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Removed buggy -smooth hack in hbond module
2015-06-23
E
r
i
k Lindahl
Removed buggy
-smooth
hack in hbond module
commit
|
commitdiff
|
tree
2015-06-22
Eri
k
Lind
a
hl
Use
M
P
I
_T
H
READ_
F
UNNE
L
ED whe
n
available
commit
|
commitdiff
|
tree
2015-06-22
Erik
Linda
h
l
Fix
s
e
gfault
i
n random a
c
cess XTC searching
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
Fix a
r
gumen
t
order error for g_rmsdist
commit
|
commitdiff
|
tree
2015-06-22
Erik L
i
ndahl
Fix gro errors with
PDB ins
e
rtion codes
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindahl
U
pdated docs for g_
g
yrate
commit
|
commitdiff
|
tree
2015-06-20
Erik Lind
a
hl
Fix
potential b
u
ffer
o
ver
f
lo
w
in pdb2gmx
commit
|
commitdiff
|
tree
2015-06-20
E
r
ik Lind
a
hl
Disallow infini
t
e e
p
silon
w
ith PME or
GB
.
commit
|
commitdiff
|
tree
2015-06-20
E
r
ik
Lindahl
Remove GMX_MAX_MPI_THR
E
ADS
commit
|
commitdiff
|
tree
2015-06-20
Eri
k
L
in
d
ahl
Fix repro
d
uci
b
ilit
y
b
ug in fft5d
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindahl
Hand
l
e m
u
ltidir/multisim with single
argument correctly
commit
|
commitdiff
|
tree
2015-06-19
Erik Lindahl
Fix inc
o
rrec
t
sh
i
ft with g
_
de
n
s
i
ty
-
cen
t
er
commit
|
commitdiff
|
tree
2014-09-30
Erik Lindahl
Avoid using f
u
ncti
o
n
calls in Op
e
nMP dire
c
tives
commit
|
commitdiff
|
tree
2014-09-20
E
r
ik
L
in
d
ahl
F
ix RelWithDebInfo name
b
ugs,
a
n
d
u
se full optimizati
o
n
.
commit
|
commitdiff
|
tree
2014-09-11
Erik L
i
ndahl
E
nabl
e
static anon namespace
workaround on path
s
cale
commit
|
commitdiff
|
tree
2014-09-04
E
r
ik Lindahl
K-com
p
uter
specific mo
d
ificatio
n
s
commit
|
commitdiff
|
tree
2014-09-03
Er
i
k Linda
h
l
F
i
xed sc_po
w
er==48
crash in s
i
n
gle precision
commit
|
commitdiff
|
tree
2014-09-03
Erik
Li
n
dahl
Fix
e
d preprocessor e
r
ror f
o
r
A
VX_
1
2
8
_
FMA s
i
m
d
commit
|
commitdiff
|
tree
2014-09-02
Eri
k
Lindahl
Fix
f
o
r
m
atting of fatal errors in
g_bar
commit
|
commitdiff
|
tree
2014-09-02
Erik Linda
h
l
Fixed stri
n
g var e
x
p
a
nsion in C
M
ake due to CMP00
5
3
commit
|
commitdiff
|
tree
2014-08-31
Erik
Lindahl
Add
e
d negative zero pr
e
pr
o
c
e
ssor c
o
nstant
s
commit
|
commitdiff
|
tree
2014-08-20
Erik
L
indahl
Add _GNU_SOURC
E
=1 to find clone() with PGI
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
F
i
x matri
x
pointer derefere
n
ce bug in upd
a
t
e
.
