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gmxapi::UsageError
2018-10-14
M
.
Eric
I
rrgang
gmx
a
pi::Usag
e
E
rror
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Irrgang
All
o
w AP
I
acc
e
s
s
t
o
s
imulation signals
.
commit
|
commitdiff
|
tree
2018-10-13
Aleksei Iupinov
Add an
d
e
nable P
M
E
OpenC
L
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eri
c
Irrgang
Add AP
I
for adding
M
D
Modu
l
e
s / R
e
straints
.
commit
|
commitdiff
|
tree
2018-10-12
Berk Hess
I
mplement ass
i
gning
b
o
nde
d
s
t
o the
G
P
U
commit
|
commitdiff
|
tree
2018-10-12
M
.
E
ric Irrgang
Add restr
a
ints frame
w
ork
.
commit
|
commitdiff
|
tree
2018-10-12
V
iach
e
sla
v
Bolny
k
h
Implement
e
d QM/MM workflow inside core G
R
O
M
ACS
commit
|
commitdiff
|
tree
2018-10-12
Mark Abra
h
am
E
xclude gmxapi source f
i
l
e
s from
i
nclud
e
s
o
rting
commit
|
commitdiff
|
tree
2018-10-11
Da
v
id van
der Spoel
Reinstated quasiharmonic e
n
t
ropy
c
alcul
a
t
i
on i
n
gmx
.
.
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
Er
i
c Irrgang
A
d
d gmxapi::Se
s
s
i
on
.
commit
|
commitdiff
|
tree
2018-10-11
Mark Abraha
m
Fix
P
add
e
d
Ve
c
tor issues
commit
|
commitdiff
|
tree
2018-10-10
P
a
u
l Bauer
Include
d
oi strings from zenodo during re
l
ease
commit
|
commitdiff
|
tree
2018-10-10
M
.
Eric
I
rrgan
g
g
mxapi expects position in
d
e
p
en
d
e
nt code
.
commit
|
commitdiff
|
tree
2018-10-10
S
z
i
lárd Páll
S
w
ap custom
OpenCL memset kernel f
o
r c
l
EnqueueF
i
llBuffer
commit
|
commitdiff
|
tree
2018-10-09
S
zilárd P
á
ll
Up
d
a
te regressiontest ref to download
commit
|
commitdiff
|
tree
2018-10-09
Viacheslav B
o
lnykh
Imple
m
ented changes to pre
p
rocessor to wor
k
wi
t
h MiMiC
.
.
.
commit
|
commitdiff
|
tree
2018-10-09
Mark Abraham
Fix
D
omdecOptions default
commit
|
commitdiff
|
tree
2018-10-09
Roland Schulz
Fix MSAN errors
commit
|
commitdiff
|
tree
2018-10-08
B
e
rk Hess
Enable update g
r
o
u
p
s
commit
|
commitdiff
|
tree
2018-10-08
Szi
l
árd Páll
Tweak FindFFTW
API che
c
ks
commit
|
commitdiff
|
tree
2018-10-08
Szilárd Pá
l
l
Fix clang-6 warnings
commit
|
commitdiff
|
tree
2018-10-08
R
ol
a
nd Sc
h
ulz
OCL: Add cons
t
to func
t
ion argum
e
n
ts
commit
|
commitdiff
|
tree
2018-10-08
Roland Schulz
Add OCL kernel t
a
r
get
commit
|
commitdiff
|
tree
2018-10-08
Mark
Abraham
D
i
sable F
P
E explicitly
f
or TPI force
c
alc
u
lation
commit
|
commitdiff
|
tree
2018-10-08
Szilár
d
Páll
Repla
c
e some NULL w
i
th
n
ullptr i
n
CUDA code
commit
|
commitdiff
|
tree
2018-10-08
Mark
A
braham
Im
p
lement PaddedV
e
ctor
commit
|
commitdiff
|
tree
2018-10-08
Paul Bau
e
r
Wo
r
karound for ICC postsubmit b
u
g
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
M
o
re update
s
t
o
test matrix
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
Fi
x
make
t
es
t
commit
|
commitdiff
|
tree
2018-10-07
Mark Abraham
Test w
i
th
g
cc 8 and cuda 10
commit
|
commitdiff
|
tree
2018-10-05
Mark Abra
h
am
C
h
ec
k
log and other file
s
differently during appending
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Berk H
e
ss
Add update group
s
to DD a
t
om d
i
s
p
lacement
commit
|
commitdiff
|
tree
2018-10-05
Mark
Abraham
Change
t
o t
e
st TS
A
N wit
h
clang and libomp
commit
|
commitdiff
|
tree
2018-10-05
R
o
land Schulz
O
C
L: Make
v
ariab
l
es
const
commit
|
commitdiff
|
tree
2018-10-05
M
.
