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QM/MM: remove optimization and trans. state search
2015-06-29
Erik Lindahl
Fix OS X open
C
L buil
d
s
commit
|
commitdiff
|
tree
2015-06-29
Erik Lindahl
Fix b
u
gs
i
n
gmx d
o
s
commit
|
commitdiff
|
tree
2015-06-29
Erik Lindahl
Replace functio
n
s
depr
e
cat
e
d in Op
e
nCL 1
.
2
commit
|
commitdiff
|
tree
2015-06-29
Erik Lindahl
Fi
x
bug r
e
mov
i
ng multiple dihedral
s
in ma
i
n rtp e
n
tries
commit
|
commitdiff
|
tree
2015-06-29
Erik Lindahl
R
e
moved gmx protonate to
o
l
commit
|
commitdiff
|
tree
2015-06-28
Erik
Li
n
dahl
Fi
x
double preci
s
ion
referenc
e
SIMD
a
nd gc
c
bug
commit
|
commitdiff
|
tree
2015-06-28
Erik
Lindah
l
Fix one erro
r
a
n
d c
o
mpiler
warnings with Cuda & c
l
ang-3
.
6
commit
|
commitdiff
|
tree
2015-06-27
Erik Lin
d
ah
l
Fix IB
M
V
SX SI
M
D compil
e
s with x
l
c
commit
|
commitdiff
|
tree
2015-06-27
Erik
L
i
n
dahl
Fix single-prec
.
softcore issue in 4
.
6 b
r
a
nch
commit
|
commitdiff
|
tree
2015-06-27
Erik
L
indahl
Merge "Mer
g
e release-5-0
i
nto
master"
commit
|
commitdiff
|
tree
2015-06-26
Erik
L
indahl
Fix co
m
p
i
le
i
ssu
e
s on K comp
u
t
er
commit
|
commitdiff
|
tree
2015-06-26
Erik Lin
d
ahl
F
ix bu
f
fer size issues in string databa
s
e
commit
|
commitdiff
|
tree
2015-06-25
Erik Lindahl
Fix e
d
r
a
p
pending
an
d
e
x
a
ct co
n
tinuat
i
on
commit
|
commitdiff
|
tree
2015-06-25
Erik Lindahl
Fix binary exact continuatio
n
for trajectories
commit
|
commitdiff
|
tree
2015-06-24
Erik
Lindahl
Avoid acce
s
sing hackblocks f
o
r x2top
commit
|
commitdiff
|
tree
2015-06-23
Er
i
k Lindahl
Upd
a
ted physical con
s
ta
n
ts from NIST 20
1
0 CODA
T
A
commit
|
commitdiff
|
tree
2015-06-23
Erik Lindahl
Removed buggy -smooth hack in hbond
module
commit
|
commitdiff
|
tree
2015-06-22
Er
i
k Lindahl
Fix c
o
m
p
iler war
n
i
ngs in cma
k
e tests
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
Use MPI_THREAD_FUNNELED when available
commit
|
commitdiff
|
tree
2015-06-22
Er
i
k Li
n
dah
l
Fi
x
segfaul
t
in random access
X
TC searching
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
Fix argu
m
e
n
t order error
for g_rmsdist
commit
|
commitdiff
|
tree
2015-06-22
Erik L
i
ndahl
Fi
x
g
ro erro
r
s with PDB insertio
n
cod
e
s
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindahl
U
p
date
d
docs
f
or g
_
gyrate
commit
|
commitdiff
|
tree
2015-06-20
Er
i
k L
i
ndahl
Fix potential
b
uffer ov
e
rflow i
n
pdb2gmx
commit
|
commitdiff
|
tree
2015-06-20
Erik Li
n
dahl
Disallow infini
t
e epsilon with PM
E
or G
B
.