c
commit
|
commitdiff
|
tree
2014-08-20
Eri
k
Lindahl
E
na
b
le SI
M
D register cal
l
ing con
v
ent
i
o
n
with gmx_
s
i
mdca
l
l
commit
|
commitdiff
|
tree
2014-08-20
Erik Lind
a
hl
Add cycle coun
t
ers for 64-
b
i
t ARM
commit
|
commitdiff
|
tree
2014-08-20
Erik Lind
a
hl
Shorten
p
lugin configuration me
s
sage
commit
|
commitdiff
|
tree
2014-08-17
Erik Lindah
l
Fix Portl
a
n
d compiler w
a
r
n
ings
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindahl
Ma
k
e int
e
rnal B
L
AS/LAPACK messages les
s
noisy
commit
|
commitdiff
|
tree
2014-08-10
Erik L
i
n
dahl
Improve Grom
a
cs
portability
commit
|
commitdiff
|
tree
2014-08-10
E
r
i
k Li
n
dahl
Replac
e
__LP64__ wi
t
h check fo
r
p
ointer size
commit
|
commitdiff
|
tree
2014-08-07
Erik Linda
h
l
Fi
x
portability issue with ArrayRef
i
nitial
i
z
er ove
r
l
oading
commit
|
commitdiff
|
tree
2014-08-07
Erik Lindahl
C
h
a
nged names of t
e
st files to
a
v
o
id Fuji
t
su compile
r
bug
commit
|
commitdiff
|
tree
2014-08-01
Er
i
k L
i
ndahl
Added te
s
ts fo
r
denormal and u
n
d
erflow for
simd exp()
commit
|
commitdiff
|
tree
2014-07-27
Eri
k
Lindah
l
Fix selection of xtc groups no
t
starting at index 0
commit
|
commitdiff
|
tree
2014-07-13
Erik Lindahl
Avoid clang/32 o
p
t
i
miza
t
ion affect
i
ng IEEE endia
n
d
e
tection
commit
|
commitdiff
|
tree
2014-07-11
Erik Lindahl
Make AVX2
check more
r
obus
t
commit
|
commitdiff
|
tree
2014-07-08
Erik Lindah
l
Mak
e
IEEE754 check more robust
commit
|
commitdiff
|
tree
2014-06-29
Erik Lindah
l
F
ix
e
d free energy with LJ-
P
ME
commit
|
commitdiff
|
tree
2014-06-29
E
r
ik
L
in
d
a
hl
Enable rtp ang
l
e/
d
ihedral entries not connec
t
e
d
b
y
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Erik Lindah
l
F
ixed CMAP g
e
nera
t
i
o
n for alanine
dipeptide special
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Always s
e
t b-state
p
o
sres, even if
ident
i
cal to a-state
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Update g_density to
h
a
ndle bilayers better
commit
|
commitdiff
|
tree
2014-06-27
E
rik Lindahl
F
i
x
LJPME Lorentz-Berthelot comb
i
nation ru
l
es
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Improve PDB I/O (keep
occupancy, b-f
a
ctor, element)
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Avo
i
d
w
arnings
a
bout coupli
n
g when f
r
ee_energ
y
=no
commit
|
commitdiff
|
tree
2014-06-25
Erik
Lindahl
Updated
A
mber GB
S
A parame
t
ers
commit
|
commitdiff
|
tree
2014-06-25
Erik Lindahl
Make
s
ou
r
c
e
compile under Linux X32
ABI
commit
|
commitdiff
|
tree
2014-06-25
E
r
ik Lindahl
Make it harder for compil
e
r to o
p
timize
a
wa
y
SIMD CMake
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Fixed GROMOS assign
m
en
t
of PRO-NH t
e
rminus
t
o
rsions
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Mak
e
su
r
e d
u
plicates
bondeds are
s
e
t from
h
ackblo
c
ks
commit
|
commitdiff
|
tree
2014-06-24
Erik
Lindahl
Clean u
p
CMAP
place
m
ent
i
n parame
t
er list
commit
|
commitdiff
|
tree
2014-06-24
Erik
L
indahl
Added
multisi
m
u
lation
i
nfo to log
/
o
u
t
put
commit
|
commitdiff
|
tree
2014-06-24
Erik L
i
ndahl
Fixed recent bug with disp
.
co
r
r
.