Eric Irrgang
Add gmxapi
:
:System
.
commit
|
commitdiff
|
tree
2018-10-05
Szilá
r
d
P
áll
Update test mat
r
ice
s
with n
e
w GPU spe
c
ifiers
commit
|
commitdiff
|
tree
2018-10-04
Berk Hess
Make
AV
X
2 p
a
ss T
S
A
N
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Extract
hel
p
er functions fo
r
pr
e
parin
g
for
appen
d
ing
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraha
m
Simpl
i
fy
E
M
u
sage of
m
debin
commit
|
commitdiff
|
tree
2018-10-03
Mark Abrah
a
m
U
s
e
f
ast returns in md5 com
p
utatio
n
commit
|
commitdiff
|
tree
2018-10-03
Magn
u
s L
u
n
d
borg
A
l
low
u
sing COM of previous step as PBC refe
r
ence
commit
|
commitdiff
|
tree
2018-10-03
M
a
r
k Abraha
m
Add end-to-end tes
t
s of energ
y
minimization
commit
|
commitdiff
|
tree
2018-10-03
Paul Bauer
Disabl
e
GMXAPI when only building mdrun
commit
|
commitdiff
|
tree
2018-10-03
M
.
E
ric
I
rrgang
Add gmxapi::Co
n
t
e
xt
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
E
r
ic Irrgang
Move mdrun mainFunc
t
i
o
n to c
l
ient code
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Irrgang
A
d
d
test d
a
ta for gmxapi
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
E
r
ic Irrg
a
ng
Add g
m
x
a
pi exceptions
.
commit
|
commitdiff
|
tree
2018-10-02
Paul Bauer
Fix
include
f
ormat
t
i
ng in
g
mxapi
commit
|
commitdiff
|
tree
2018-10-02
Roland Schulz
Use subgroup shuffle for reduction
commit
|
commitdiff
|
tree
2018-10-02
Berk Hess
Update
DD cutoffs fo
r
u
pdate grou
p
s
commit
|
commitdiff
|
tree
2018-10-02
M
a
r
k
Abraham
Red
u
c
e
mdrun
t
es
t
s using group scheme
commit
|
commitdiff
|
tree
2018-10-01
Mark Abraham
F
i
x gcc-
8
wa
r
ning
s
about
s
trings
commit
|
commitdiff
|
tree
2018-10-01
Paul Baue
r
Change get_at
o
m_index to return
i
nt
commit
|
commitdiff
|
tree
2018-10-01
Ma
r
k
Ab
r
aha
m
Add rele
a
se
n
ot
e
s for r
e
moving n
o
n-repro
d
ucible asp
e
cts
commit
|
commitdiff
|
tree
2018-10-01
Mark
A
brah
a
m
Tests for
m
d
5 computatio
n
on op
e
n fil
e
s
commit
|
commitdiff
|
tree
2018-09-29
Mark
A
brah
a
m
S
to
p
ICC ICE
commit
|
commitdiff
|
tree
2018-09-29
B
erk H
e
ss
Ad
d
Upd
a
teGro
u
psCog t
o
DD
commit
|
commitdiff
|
tree
2018-09-28
Mar
k
A
braham
Us
e
more default
initi
a
li
z
a
tion of mdrun structs
commit
|
commitdiff
|
tree
2018-09-28
Mark Abraham
Make some s
y
mbo
l
s in gmx
p
re-con
f
ig
.
h always
d
efined
commit
|
commitdiff
|
tree
2018-09-27
Kevi
n
B
o
yd
R
e
d
u
c
e prep
r
ocessor depend
e
n
cy in re
s
ourc
e
divisio
n
.
cpp
commit
|
commitdiff
|
tree
2018-09-26
Berk Hes
s
E
xtract settle test water coord
i
nates
commit
|
commitdiff
|
tree
2018-09-26
Mag
n
us Lu
n
d
b
org
Added pullCheckP
b
cW
i
thinG
r
o
u
p() to check
one
group
commit
|
commitdiff
|
tree
2018-09-26
Mark Abraham
Cla
r
ify
distinct p
a
ths for mdrun log file
h
andlin
g
commit
|
commitdiff
|
tree
2018-09-25
Be
r
k Hes
s
Add Up
d
ateGr
o
upsCog class
commit
|
commitdiff
|
tree
2018-09-25
P
a
s
c
a
l
Merz
Remove obsolete brace
s
in do_md
(
)
commit
|
commitdiff
|
tree
2018-09-25
Pascal Merz
Re
m
o
v
e
r
e
run f
r
om do_md
commit
|
commitdiff
|
tree
2018-09-24
M
.
