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Updates to documentation
2016-06-07
Mark
Abraha
m
Update
s
t
o docum
e
nt
a
t
i
on
commit
|
commitdiff
|
tree
2016-06-07
Berk Hess
Fix d
a
ta
r
ace in hwinfo with thre
a
d-MPI
commit
|
commitdiff
|
tree
2016-06-02
Mark Abraham
F
i
x c
o
mp
a
tibilit
y
w
i
th
o
lder CMake
commit
|
commitdiff
|
tree
2016-05-31
Mark
A
braham
Fix reference to
v
m
dio
.
c t
o
be
vmd
i
o
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mar
k
Abraham
Se
c
o
n
d
2016 b
e
ta rele
a
se
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Repositio
n
n
bnxn filler particles
commit
|
commitdiff
|
tree
2016-05-31
B
e
rk Hes
s
Avoid
n
umerical overfl
o
w w
i
th
overlappi
n
g atoms
commit
|
commitdiff
|
tree
2016-05-31
B
erk H
e
ss
Add check
for finite energ
i
es
commit
|
commitdiff
|
tree
2016-05-28
R
o
land Schulz
Fi
x
bu
i
ld wi
t
h
cl
a
n
g
3
.
1+3
.
2
commit
|
commitdiff
|
tree
2016-05-26
Ma
r
k
Abraham
New quote
commit
|
commitdiff
|
tree
2016-05-21
Er
i
k Lindahl
D
i
sa
b
le automated FFT
W
3 builds
on
Windows
commit
|
commitdiff
|
tree
2016-05-17
Roland Schulz
Add refere
n
ce to
Topo
T
ools 1
.
6
commit
|
commitdiff
|
tree
2016-05-17
T
e
emu Murtola
Fix some th
r
ead a
f
finity
c
ases
commit
|
commitdiff
|
tree
2016-05-13
Roland Schulz
Don't use abort
f
or
fatal err
o
r
s
commit
|
commitdiff
|
tree
2016-05-12
Mark Ab
r
aham
Merge bra
n
c
h release-5-1
i
nto rele
a
se-2016
commit
|
commitdiff
|
tree
2016-05-12
Mark Abra
h
am
G
R
OM
A
CS 201
6
beta1 r
e
lease
commit
|
commitdiff
|
tree
2016-05-12
V
edran Milet
i
ć
Remove static function qu
a
lifie
r
in OpenCL kernel
u
t
il
s
commit
|
commitdiff
|
tree
2016-05-10
T
eemu Murto
l
a
Add
i
tional Jenki
n
s documentat
i
on
commit
|
commitdiff
|
tree
2016-05-10
M
ark
Abrah
a
m
Bump cl
a
ng stat
i
c a
n
aly
z
er to
v
ersio
n
3
.
8
commit
|
commitdiff
|
tree
2016-05-10
M
a
rk Abraham
Minor update to sphinx dependency
commit
|
commitdiff
|
tree
2016-05-10
Teemu Murtola
Include re
l
eng
d
o
cume
n
tation to de
v
eloper g
u
ide
commit
|
commitdiff
|
tree
2016-05-10
Er
i
k
L
i
n
dah
l
Fix precision
l
oss in tabulated
normal distribu
t
ion
commit
|
commitdiff
|
tree
2016-05-10
Mark
A
b
raham
Facilitate l
i
nking with
l
ibcxx
commit
|
commitdiff
|
tree
2016-05-10
Erik Li
n
dahl
F
l
us
h
streams when not writing newline character
commit
|
commitdiff
|
tree
2016-05-10
B
e
rk Hess
O
ptimized t
h
e
vsite
t
hr
e
ading
commit
|
commitdiff
|
tree
2016-05-10
Rolan
d
Schulz
Add O
p
enMP fo
r
functio
n
s limiting scaling
commit
|
commitdiff
|
tree
2016-05-08
Mark Abra
h
am
F
i
xes for
c
lang 3
.
7 on PowerPC
commit
|
commitdiff
|
tree
2016-05-08
James
W
.
B
a
r
n
e
t
t
Correc
t
and c
l
ar
i
fy
o
u
tput units for fluct
_
props
commit
|
commitdiff
|
tree
2016-05-08
E
rik Linda
h
l
Fix Luzar/Chander li
t
erature
refer
e
nce in g_h
b
ond
commit
|
commitdiff
|
tree
2016-05-08
Davi
d
van der Spo
e
l
Modify lmfit
l
i
b
rary
to a
v
oid clashes with othe
r
ver
s
ions
.