commit
|
commitdiff
|
tree
2015-06-20
Erik
L
ind
a
hl
Remove GMX_M
A
X_MPI_THREADS
commit
|
commitdiff
|
tree
2015-06-20
Erik Linda
h
l
Fix reproducibi
l
ity bug
i
n fft5d
commit
|
commitdiff
|
tree
2015-06-20
Erik
Lin
d
ahl
Handle m
u
ltidi
r
/multisim with single argument correct
l
y
commit
|
commitdiff
|
tree
2015-06-19
Erik Lindahl
Fix incorrec
t
shift with
g_density -c
e
nter
commit
|
commitdiff
|
tree
2015-06-16
Erik Lin
d
a
hl
Fix
C
U
D
A ve
r
sion info in
NVML
app
l
ic
a
tion
c
lock
w
arnin
g
commit
|
commitdiff
|
tree
2015-06-16
Er
i
k Lindahl
Add memb
r
ane emb
e
dding
d
ocs
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Updated FFTW recommendations in install-g
u
ide
.
commit
|
commitdiff
|
tree
2015-06-16
Erik Lindahl
Fix se
g
fault with
tim
e
r reset and
-
nb cpu
commit
|
commitdiff
|
tree
2015-06-16
E
r
i
k Lindahl
Avo
i
d warning about
a
f
f
inity on Blue
G
ene, reduc
e
warn
i
ngs
commit
|
commitdiff
|
tree
2015-06-15
Erik Lin
d
ahl
F
i
x OS X FFTW
bu
i
l
d
failures introduc
e
d 86a772
commit
|
commitdiff
|
tree
2015-06-15
Erik Lindahl
Fixed SIMD det
e
ction and flags
c
ommon for IBM archs
commit
|
commitdiff
|
tree
2015-06-07
Erik
Lind
a
hl
Fix out-of
-
range i
n
teger literal
s
for th
r
ee
f
ry
commit
|
commitdiff
|
tree
2015-06-04
E
rik Linda
h
l
More new
quo
t
es
commit
|
commitdiff
|
tree
2015-05-17
Erik L
i
ndahl
Added ha
c
ks for SIMD rvec
/
load store in linc
s
&
bonded
s
commit
|
commitdiff
|
tree
2015-03-30
Erik L
i
nda
h
l
Quote from Szilard's talk
a
t GTC2015
commit
|
commitdiff
|
tree
2015-03-25
Erik
Lindahl
Quote fro
m
Jen-Hsun a
t
t
he
NVI
D
IA GTC
c
onfer
e
nce 20
1
5
commit
|
commitdiff
|
tree
2015-03-03
Erik Lindahl
Added sin
g
le-accuracy SIMD double ma
t
h functions
commit
|
commitdiff
|
tree
2015-02-24
Eri
k
L
indahl
Add
e
d AVX-512ER SIMD support
commit
|
commitdiff
|
tree
2015-02-24
Eri
k
Lind
a
h
l
Ad
d
AVX-512F S
I
MD
support
commit
|
commitdiff
|
tree
2015-02-20
Erik Lin
d
ahl
Famous quot
e
fro
m
Colleen McCu
l
lou
g
h
commit
|
commitdiff
|
tree
2015-02-20
Erik Lindahl
Added two
p
op-cultu
r
e quote
s
from
Andy Warhol
.
commit
|
commitdiff
|
tree
2015-01-19
Erik
L
i
n
d
ahl
Added two
quotes from
J
ulie Ber
n
aue
r
habilitatio
n
commit
|
commitdiff
|
tree
2014-09-30
Er
i
k Lin
d
ah
l
Add
Power8
V
SX SIMD s
u
pport
commit
|
commitdiff
|
tree
2014-09-30
Er
i
k Linda
h
l
Avoid using funct
i
on call
s
in Ope
n
M
P
d
i
r
ectiv
e
s
commit
|
commitdiff
|
tree
2014-09-22
Er
i
k
L
indahl
M
ore
q
uotes
commit
|
commitdiff
|
tree
2014-09-20
Er
i
k
L
inda
h
l
Fix R
e
lWith
D
ebInfo
n
ame
b
ugs
,
a
n
d us
e
full optimi
z
ation
.
