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Move gmx_ffparams_t to forcefieldparameters
2018-10-16
Ma
g
nus Lundborg
Move gmx_ff
p
arams_t to
for
c
efiel
d
para
m
eters
commit
|
commitdiff
|
tree
2018-10-16
Mark Abraham
Task assig
n
ment for bond
e
d int
e
raction
s
on
CUDA GPUs
commit
|
commitdiff
|
tree
2018-10-16
Mark
A
b
raham
F
i
x c
o
m
p
iler issues
commit
|
commitdiff
|
tree
2018-10-16
M
a
r
k Abr
a
ham
Re
m
oved su
p
port fo
r
NVIDIA
C
C 2
.
x
devi
c
es (coden
a
me
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
Mark
Abraham
Create Exclusi
o
nB
l
ocks
commit
|
commitdiff
|
tree
2018-10-15
M
a
rk Abraham
De-d
u
plicati
n
g mdrun setup
commit
|
commitdiff
|
tree
2018-10-15
Magnus Lu
n
dborg
Enabl
e
output of average pull f
o
rc
e
and posit
i
ons
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Ir
r
gang
Resolve some li
n
ter wa
r
ning
s
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
E
ric Ir
r
gang
Test signali
n
g fac
i
lity throu
g
h sess
i
on r
e
so
u
rc
e
s
.
commit
|
commitdiff
|
tree
2018-10-14
Szilárd
Páll
Moderniz
e
O
p
enCL me
m
ory
a
llocatio
n
flags
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Irrgang
Cle
a
n up gmxapi
t
estsupport output
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
I
rrgan
g
gmxapi::U
s
ageError
commit
|
commitdiff
|
tree
2018-10-14
M
.
Er
i
c
I
r
r
g
a
ng
Allow API acce
s
s
t
o s
i
m
ulation
s
ignals
.
commit
|
commitdiff
|
tree
2018-10-13
Aleksei
I
upinov
A
d
d an
d
enable PME OpenCL
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Irr
g
ang
A
d
d API for ad
d
ing MDModule
s
/ Restraints
.
commit
|
commitdiff
|
tree
2018-10-12
Ber
k
Hess
Imple
m
ent assign
i
ng bo
n
de
d
s to the GPU
commit
|
commitdiff
|
tree
2018-10-12
M
.
E
r
ic Irrgang
A
d
d restraints
framework
.
commit
|
commitdiff
|
tree
2018-10-12
Viache
s
lav Bolny
k
h
Implemented QM/MM workfl
o
w
inside core GR
O
MACS
commit
|
commitdiff
|
tree
2018-10-12
Mark Abraham
Exclude
g
m
x
api source files f
r
o
m
includ
e
sort
i
ng
commit
|
commitdiff
|
tree
2018-10-11
David van der Sp
o
e
l
Reinstated quasihar
m
onic entro
p
y calcu
l
ation in gm
x
.
.
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
Eric Irrgang
A
d
d gmxapi
:
:S
e
ssion
.
commit
|
commitdiff
|
tree
2018-10-11
Mark Abrah
a
m
Fix PaddedVector issues
commit
|
commitdiff
|
tree
2018-10-10
Paul Bauer
Includ
e
doi strings fro
m
zenodo dur
i
ng rel
e
ase
commit
|
commitdiff
|
tree
2018-10-10
M
.
Eric Irrgang
gmxapi
ex
p
ects p
o
sition independent cod
e
.
commit
|
commitdiff
|
tree
2018-10-10
Szilárd Páll
Sw
a
p
custom OpenCL
m
emse
t
k
e
rnel
for
clEnqueueFillBuffer
commit
|
commitdiff
|
tree
2018-10-09
Szilárd Páll
Update regressiontest ref to
d
ownl
o
ad
commit
|
commitdiff
|
tree
2018-10-09
V
i
achesl
a
v Bolny
k
h
Implemented changes to preprocess
o
r to work with MiMiC
.
.