commit
|
commitdiff
|
tree
2016-04-28
Teemu Murtola
Us
e
HardwareTo
p
ology to set nthreads_hw_avail
commit
|
commitdiff
|
tree
2016-04-28
Teemu Mu
r
tola
Remove gmx_hw_info_t::ncore
commit
|
commitdiff
|
tree
2016-04-28
Szilárd
P
áll
Workaround for gcc f
a
l
se positiv
e
warning
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtol
a
I
mprove re
l
ease wor
k
flow testing
commit
|
commitdiff
|
tree
2016-04-27
Teemu Murtol
a
Di
s
able multipl
e
ranks for non-MP
I
unit tests
commit
|
commitdiff
|
tree
2016-04-27
Mark Abraham
M
e
r
g
e b
r
anch rele
a
se-5-1
commit
|
commitdiff
|
tree
2016-04-27
Szilár
d
Pá
l
l
Fix multip
l
e
M
PI ra
n
ks per node with O
p
enC
L
commit
|
commitdiff
|
tree
2016-04-27
T
eemu Murto
l
a
Fi
x
i
ss
u
es with failing
t
hread affinity setting
commit
|
commitdiff
|
tree
2016-04-19
Roland Schulz
F
ix numerica
l
ly unstable selecti
o
n test
commit
|
commitdiff
|
tree
2016-04-19
Szi
l
árd Páll
Mo
v
e out CUDA profiler triggers
from NBNX
N
commit
|
commitdiff
|
tree
2016-04-19
Berk H
e
ss
Al
l
ow rcoulomb>rvdw with PM
E
commit
|
commitdiff
|
tree
2016-04-19
Mark Abrah
a
m
R
ep
l
ace libxml2
w
ith tinyxml2 f
o
r
use in test cod
e
commit
|
commitdiff
|
tree
2016-04-19
Roland
S
chulz
Tune nstlist in
c
r
ease for KNL
commit
|
commitdiff
|
tree
2016-04-19
Ma
r
k Abraham
Fix
parse_d
i
gits_from_st
r
i
n
g
commit
|
commitdiff
|
tree
2016-04-19
B
e
rk Hess
B
r
oadcast pull
e
x
ternal po
t
ential p
r
ovider string
commit
|
commitdiff
|
tree
2016-04-19
Mark Abrah
a
m
Fi
x
mdp label generation
commit
|
commitdiff
|
tree
2016-04-19
Berk H
e
ss
Fix gmx h
b
ond
g
r
oup ov
e
r
l
a
p check
commit
|
commitdiff
|
tree
2016-04-14
M
a
rk A
b
r
a
ha
m
Merge branch release-5-1
commit
|
commitdiff
|
tree
2016-04-14
C
ar
s
t
e
n Kutzner
Corrected value o
f
electric conversion factor f in
.
.
.
commit
|
commitdiff
|
tree
2016-04-06
Ro
l
and Sc
h
ulz
AVX51
2
transposeScatterI
n
cr
/
DecrU with loa
d
/store
commit
|
commitdiff
|
tree
2016-04-04
Erik Lindahl
Fix compi
l
e
e
rror for
IBM VMX on p
p
c64
commit
|
commitdiff
|
tree
2016-04-04
Eri
k
L
inda
h
l
Fix SIMD d
e
tection on new AMD AVX CPUs w/
o
f
ma
commit
|
commitdiff
|
tree
2016-04-03
Erik Lindahl
Fix
u
nit
test segfau
l
ts
with gcc-6
.
0
commit
|
commitdiff
|
tree
2016-04-03
Eri
k
L
i
n
d
ahl
Fix incorrect
r
et
u
rn typ
e
for scalar versi
o
n o
f
simd
.
.
.
commit
|
commitdiff
|
tree
2016-04-03
Sem
e
n Yesyl
e
vskyy
Added re
f
erences to Pr
o
tSqu
e
eze and g_memb
e
d to
t
he
.
.
.
commit
|
commitdiff
|
tree
2016-04-02
Rol
a
n
d
Schulz
Fix coolqu
o
tes
commit
|
commitdiff
|
tree
2016-04-01
Mark
Abraham
Re
v
ert
t
o treating -1
as
"generate
a
seed" in
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
B
erk Hess
A
dd option f
o
r exter
n
al pull potential
commit
|
commitdiff
|
tree
2016-03-31
J
ames W
.
Barnett
Reve
r
t behavior for
handling SETTLE errors
commit
|
commitdiff
|
tree
2016-03-31
Szil
á
rd Páll
refa
c
t
o
r CUDA textu
r
e-based t
a
ble i
n
i
tialization
commit
|
commitdiff
|
tree
2016-03-31
Szilard P
a
l
l
a
v
o
id C
P
U o
v
ersubscription wi
t
h G
P
Us
commit
|
commitdiff
|
tree
2016-03-30
S
zilár
d
Páll
LJ combination rul
e
kernels f
o
r OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
Re-en
a
ble i-ato
m
t
y
pe
local mem
p
r
efetch in OpenCL
commit
|
commitdiff
|
tree
2016-03-30
Berk H
e
s
s
C
o
r
r
e
c
t mdrun tMPI (non-)parallel
e
rr
o
r me
s
sage
commit
|
commitdiff
|
tree
2016-03-30
Teemu Murtola
Make includ
e
so
r
te
r
.
py
w
o
rk with
D
oxygen 1
.
