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Use std::vector for checkpoint outputfiles
2018-02-14
M
ark Abraham
Use std::ve
c
tor for che
c
kpoint o
u
tputfil
e
s
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iu
p
inov
Repla
c
e the re
m
aining EXP
E
CT_DEA
T
H
with EXPECT_DEA
T
H_IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
A
l
eksei Iupin
o
v
Add DeviceBu
f
fer as a typed
e
f for
cl_mem/d
e
v
i
ce ponter
commit
|
commitdiff
|
tree
2018-02-14
Szi
l
á
rd Páll
Remove
ba
r
riers preventing
textur
e
reference races
commit
|
commitdiff
|
tree
2018-02-13
Mark Abraham
Se
p
ara
t
e multisim
f
rom commrec
commit
|
commitdiff
|
tree
2018-02-12
M
a
r
k
Abraham
Ana
l
yse
t
hreads
o
n
n
od
e
bef
o
re
s
e
t
ting
a
f
finities
commit
|
commitdiff
|
tree
2018-02-12
Mark Abr
a
ham
Fix rea
d
ing o
l
d fo
r
ce
f
ield
f
iles
commit
|
commitdiff
|
tree
2018-02-09
Mark Abr
a
h
am
Merge branch rel
e
ase-201
8
commit
|
commitdiff
|
tree
2018-02-08
M
ark Abraham
Me
r
ge "
M
erg
e
branc
h
re
l
e
a
s
e-20
1
6 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Mark Abrah
a
m
M
er
g
e branch re
l
ease-
2
016
into release-2018
commit
|
commitdiff
|
tree
2018-02-08
Aleksei Iupinov
Enable
debug FP ex
c
ept
i
o
n
s with
o
ut TP
I
,
no
t
wi
t
h TPI
commit
|
commitdiff
|
tree
2018-02-08
Mark Ab
r
aham
Merge "M
e
rge branch '
r
ele
a
se-201
8
' into master"
commit
|
commitdiff
|
tree
2018-02-06
Mark Abr
a
ham
Prevent
log file energy
a
ve
r
a
g
e printing dividing by
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleks
e
i
Iupinov
Don't prin
t
impossible C
U
DA version numbers i
n
absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-01
Paul Bauer
Add in
f
ormation for n2t file format
commit
|
commitdiff
|
tree
2018-01-27
Ma
r
k Ab
r
aham
Remove unu
s
ed dec
l
a
r
ation
commit
|
commitdiff
|
tree
2018-01-25
M
a
r
k
Abraham
Remove unuse
d
fields of t
_
commrec
commit
|
commitdiff
|
tree
2018-01-25
Mark Abraham
R
educed i
n
c
ludes o
f
c
o
mmon header
s
i
n
heade
r
s
commit
|
commitdiff
|
tree
2018-01-25
Ma
r
k
Abraham
Removed md
r
u
n
-
multi
commit
|
commitdiff
|
tree
2018-01-24
M
a
r
k
Abra
h
am
C
h
ang
e
multi
-
sim te
s
ts to use -mul
t
idir
commit
|
commitdiff
|
tree
2018-01-24
Mar
k
A
b
r
aham
Re
m
ove gmx_inline
commit
|
commitdiff
|
tree
2018-01-24
Mark Ab
r
aha
m
Teach include
sorter
to i
g
nore cmake-test
f
il
e
s
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
Move W
i
nd
o
ws icc conf
i
g
to post-s
u
bmit t
e
sting
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
Replace gmx_bool w
i
th bool in
b
itmask fun
c
tions
commit
|
commitdiff
|
tree
2018-01-23
Mark Abraham
Remove sup
p
ort for implicit
solv
a
tio
n
commit
|
commitdiff
|
tree
2018-01-23
Mark Ab
r
aham
R
e
m
ove topology
suppo
r
t for implicit solvat
i
on
commit
|
commitdiff
|
tree
2018-01-23
A
leksei I
u
pi
n
o
v
Test PME CPU/GPU with walls a
n
d b
o
x
scal
i
ng
commit
|
commitdiff
|
tree
2018-01-23
Al
e
ksei
I
upinov
Wrap
t
h
e PME
t
e
s
ting
l
oop in a meth
o
d for extensibility
commit
|
commitdiff
|
tree
2018-01-23
Mark Abrah
a
m
Prelimina
r
y cleanup befor
e
remo
v
ing
i
f
d
e
f cplusplus
commit
|
commitdiff
|
tree
2018-01-19
Al
e
k
s
e
i Iupinov
Add a
d
e
a
th test for the duplicate inp
u
trec
keys che
c
k
i
n
g
commit
|
commitdiff
|
tree
2018-01-19
Mark Abrah
a
m
Merge "Merge branch
'
release-2018'
into master"
commit
|
commitdiff
|
tree
2018-01-19
A
l
ekse
i
I
upinov
R
e
name
class BiasReader to struct BiasOutputSetup
commit
|
commitdiff
|
tree
2018-01-19
Mark A
b
raham
Add d
e
v-guide do
c
s for automatic upd
a
te of regre
s