.
commit
|
commitdiff
|
tree
2018-10-09
Mark Abraham
Fix DomdecOptions def
a
ult
commit
|
commitdiff
|
tree
2018-10-09
Roland Schulz
Fix MSAN errors
commit
|
commitdiff
|
tree
2018-10-08
Be
r
k Hess
Enable update groups
commit
|
commitdiff
|
tree
2018-10-08
Szilár
d
P
á
ll
T
w
eak FindFFTW API
c
hec
k
s
commit
|
commitdiff
|
tree
2018-10-08
Szilárd Pál
l
Fix clang-6 warnings
commit
|
commitdiff
|
tree
2018-10-08
Roland Schulz
OCL
:
A
d
d
const to function argum
e
nts
commit
|
commitdiff
|
tree
2018-10-08
Roland Schulz
Add O
C
L kernel
t
arget
commit
|
commitdiff
|
tree
2018-10-08
Mark Abr
a
h
a
m
D
i
s
a
b
l
e FP
E
e
x
p
l
i
c
itl
y
for TPI f
o
r
c
e cal
c
u
lat
i
o
n
commit
|
commitdiff
|
tree
2018-10-08
Szilárd Páll
Replace
s
o
me N
U
LL wit
h
n
u
llptr in
C
UDA code
commit
|
commitdiff
|
tree
2018-10-08
Mark
A
braham
I
m
plement PaddedVector
commit
|
commitdiff
|
tree
2018-10-08
Paul Bauer
Workarou
n
d for ICC postsubmi
t
bug
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
More u
p
dates
t
o
test
m
atr
i
x
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
Fix
m
ake test
commit
|
commitdiff
|
tree
2018-10-07
M
a
rk Abraham
T
est with
g
cc
8
and cu
d
a 10
commit
|
commitdiff
|
tree
2018-10-05
M
ark
A
braham
Check log and othe
r
files differently during ap
p
end
i
ng
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Be
r
k Hess
A
d
d update g
r
oups
to DD at
o
m
displacement
commit
|
commitdiff
|
tree
2018-10-05
Mark
A
b
r
aham
C
hang
e
to test TSAN
w
i
t
h
c
l
ang and libomp
commit
|
commitdiff
|
tree
2018-10-05
R
ol
a
nd Schulz
OCL: Make variables
const
commit
|
commitdiff
|
tree
2018-10-05
M
.
Eric Irrgang
Add gmx
a
p
i::System
.
commit
|
commitdiff
|
tree
2018-10-05
Szilárd Páll
Update te
s
t matrices w
i
th new
G
PU s
p
e
c
ifiers
commit
|
commitdiff
|
tree
2018-10-04
Berk
H
e
s
s
M
ak
e
AVX2
p
ass TSAN
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
E
x
tract helper f
u
nctions for prep
a
ring for app
e
nd
i
n
g
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Simplify EM usage
o
f mdebin
commit
|
commitdiff
|
tree
2018-10-03
Mark A
b
raham
Use
fast returns in md5
computation
commit
|
commitdiff
|
tree
2018-10-03
M
a
g
nus Lund
b
org
A
l
low u
s
ing
C
O
M of p
r
evious step as PBC ref
e
rence
commit
|
commitdiff
|
tree
2018-10-03
Mark Abr
a
ham
Add end-
t
o-end
t
e
st
s
o
f
energy mi
n
imization
commit
|
commitdiff
|
tree
2018-10-03
Paul Ba
u
er
D
i
sable GMXAPI when only
buildin
g
m
drun
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric I
r
r
gang
Add g
m
xa
p
i::Con
t
ext
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
E
r
ic Irrgan
g
Move mdru
n
m
a
inFunc
t
ion to client code
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Ir
r
gan
g
Add test data f
o
r
g
mxapi
.
commit
|
commitdiff
|
tree
2018-10-03
M
.
Eric Irrg
a
ng
Add gmxapi exceptions
.
commit
|
commitdiff
|
tree
2018-10-02
Pau
l
Bauer
Fix include formattin
g
in gmxa
p
i
commit
|
commitdiff
|
tree
2018-10-02
Roland
Sch
u
lz
Use subgroup s
h
uf
f
le for red
u
ction
commit
|
commitdiff
|
tree
2018-10-02
Berk
H
ess
Updat
e
D
D cutoffs
f
or update g
r
oups
commit
|
commitdiff
|
tree
2018-10-02
Mark Abraham
Red
u
c
e
md
r
un te
s
ts usi
n
g g
r
oup s
c
heme
commit
|
commitdiff
|
tree
2018-10-01
Mark
A
braham
Fix gcc-8 warnings a
b
out strings
commit
|
commitdiff
|
tree
2018-10-01
Paul Bau
e
r
Change
g
e
t_atom
_
i
ndex to return int
commit
|
commitdiff
|
tree
2018-10-01
Mark Abra
h
a
m
Add release notes for removing non-r
e
producible
a
s
pects
commit
|
commitdiff
|
tree
2018-10-01
Mark Abraham
Te
s
ts
f
or md5 computat
i
on on open
fi
l
es
commit
|
commitdiff
|
tree
2018-09-29
Mark Ab
r
a
ham
Stop ICC ICE
commit
|
commitdiff
|
tree
2018-09-29
Berk
H
es
s
Add
U
p
dateGroupsCog to DD
commit
|
commitdiff
|
tree
2018-09-28
Mark Abraham
Use more default in
i
t
i
alizati
o
n of mdrun str
u
cts
commit
|
commitdiff
|
tree
2018-09-28
Mar
k
A
braham
Ma
k
e so
m
e sym
b
ols i
n
g
m
x
pre-config
.