a
n
d
v
d
w
type=shift
commit
|
commitdiff
|
tree
2014-06-23
E
rik
L
in
d
ahl
Enable termi
n
us-specific
a
tom translation
commit
|
commitdiff
|
tree
2014-06-23
E
r
ik Lindahl
E
n
ab
l
e 4-
l
et
t
e
r
r
esname in PDB
output
,
keeps more pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
Eri
k
L
i
ndah
l
Detect non-fata
l
warning
s
whe
n
trying CFlags for source
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
En
a
ble x
v
gr ou
t
p
ut and labels for g_
p
rin
c
i
p
al
commit
|
commitdiff
|
tree
2014-06-23
Erik Lind
a
hl
Disal
l
ow extrac
t
in
g
V/F
f
rom XT
C
f
i
l
e
s in g_
t
raj
commit
|
commitdiff
|
tree
2014-06-23
E
r
ik Lin
d
ahl
Warn i
f
using nsteps
=
0 without continuation=yes
commit
|
commitdiff
|
tree
2014-06-22
Erik Lindahl
Make
log file option listing similar to mdp names
commit
|
commitdiff
|
tree
2014-06-21
Erik Lindahl
Make sure masses a
r
e copied from
t
ermini
d
atab
a
ses
commit
|
commitdiff
|
tree
2014-06-18
Eri
k
L
i
ndahl
Fix
e
d CMake 2
.
8
.
12+ CUDA
dylib bug
s
and
warnings
on
.
.
.
commit
|
commitdiff
|
tree
2014-06-17
Erik Li
n
dah
l
Disabled replica e
x
change w
h
en T not in order
commit
|
commitdiff
|
tree
2014-06-14
Erik Lindahl
Make sure figu
r
e legends are
a
d
apt
e
d t
o
xmgr/xm
g
race
commit
|
commitdiff
|
tree
2014-06-13
Erik Lin
d
ahl
Force
g
_bond to
u
s
e
structure f
i
l
e
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
Adde
d
dummy
mass for
c
h
ar
m
m T
Y
R aromatic vsit
e
s
commit
|
commitdiff
|
tree
2014-06-12
Erik Lin
d
ah
l
Mak
e
sure g
e
nrestr
u
s
e
s the disre_up2
parameter
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindah
l
Remo
v
ed undocumen
t
ed
-
m
ap and -mdata options from g_sham
.
commit
|
commitdiff
|
tree
2014-06-12
Erik Lindahl
A
l
wa
y
s write output f
r
om genion
commit
|
commitdiff
|
tree
2014-06-11
Eri
k
Linda
h
l
Av
o
i
d
writing xvgr
f
ormatting with -
x
vg
none
commit
|
commitdiff
|
tree
2014-06-10
Erik
L
inda
h
l
Process
n
egative sigma correctly with combrule 2 or
3
commit
|
commitdiff
|
tree
2014-06-09
Erik Lindahl
Fixed th
e
output format of g_princi
p
a
l
commit
|
commitdiff
|
tree
2014-06-09
Erik
L
indahl
Modify singl
e
/dou
b
le EPS to agr
e
e wi
t
h
ISO C
commit
|
commitdiff
|
tree
2014-06-07
Er
i
k
L
i
n
dahl
Adde
d
p
a
ck
a
ge versi
o
n to tn
g
_
i
o
CMak
e
li
s
ts
.
txt
commit
|
commitdiff
|
tree
2014-06-02
Eri
k
Lin
d
a
h
l
Added
grom
p
p
checks
f
or
ze
r
o atom masses in state B
commit
|
commitdiff
|
tree
2014-06-01
Erik Lin
d
ahl
F
ixed
t
ypo
in man
u
al
commit
|
commitdiff
|
tree
2014-06-01
E
r
ik Lindahl
T
wo quotes co
n
tr
i
buted by
V
e
dran Miletic
commit
|
commitdiff
|
tree
2014-04-07
Erik Lindah
l
Make sure wa
t
er opti
m
i
z
ati
o
n i
s
disabled for esot
e
ri
c
.