sionte
s
ts
commit
|
commitdiff
|
tree
2018-01-19
Alek
s
ei I
u
pinov
Make the re
f
erenc
e
data variables loca
l
in GetIrTest
commit
|
commitdiff
|
tree
2018-01-19
Ma
r
k Abraham
F
ixes for
issues fo
u
nd by cl
a
ng 6
commit
|
commitdiff
|
tree
2018-01-18
Mar
k
Abraham
Remov
e
su
p
port
f
or BlueGene
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
F
i
x COMM r
e
mova
l
on part of the system
commit
|
commitdiff
|
tree
2018-01-18
Paul Bauer
Add
c
ontribu
t
ion inf
o
rma
t
ion to webp
a
ge
commit
|
commitdiff
|
tree
2018-01-17
Aleksei Iupinov
F
ix b
o
x scaling
i
n
PME mixed
m
ode
commit
|
commitdiff
|
tree
2018-01-17
Ber
k
Hess
Re
-
e
n
able GPU
with walls and 1 energy group
commit
|
commitdiff
|
tree
2018-01-16
M
a
r
k Abrah
a
m
Merge
"Merge re
l
ease-
2
01
8
into m
a
st
e
r"
commit
|
commitdiff
|
tree
2018-01-16
Rolan
d
Schulz
M
erge
r
elease-2
0
18
i
nto master
commit
|
commitdiff
|
tree
2018-01-16
Be
r
k
Hess
Avoid
mdrun e
c
h
oing
"
N
o option -multi"
commit
|
commitdiff
|
tree
2018-01-11
M
a
rk
Abraham
Bumped v
e
rsio
n
for next patch rele
a
se
commit
|
commitdiff
|
tree
2018-01-11
Ma
r
k Abrah
a
m
V
e
rsi
o
n
2
018
commit
|
commitdiff
|
tree
2018-01-11
Mark A
b
raham
Announ
c
e
in user log fi
l
es
t
hat featu
r
e
s are dep
r
ecated
.
commit
|
commitdiff
|
tree
2018-01-11
Roland Schulz
Fix GMX_E
N
A
BLE_A
V
X5
1
2_TESTS
b
eing i
n
ternal
commit
|
commitdiff
|
tree
2018-01-10
Mark Abraham
Fix automa
t
ed GPU
I
D ass
i
g
n
me
n
t
commit
|
commitdiff
|
tree
2018-01-10
Szilárd
P
áll
U
s
er guide update
s
to GPU section
commit
|
commitdiff
|
tree
2018-01-10
S
z
i
l
árd P
á
ll
Release n
o
tes tw
e
aks
commit
|
commitdiff
|
tree
2018-01-10
Mark Abraham
Add release notes
t
o
source repo
commit
|
commitdiff
|
tree
2018-01-10
Erik
L
i
ndahl
Improve
pdb2gmx for nonstandard residue t
y
p
es
commit
|
commitdiff
|
tree
2018-01-10
S
z
ilárd
Páll
Ins
t
all guide updates
commit
|
commitdiff
|
tree
2018-01-10
Szilárd Páll
En
v
ironment variable docs m
a
i
ntenance
commit
|
commitdiff
|
tree
2018-01-10
Aleksei Iupinov
Do not
p
rint PME c
o
unter breakdown if
i
t
'
s
e
m
pty
commit
|
commitdiff
|
tree
2018-01-10
Mark Ab
r
aham
H
andle erroneous comm
a
nd
line args better
commit
|
commitdiff
|
tree
2018-01-10
Erik Linda
h
l
Cl
a
r
ified gmx rmsf documentation
commit
|
commitdiff
|
tree
2018-01-09
Mark
A
braham
C
l
e
a
n up user
g
u
i
de for
r
elease
commit
|
commitdiff
|
tree
2018-01-09
Ma
r
k Abraham
Merge
branch rele
a
se-2016
into re
l
ea
s
e
-20
1
8
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do no
t
turn
o
n DLB at replic
a
exchange
commit
|
commitdiff
|
tree
2018-01-04
Mark Abraham
Me
r
g
e branch release-2018
commit
|
commitdiff
|
tree
2018-01-04
Erik Lindahl
Implemen
t
changes fo
r
CM
a
ke po
l
icy
0
068
commit
|
commitdiff
|
tree
2018-01-04
M
a
rk
Abraham
A
dd
test con
f
ig of GPU build on
s
lave wit
h
o
ut
GPU
commit
|
commitdiff
|
tree
2018-01-04
Paul B
a
uer
Fix gmx msd when
u
sing C
O
M rem
o
val a
n
d m
o
lecules
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindahl
F
i
x index err
o
r in gmx chi
commit
|
commitdiff
|
tree
2018-01-03
Paul B
a
uer
Correct dihedral res
t
r
aint section in Manual
commit
|
commitdiff
|
tree
2018-01-03
Erik Lind
a
h
l
Avoid
F
T
Z t
r
iggeri
n
g simd test failures
commit
|
commitdiff
|
tree
2018-01-02
Erik Lind
a
hl
Fix
O
penCL
c
ompiles on
M
ac OS
commit
|
commitdiff
|
tree
2018-01-02
Erik L
i
ndah
l
Improve
m
an
u
al
from comments
b
y Gang Li
u
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindah
l
M
ake it explicit
tha
t
ti
m
e uni
t
s
a
pply to begin/end
.