h
always defin
e
d
commit
|
commitdiff
|
tree
2018-09-27
K
e
vin Bo
y
d
R
e
duce pre
p
rocessor dependency in resourcedivis
i
on
.
cpp
commit
|
commitdiff
|
tree
2018-09-26
Berk Hess
Extract
s
ettl
e
tes
t
water coordinates
commit
|
commitdiff
|
tree
2018-09-26
Magnus Lun
d
borg
Added pullCheck
P
bcWithinGroup() to check one grou
p
commit
|
commitdiff
|
tree
2018-09-26
Mark Abra
h
am
C
larify distin
c
t paths for mdrun lo
g
file handl
i
ng
commit
|
commitdiff
|
tree
2018-09-25
Berk H
e
s
s
Add
U
pdateGr
o
upsCog class
commit
|
commitdiff
|
tree
2018-09-25
Pascal
Merz
Remove
o
bsole
t
e
b
races
in do
_
md()
commit
|
commitdiff
|
tree
2018-09-25
Pascal
M
e
rz
Remove re
r
un from do_md
commit
|
commitdiff
|
tree
2018-09-24
M
.
Eric Ir
r
gang
F
ix g
m
xapi::Vers
i
on t
e
s
t regression
.
commit
|
commitdiff
|
tree
2018-09-24
Berk Hess
Fix performance
r
e
port
w
hen init_step!=0
commit
|
commitdiff
|
tree
2018-09-24
Mark Abraham
Fi
x
D
oxyg
e
n links
commit
|
commitdiff
|
tree
2018-09-23
Mark Abraham
Leak less from gromppp with
c
m
a
p
commit
|
commitdiff
|
tree
2018-09-22
B
e
rk
Hess
Add u
p
date gr
o
ups boolean to DD
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
R
e
name D
D
constr
a
int boo
l
e
a
ns
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
A
d
d update groups
commit
|
commitdiff
|
tree
2018-09-21
Szilá
r
d Páll
Bu
m
p tes
t
timeout only for OpenC
L
integration tests
commit
|
commitdiff
|
tree
2018-09-21
Rola
n
d
S
ch
u
lz
F
ix cl
a
n
g
-
t
idy w
a
rni
n
gs for c
l
ang 7
commit
|
commitdiff
|
tree
2018-09-20
Mark Abraham
Update to test w
i
th clang
-
7
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Change pul
l
buffers to std:
:
vector
commit
|
commitdiff
|
tree
2018-09-18
Berk Hess
I
ntroduce
e
xtractILists h
e
lper
function
commit
|
commitdiff
|
tree
2018-09-18
Mark Abr
a
ham
S
e
pa
r
ated
p
a
r
titioni
n
g and
dl
b
code
within domd
e
c
commit
|
commitdiff
|
tree
2018-09-18
Pas
c
al Merz
I
n
troduce stop handler
commit
|
commitdiff
|
tree
2018-09-18
P
ascal Merz
Introduce c
h
eck
p
oi
n
t handler
commit
|
commitdiff
|
tree
2018-09-18
Pas
c
al Merz
Introdu
c
e
r
eset handler
commit
|
commitdiff
|
tree
2018-09-18
Mark Abr
a
ham
Add not_nul
l
f
r
om GSL
commit
|
commitdiff
|
tree
2018-09-18
Roland Schulz
Fix bitmask
p
rinting
commit
|
commitdiff
|
tree
2018-09-17
M
.
Eric Irrgang
F
r
a
m
e
wor
k
in
which to buil
d
gmxapi
.
commit
|
commitdiff
|
tree
2018-09-17
Pau
l
Bau
e
r
Proper
l
y in
i
tiali
z
e idef i
n
topo
l
ogies
commit
|
commitdiff
|
tree
2018-09-17
B
e
rk
H
ess
Move ifunc stuff
fr
o
m id
e
f
.
h
to ifunc
.
h
commit
|
commitdiff
|
tree
2018-09-17
Kevin Boyd
Adde
d
basic
tests fo
r
gmx
msd
commit
|
commitdiff
|
tree
2018-09-16
J
o
e Jordan
M
o
ve variables around in p
d
b2gmx
commit
|
commitdiff
|
tree
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