E
r
ic Irrgang
F
ix gmxapi::Ver
s
io
n
te
s
t regres
s
ion
.
commit
|
commitdiff
|
tree
2018-09-24
Berk Hess
Fix perfo
r
man
c
e
report
w
h
e
n
init_ste
p
!
=
0
commit
|
commitdiff
|
tree
2018-09-24
Mark Abraham
Fix Doxygen links
commit
|
commitdiff
|
tree
2018-09-23
M
a
r
k Abr
a
ham
Leak
less from gr
o
mpp
p
w
i
th cmap
commit
|
commitdiff
|
tree
2018-09-22
Berk He
s
s
Add update groups boo
l
ean to DD
commit
|
commitdiff
|
tree
2018-09-22
B
e
r
k Hess
R
ename DD
constrai
n
t boolean
s
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
Add update groups
commit
|
commitdiff
|
tree
2018-09-21
Sz
i
lárd Páll
Bump
test time
o
ut only for
OpenCL in
t
egrati
o
n
tests
commit
|
commitdiff
|
tree
2018-09-21
Ro
l
a
nd
S
chulz
F
i
x clang-tidy w
a
rning
s
for clang 7
commit
|
commitdiff
|
tree
2018-09-20
Mark Abrah
a
m
Up
d
a
t
e t
o
t
e
st wi
t
h clang-7
commit
|
commitdiff
|
tree
2018-09-20
Berk
H
ess
Change pull
buffers
to
st
d
::vec
t
or
commit
|
commitdiff
|
tree
2018-09-18
Berk Hess
Introduce ex
t
ractIL
i
sts helpe
r
fun
c
tion
commit
|
commitdiff
|
tree
2018-09-18
Mark Abraham
Separated p
a
rt
i
tioning an
d
dlb code within do
m
dec
commit
|
commitdiff
|
tree
2018-09-18
Pascal Merz
I
ntroduc
e
stop han
d
ler
commit
|
commitdiff
|
tree
2018-09-18
P
a
scal Mer
z
Introduce che
c
kpoint handler
commit
|
commitdiff
|
tree
2018-09-18
Pascal
Me
r
z
I
n
t
roduce re
s
et handler
commit
|
commitdiff
|
tree
2018-09-18
Mark A
b
raham
Add no
t
_
n
ull from
GSL
commit
|
commitdiff
|
tree
2018-09-18
Roland Schulz
Fix bitmask printing
commit
|
commitdiff
|
tree
2018-09-17
M
.
Eric Irrgang
Framework
i
n
which
t
o bu
i
ld
g
mxapi
.
commit
|
commitdiff
|
tree
2018-09-17
P
a
ul Bauer
P
r
o
p
e
r
ly initial
i
ze idef i
n
top
o
l
o
g
ies
commit
|
commitdiff
|
tree
2018-09-17
Berk Hess
Move
ifunc stuff f
r
om idef
.
h
to ifu
n
c
.
h
commit
|
commitdiff
|
tree
2018-09-17
K
e
vin
Boyd
Ad
d
ed basic
t
ests for
g
mx
msd
commit
|
commitdiff
|
tree
2018-09-16
Joe
J
orda
n
Mo
v
e
variables around in pd
b
2g
m
x
commit
|
commitdiff
|
tree
2018-09-14
M
.
Eric Irrg
a
ng
Rea
r
ra
n
ge mdrun/runner
.
h
commit
|
commitdiff
|
tree
2018-09-14
Pau
l
Bauer
Int
r
oduce gmx repo
r
t
-
methods
commit
|
commitdiff
|
tree
2018-09-13
Berk Hess
A
d
d
C
++ versi
o
n of
t
_ilist
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Convert vsit
e
s
tructs to C++
commit
|
commitdiff
|
tree
2018-09-12
M
.
Eric Irrgang
Simplif
y
add_suffix_to_output_na
m
es()
commit
|
commitdiff
|
tree
2018-09-12
Roland Schulz
Remove cplusc
p
lus if
d
efs
commit
|
commitdiff
|
tree
2018-09-12
Roland
S
c
h
ulz
Fix clang-tidy warning
s
for OCL
commit
|
commitdiff
|
tree
2018-09-12
Be
r
k Hess
C
o
nvert DD gmx_reverse_top_t to C++
commit
|
commitdiff
|
tree
2018-09-11
Ma
r
k Abraham
Rep
l
ace C-style li
b
rar
y
file h
a
ndling with R
A
II
approache
s
commit
|
commitdiff
|
tree
2018-09-11
Ma
r
k Abraham
Improve DD logging
commit
|
commitdiff
|
tree
2018-09-11
Roland Schulz
Compil
e
nonbonded kernels as C++
commit
|
commitdiff
|
tree
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