
Berk Hess
Store nbnxm gridSet da
t
a in
GridSe
t
Data
commit
|
commitdiff
|
tree
2019-07-05
Mark
A
braha
m
Mod
e
rnize Find
H
w
l
oc
.
cmake
commit
|
commitdiff
|
tree
2019-07-05
M
.
Eric
Irr
g
ang
Python b
i
n
d
ings f
o
r m
d
run
.
commit
|
commitdiff
|
tree
2019-07-04
M
ark Abraham
Furth
e
r cl
a
ng-tidy-
7
fi
x
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Combine C
U
DA Leap-Frog
,
LI
N
CS and SETTL
E
.
II
.
commit
|
commitdiff
|
tree
2019-07-03
Kevin Boyd
Updates to m
a
th/ve
c
.
h
commit
|
commitdiff
|
tree
2019-07-02
Mark Abraham
Clarify wo
r
di
n
g of relea
s
e note
s
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
R
e
-enable affinity diagonostics with MPI
commit
|
commitdiff
|
tree
2019-07-02
Kev
i
n
Boy
d
A
dd
functio
n
for c
a
lculating 3x3
ma
t
rix determin
a
nt
commit
|
commitdiff
|
tree
2019-07-02
Kevin Boyd
Remove refer
e
nces to
e
cutsG
R
O
U
P
commit
|
commitdiff
|
tree
2019-07-01
Pascal
M
erz
Fix m
o
dule
detection
fo
r
p
hysical v
a
l
ida
t
io
n
commit
|
commitdiff
|
tree
2019-07-01
S
zilárd
Páll
Refactor
tracking of GPU short-ran
g
e work/skipping
commit
|
commitdiff
|
tree
2019-07-01
Berk H
e
ss
Fix MP
I
de
a
dlock in
a
ffinity setting
commit
|
commitdiff
|
tree
2019-07-01
M
.
Eric Irr
g
ang
gmxapi Python package
d
ocumentati
o
n
i
nf
r
astruct
u
re
.
commit
|
commitdiff
|
tree
2019-06-30
Szi
l
árd Páll
Creat
e
ded
i
cated subco
u
nter for non
b
o
nded FEP
commit
|
commitdiff
|
tree
2019-06-30
Kev
i
n Boyd
Re
m
ove group s
c
heme ch
e
cks from runner
commit
|
commitdiff
|
tree
2019-06-30
Magnus Lundborg
Cleaning
u
p the
G
PU bonded kernel
commit
|
commitdiff
|
tree
2019-06-20
P
aul
B
auer
Use I
S
er
i
a
l
izer fo
r
T
PR f
i
le IO
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Temp
l
ate free-energy kernel
o
n sof
t
-core
commit
|
commitdiff
|
tree
2019-06-20
Christi
a
n Blau
Add BasicVe
c
t
o
r scal
i
n
g, max, min an
d
toIvec
commit
|
commitdiff
|
tree
2019-06-19
Szilárd P
á
ll
D
i
s
a
ble P
M
E
GPU
on Appl
e
OpenCL
commit
|
commitdiff
|
tree
2019-06-19
B
e
rk Hess
Refa
c
tor PME atom handling
commit
|
commitdiff
|
tree
2019-06-19
Paul B
a
uer
Split t
p
r h
e
ader reading reading
from t
p
r b
o
dy
commit
|
commitdiff
|
tree
2019-06-19
Berk H
e
ss
Remove
d
u
nused code
p
aths i
n
the NB FE k
e
rnel
commit
|
commitdiff
|
tree
2019-06-18
Paul
B
au
e
r
Fix gmx d
u
m
p
commit
|
commitdiff
|
tree
2019-06-18
Mark A
b
raha
m
Move cod
e
handling m
d
r
un -g
p
u_id to
t
a
s
kassig
n
m
ent
.
.