8
.
1
0
+
commit
|
commitdiff
|
tree
2016-03-30
Szilárd Páll
Describe AMD APPSDK 3
.
0 iss
u
es in the g
u
ide
commit
|
commitdiff
|
tree
2016-03-30
Teemu M
u
rtola
F
i
x
e
rr
o
r reporting for documentati
o
n
build
commit
|
commitdiff
|
tree
2016-03-30
Mark Abraham
Clean up vsite
co
d
e
commit
|
commitdiff
|
tree
2016-03-22
C
a
rsten Kutzner
C
l
ea
n
-up code for swapcoords
.
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
L
J co
m
binati
o
n rule kernels for C
U
DA
commit
|
commitdiff
|
tree
2016-03-19
Mark Abra
h
am
Add more const corre
c
tness
commit
|
commitdiff
|
tree
2016-03-19
Mark Abra
h
am
I
mproved some m
d
r
u
n integratio
n
tests
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Warn
about OpenMPI 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix non-no
r
malization of FFT a
u
to
c
orr
commit
|
commitdiff
|
tree
2016-03-18
Mark Abr
a
ha
m
Fix typo
i
n
Fourier dihedral
e
qu
a
tion
commit
|
commitdiff
|
tree
2016-03-18
V
i
ve
c
a Lindahl
A
d
ded pu
l
l coordinate geometry angle
.
commit
|
commitdiff
|
tree
2016-03-18
D
a
v
id van der
S
poel
Fixed div
i
sio
n
b
y
z
ero in pol
a
rize
.
commit
|
commitdiff
|
tree
2016-03-18
Ni
c
h
o
la
s
Breen
Various mino
r
s
pelling fixes -
messages
a
nd code comments
.
.
.
commit
|
commitdiff
|
tree
2016-03-17
Ca
r
sten Ku
t
zner
Fix membed i
n
itializat
i
on
commit
|
commitdiff
|
tree
2016-03-15
Mark Abraham
Merge bra
n
ch rel
e
a
s
e-5-0 into
r
elease-5
-
1
commit
|
commitdiff
|
tree
2016-03-11
M
a
r
k
Ab
r
a
h
am
Merge branch re
l
eas
e
-5-0 into release-
5
-1
commit
|
commitdiff
|
tree
2016-03-10
M
ark Abraham
Require
2
015
v
ersion fo
r
MSVC
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Remove epsfac from G
P
U kernel inn
e
r-l
o
o
p
s
commit
|
commitdiff
|
tree
2016-02-23
Mar
k
Abr
a
ham
Repla
c
e cppchec
k
s
u
ppres
s
ion in checkpoint
c
ode
commit
|
commitdiff
|
tree
2016-02-16
Mark
Abraham
Merge
b
r
a
nch
r
e
lease-5-0 into r
e
le
a
se-5-1
commit
|
commitdiff
|
tree
2016-02-14
Ma
r
k
Abra
h
am
R
e-gene
r
ated
eps for figure
4
.
8
commit
|
commitdiff
|
tree
2016-02-10
M
a
rk
A
b
r
aha
m
R
e-remove *_stoc
h
d
_state
f
un
c
tion declarations
commit
|
commitdiff
|
tree
2016-02-10
Er
i
k Linda
h
l
S
c
alar
functions mimicking the SIM
D
interface
commit
|
commitdiff
|
tree
2016-02-08
Mark Abraham
Mer
g
e
b
ranch r
e
l
ease-5-
0
into releas
e
-5
-
1
commit
|
commitdiff
|
tree
2016-02-06
Mark Abraham
Merge bra
n
c
h release-5-1
commit
|
commitdiff
|
tree
2016-02-03
M
a
rk Abraham
B
umped pat
c
h num
b
er to prepare for futur
e
5
.
1
.
3 release
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Version 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
Mar
k
A
brah
a
m
Merge release-5-0
i
nto
r
ele
a
s
e
-5-1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abr
a
ham
Merge
b
r
a
nch
r
el
e
ase-5-1
commit
|
commitdiff
|
tree
2016-01-28
M
ark Abraham
A
void FP ex
c
eption
commit
|
commitdiff
|
tree
2016-01-27
Mark
Abraham
Merge b
r
anc
h
release-
5
-1
commit
|
commitdiff
|
tree
2016-01-27
Mark Abrah
a
m
Remove
bNotLa
s
tFrame
commit
|
commitdiff
|
tree
2016-01-26
Mark
A
b
raham
Fix de
f
ault for GMX_USE_NVML
commit
|
commitdiff
|
tree
2016-01-25
M
a
rk
A
braham
M
er
g
e branch release-5-1
commit
|
commitdiff
|
tree
2016-01-12
Ma
r
k Abraham
Merge branch rele
a
se
-
5
-0 in
t
o release-5-
1
commit
|
commitdiff
|
tree
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