.
.
commit
|
commitdiff
|
tree
2018-01-02
E
r
ik
L
i
ndahl
Do
n
't require m
a
tc
h
ing nam
e
s
between
rtp and tdb fi
l
es
commit
|
commitdiff
|
tree
2018-01-02
Erik Li
n
dahl
D
on't write r
e
ference pu
l
l gro
u
p 0 to log
commit
|
commitdiff
|
tree
2017-12-30
Mark Abraham
Fi
r
st rele
a
se c
a
ndida
t
e for vers
i
on 201
8
commit
|
commitdiff
|
tree
2017-12-26
Erik
L
indahl
Fi
x
builds on ARM & clari
f
y (ARM
)
GPU suppo
r
t
commit
|
commitdiff
|
tree
2017-12-22
Mark Abraham
M
e
rge bra
n
ch release-2016 into release-2018
commit
|
commitdiff
|
tree
2017-12-21
M
a
r
k
Abraha
m
M
erge branch
release-5-1 into release
-
2016
commit
|
commitdiff
|
tree
2017-12-21
M
ark A
b
raha
m
Bump minor ve
r
sion for
t
h
e
oretical new re
l
ease
commit
|
commitdiff
|
tree
2017-12-21
Pascal Merz
Docum
e
nt
a
tion and fix
e
s
for physi
c
al
v
alidation
commit
|
commitdiff
|
tree
2017-12-21
M
a
rk Abraham
Update double-prec
i
sion te
s
t configu
r
ations
commit
|
commitdiff
|
tree
2017-12-21
Rola
n
d Schulz
Up
d
ate
c
hecks f
o
r BuildOwnFFT
commit
|
commitdiff
|
tree
2017-12-20
Mark Abraham
Use new default
R
e
a
lTol
e
rance() to s
t
abilise som
e
tests
commit
|
commitdiff
|
tree
2017-12-20
Mark
A
braham
Merge "Merge
b
ranch release-2016
into release
-
2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-20
Mark Abraham
Me
r
ge branch relea
s
e-2016 into release-
2
0
18
commit
|
commitdiff
|
tree
2017-12-19
M
ar
k
A
b
r
aham
Third beta
r
elease of 2018
commit
|
commitdiff
|
tree
2017-12-19
Mark
Abraha
m
Fix table tests and improve ta
b
le constructio
n
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Ma
k
e oversubsc
r
ip
t
ion warnin
g
consistent
commit
|
commitdiff
|
tree
2017-12-19
C
ars
t
en Kut
z
ner
F
i
x
electric fie
l
d
.
m
dp do
c
um
e
ntation
commit
|
commitdiff
|
tree
2017-12-19
Erik Lindahl
Use reduced defaul
t
tole
r
ances fo
r
tpx compa
r
ison
commit
|
commitdiff
|
tree
2017-12-18
Roland Sch
u
l
z
F
i
x
c
make error with
emacs
lock files in place
commit
|
commitdiff
|
tree
2017-12-17
Ro
l
and Schulz
Chan
g
e avx
_
1
2
8_fma build to double
commit
|
commitdiff
|
tree
2017-12-17
Roland Schulz
Support Simd4N for Simd
R
e
alWi
d
th<4
commit
|
commitdiff
|
tree
2017-12-14
E
r
ik Lindahl
Fix PBC error in
gmx_spat
i
al
commit
|
commitdiff
|
tree
2017-12-14
Mark A
b
raham
Merge
"Merge branch
r
elease-2016
i
nt
o
release-2
0
1
8
.
.
.
commit
|
commitdiff
|
tree
2017-12-12
Erik Lind
a
hl
Disa
l
low ascii
for
m
ats for gm
x
trj
c
a
t
commit
|
commitdiff
|
tree
2017-12-12
Mark
A
bra
h
am
I
mprove grompp missing-parameters erro
r
m
essage
commit
|
commitdiff
|
tree
2017-12-12
Mark Abraha
m
Merge branch r
e
lease-2016
into r
e
lease-2
0
1
8
commit
|
commitdiff
|
tree
2017-12-11
Mark Abraham
Second beta release of
2018
commit
|
commitdiff
|
tree
2017-12-11
Erik Lindahl
Remove duplicated line
s
from O
P
LS ffbonded
.
itp
commit
|
commitdiff
|
tree
2017-12-11
Roland Sch
u
lz
Replace in
t
rinsic wi
t
h inline asm for AVX
5
12 unit test
commit
|
commitdiff
|
tree
2017-12-11
Erik Lin
d
ahl
D
on't warn about NVML clocks that
a
re at max
commit
|
commitdiff
|
tree
next