.
commit
|
commitdiff
|
tree
2019-06-18
Berk Hess
Make for
c
erec c
o
nst in dis
p
atchNonbondedKernel()
commit
|
commitdiff
|
tree
2019-06-18
Christian
Blau
Mrc format hea
d
er
t
o lattice coordinate
t
ransf
o
rm
commit
|
commitdiff
|
tree
2019-06-18
C
h
ristian Blau
Densi
t
y similari
t
y
m
ea
s
ure and gradient
commit
|
commitdiff
|
tree
2019-06-18
M
.
Eric Irrgang
Reduce
d
o
cker image size for gmxap
i
CI
.
commit
|
commitdiff
|
tree
2019-06-18
Artem
Zhm
u
rov
Bug fix
:
Constraints tests are not inst
a
nt
i
ated with
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark Abr
a
ham
Fix p
y
gments detection
for sphinx
fo
r
docs bui
l
d
commit
|
commitdiff
|
tree
2019-06-11
Mar
k
A
braham
Use RAII app
r
oac
h
e
s
for
hardware information detection
commit
|
commitdiff
|
tree
2019-06-11
Ma
r
k Abraham
Clean up mu
l
tisim, communication, a
n
d REMD code
commit
|
commitdiff
|
tree
2019-06-11
M
ark A
b
raham
Initialize all of gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-06-11
P
aul Bauer
Fix r
e
sidu
e
an
d
molecu
l
e indexing i
n
sele
c
tion
s
commit
|
commitdiff
|
tree
2019-06-11
Berk Hess
Allow AWH geometry 'dire
c
tion' to
b
e periodic
commit
|
commitdiff
|
tree
2019-06-11
Paul Ba
u
er
Add check for too m
a
ny grid
p
o
ints
in hbond
commit
|
commitdiff
|
tree
2019-06-05
B
erk Hess
F
i
x refer
e
nce SIMD memory ali
g
n
m
e
nt
commit
|
commitdiff
|
tree
2019-05-29
Berk Hess
Fix mi
s
sing inter
m
olecul
a
r inte
r
a
c
tions w
i
th DD
commit
|
commitdiff
|
tree
2019-05-29
Szil
á
rd Páll
Temp
l
ate x buf
f
er ops call
on whether GPU is used
commit
|
commitdiff
|
tree
2019-05-27
Pascal Merz
C
lean u
p
renamed sim
u
lator
.
h
file
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
Remove dependence of mdoutf_w
r
ite
_
t
o_trajectory_files
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
Ren
a
me Integrator c
l
as
s
commit
|
commitdiff
|
tree
2019-05-24
Artem Z
h
mu
r
ov
Clar
i
fy the Energy
O
utput
I
II
commit
|
commitdiff
|
tree
2019-05-24
A
rt
e
m Zhmurov
Cl
a
rify t
h
e EnergyOutput II
commit
|
commitdiff
|
tree
2019-05-24
Mark
Abraham
Reo
r
de
r
code before
thread-MP
I
spawns threads
commit
|
commitdiff
|
tree
2019-05-23
Szilá
r
d Pál
l
Fix m
u
litpl
e
link refs in d
e
v
-manual
commit
|
commitdiff
|
tree
2019-05-23
Mark Abraham
Te
a
ch Array
R
efWit
h
Padding t
o
m
a
k
e
a
const flav
o
ur
commit
|
commitdiff
|
tree
2019-05-23
B
erk H
e
ss
Fix
SHAKE dH/dlambda contributions
commit
|
commitdiff
|
tree
2019-05-22
Mark
Abrah
a
m
Rewrite startin
g
b
e
havior
commit
|
commitdiff
|
tree
2019-05-22
Mark
A
b
raham
Introduce tri-state e
n
ums for restarts
commit
|
commitdiff
|
tree
2019-05-22
Alan Gray
Pi
n
X b
u
ffer w
i
th DD
and u
s
e proper
abstr
a
ction in
.
.
.
commit
|
commitdiff
|
tree
2019-05-22
Jin
k
e Fan
Add support for Hyg
o
n Dhya
n
a processo
r
commit
|
commitdiff
|
tree
next