commit
|
commitdiff
|
tree
2014-09-20
Erik Lin
d
ahl
Added a bunch of n
e
w
a
n
d
old quotes
.
commit
|
commitdiff
|
tree
2014-09-18
Erik Lindahl
Add Power/Powe
r
PC V
M
X SIMD support
commit
|
commitdiff
|
tree
2014-09-11
Erik L
i
ndahl
Enable static anon names
p
a
c
e
worka
r
ound on p
a
thscale
commit
|
commitdiff
|
tree
2014-09-10
E
rik Lindahl
Improve per
f
ormance of MIC
e
xponent
i
al
commit
|
commitdiff
|
tree
2014-09-08
Er
i
k Linda
h
l
Add
64-bit AA
r
c
h
6
4 asimd SIMD support
commit
|
commitdiff
|
tree
2014-09-08
Erik
L
in
d
a
h
l
Add
3
2-bit ARM Neon SIMD support
commit
|
commitdiff
|
tree
2014-09-04
E
rik Lindahl
K-
c
omputer sp
e
c
i
fic
m
odifications
commit
|
commitdiff
|
tree
2014-09-03
Erik Lindahl
Fi
x
ed sc_p
o
wer==
4
8 cras
h
in sin
g
le p
r
ecision
commit
|
commitdiff
|
tree
2014-09-03
Erik
Lindahl
Fi
x
ed pr
e
process
o
r error for
A
VX_128
_
FMA simd
commit
|
commitdiff
|
tree
2014-09-02
Erik Lindahl
F
i
x formatting of
f
a
t
al er
r
ors in g_bar
commit
|
commitdiff
|
tree
2014-09-02
Erik Lin
d
ahl
F
i
xed strin
g
var expansio
n
in CMake due
to C
M
P
0053
commit
|
commitdiff
|
tree
2014-08-31
Erik Lindahl
A
d
ded
n
e
gative zero
p
r
epr
o
cessor constants
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Add _GNU
_
SOURCE=1 to find clone() with PGI
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Fi
x
matri
x
pointer dere
f
e
rence
b
u
g i
n
update
.
c
commit
|
commitdiff
|
tree
2014-08-20
Erik Linda
h
l
Enable SIMD
r
egister calling c
o
nventi
o
n with gmx_si
m
d
call
commit
|
commitdiff
|
tree
2014-08-20
Erik Lin
d
ahl
Add c
y
c
l
e counter
s
fo
r
64-bit A
R
M
commit
|
commitdiff
|
tree
2014-08-20
E
r
ik Lin
d
ahl
Shorten p
l
ugin c
o
n
f
i
g
uration message
commit
|
commitdiff
|
tree
2014-08-17
Erik Li
n
dahl
Fix Po
r
tlan
d
compi
l
er
w
ar
n
in
g
s
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindahl
M
a
k
e internal BLAS/LAPACK messages less noi
s
y
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindahl
I
m
prov
e
Gromacs po
r
tabi
l
i
ty
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindahl
Re
p
lace __LP64__ with
check for point
e
r si
z
e
commit
|
commitdiff
|
tree
2014-08-07
Erik
Lindahl
Fix p
o
rtability issue with A
r
rayRef
i
nitialize
r
overloading
commit
|
commitdiff
|
tree
2014-08-07
Er
i
k Lindahl
Chan
g
e
d names of
t
est files to avoid Fu
j
itsu compiler bug
commit
|
commitdiff
|
tree
2014-08-01
Erik
L
i
ndahl
Added tests fo
r
denormal
and underflow for simd exp(
)
commit
|
commitdiff
|
tree
2014-07-27
Erik
L
ind
a
h
l
Fix selection of xtc groups not st
a
rt
i
ng at index 0
commit
|
commitdiff
|
tree
2014-07-13
E
ri
k
L
i