.
.
commit
|
commitdiff
|
tree
2014-03-16
Erik Lindahl
Us
e
a constant instead o
f
siz
e
o
f
(
in
t
) for SSE2 imme
d
iate
.
.
.
commit
|
commitdiff
|
tree
2014-02-26
Erik Li
n
d
ahl
Ad
d
ed
message to w
a
r
n
tha
t
group kernels are deprecated
.
commit
|
commitdiff
|
tree
2014-02-26
Erik Lind
a
hl
Redesigned SIMD module and unit te
s
ts
.
commit
|
commitdiff
|
tree
2014-02-11
Erik Lin
d
ahl
F
irst part of commit for re
d
esigned SIMD
m
odule - namec
h
anges
.
commit
|
commitdiff
|
tree
2014-02-01
E
r
ik Linda
h
l
Added AVX2 det
e
c
tion to
c
mak
e
a
n
d created CPU acce
l
er
a
tion
.
.
.
commit
|
commitdiff
|
tree
2014-02-01
Erik Lindahl
Use pseudo-r
a
ndom instead of random streams to intializ
e
.
.
.
commit
|
commitdiff
|
tree
2013-12-17
Erik Li
n
dahl
Ad
d
e
d a bunch
of q
u
otes from t
h
e 2013 Nobel lectures
commit
|
commitdiff
|
tree
2013-12-16
Erik Lindahl
Moved shared/
s
tatic
li
b
rary
d
e
tection to s
e
parate module
commit
|
commitdiff
|
tree
2013-12-16
E
rik Lindah
l
Moved
F
FT l
i
brary processing to se
p
arate module
commit
|
commitdiff
|
tree
2013-12-16
Erik Lindah
l
M
o
ve
d
c
ompiler problem de
t
ection into
s
e
p
arate modu
l
e
commit
|
commitdiff
|
tree
2013-12-16
Erik Lindah
l
Mo
v
ed OpenMP detection to separate file
.
commit
|
commitdiff
|
tree
2013-11-15
E
rik Lindahl
Merge "Merge
b
r
a
n
ch rel
e
ase-4-6"
commit
|
commitdiff
|
tree
2013-09-25
Eri
k
Li
n
dahl
Fix bug in (
l
ong)
neighborlist SIMD p
a
ddin
g
w
h
en adding
.
.
.
commit
|
commitdiff
|
tree
2013-05-21
Erik Lindahl
Fujitsu S
p
arc64 accel
e
ration and gene
r
al fixe
s
for
.
.
.
commit
|
commitdiff
|
tree
2013-01-18
Erik
Lindahl
Merge "rem
o
ve unne
c
e
ssar
y
cma
k
e messages" into re
l
eas
e
-4-6
commit
|
commitdiff
|
tree
2013-01-18
E
r
ik Li
n
dahl
Merge
"
fi
x
Open
M
P detection on Mac OS bro
k
e
n
by a6fee0b
.
.
.
commit
|
commitdiff
|
tree
2013-01-16
Erik Lindahl
F
i
xed GB interactions for release
-
4-6
commit
|
commitdiff
|
tree
2013-01-11
Erik
L
inda
h
l
Mer
g
e "made SHAKE
w
ork again w
i
th parti
c
l
e
d
ecompostion
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Erik Lindahl
Added basic CP
U
topology
informa
t
i
o
n t
o
cpuid co
d
e
commit
|
commitdiff
|
tree
2013-01-11
Erik Lindahl
M
e
rge "
f
ixed
n
bnx
n
n
o
LJ co
m
b
.
rule AVX25
6
PME kernel
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
Fixed flop-accounting for
p
eriodic i
m
proper dihed
r
als
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
Disallow the use of Cl
a
ng to comp
i
le AVX_12
8
_FMA
commit
|
commitdiff
|
tree
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