n
dahl
Avoid
cl
a
ng/32 optimization af
f
ecting
IEEE endian d
e
tection
commit
|
commitdiff
|
tree
2014-07-11
Eri
k
Li
n
dahl
Make AVX2
c
heck more
robust
commit
|
commitdiff
|
tree
2014-07-08
Erik
Li
n
dahl
Make IEEE75
4
c
h
eck mo
r
e
robust
commit
|
commitdiff
|
tree
2014-06-29
E
rik Lindahl
Fixed free energy with LJ-PME
commit
|
commitdiff
|
tree
2014-06-29
Erik Lindahl
Enable rtp angle/d
i
hedral
entries not c
o
n
n
ected by
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
E
r
ik Linda
h
l
Fixed CMA
P
gen
e
rat
i
on for a
l
ani
n
e dipeptide specia
l
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
E
r
ik Lin
d
ahl
Always set b
-
sta
t
e posr
e
s
,
even if i
d
en
t
ical t
o
a-state
commit
|
commitdiff
|
tree
2014-06-27
Eri
k
Lindahl
Update g_density to handle bilayers
b
etter
commit
|
commitdiff
|
tree
2014-06-27
E
rik Li
n
dahl
Fix LJP
M
E Lor
e
ntz-Be
r
thel
o
t combinatio
n
r
ule
s
commit
|
commitdiff
|
tree
2014-06-27
Erik L
i
ndahl
Improve PDB I/
O
(
keep
occupancy, b-fact
o
r,
element)
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Avoid
w
a
rnings abo
u
t
coup
l
ing when fre
e
_e
n
ergy=
n
o
commit
|
commitdiff
|
tree
2014-06-25
Erik
Lind
a
hl
U
pdated Amber GBSA
p
arameters
commit
|
commitdiff
|
tree
2014-06-25
Erik Lindahl
Make
s
ourc
e
compile
u
n
d
e
r L
i
nux X32 ABI
commit
|
commitdiff
|
tree
2014-06-25
E
r
i
k
L
indahl
Make it harder for c
o
mpil
e
r to optimize away SIMD CMa
k
e
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindah
l
Fixed GROM
O
S a
s
signm
e
nt
of
P
R
O
-NH termin
u
s tors
i
o
n
s
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Make su
r
e
duplicate
s
bondeds are se
t
from hackblocks
commit
|
commitdiff
|
tree
2014-06-24
Erik Linda
h
l
C
l
e
an u
p
CMAP pl
a
c
ement in parameter list
commit
|
commitdiff
|
tree
2014-06-24
Erik L
i
ndahl
Added multisimulation i
n
fo to log/out
p
ut
commit
|
commitdiff
|
tree
2014-06-24
Erik Li
n
dahl
Fixe
d
rece
n
t bug with disp
.
corr
.
and vdwtyp
e
=
shift
commit
|
commitdiff
|
tree
2014-06-23
Er
i
k
Lin
d
ahl
Enable term
i
nus-specifi
c
atom
t
ranslation
commit
|
commitdiff
|
tree
2014-06-23
E
r
i
k Lindahl
Ena
b
l
e 4-le
t
ter
r
esname in
PDB outpu
t
, keeps mor
e
pdbin
f
o
.
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Det
e
ct non-fatal wa
r
n
i
ngs when t
r
ying CFlags for so
u
r
ce
commit
|
commitdiff
|
tree
2014-06-23
Erik
L
indahl
E
n
able xvgr outp
u
t an
d
labels for g_
p
ri
n
ci
p
al
commit
|
commitdiff
|
tree
2014-06-23
Erik Lin
d
ahl
Disal
l
ow extracti
n
g V/F fr
o
m
X
T
C
files in
g
_
traj
commit
|
commitdiff
|
tree
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