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Change use of t_inpfile to std::vector
2016-07-07
Szilárd
P
ál
l
Add user guide info
o
n CU
D
A
a
p
p
l
i
c
ation clocks
commit
|
commitdiff
|
tree
2016-07-07
M
a
rk Abraham
Fix build if
l
ibc
u
d
a is foun
d
but nvcc
i
s n
o
t
commit
|
commitdiff
|
tree
2016-06-07
Seme
n
Y
e
sylev
s
kyy
A
d
ded manual
sec
t
ion about emb
e
ddin
g
p
roteins to membranes
.
commit
|
commitdiff
|
tree
2016-06-05
Sz
i
lárd Páll
Add support fo
r
CUDA CC 6
.
0/6
.
1
commit
|
commitdiff
|
tree
2016-06-03
Berk Hess
Handle partially fr
o
zen and
c
onst
r
ained atoms
commit
|
commitdiff
|
tree
2016-06-02
Szilárd Páll
Add env
.
va
r
.
to enab
l
e Open
C
L cachin
g
commit
|
commitdiff
|
tree
2016-06-02
Szilárd Páll
Fix OpenCL b
i
nary cache fil
e
name generati
o
n
commit
|
commitdiff
|
tree
2016-06-02
R
o
l
and
Schulz
F
ix ICC
16u3 build
commit
|
commitdiff
|
tree
2016-06-02
Patrick
W
elche
E
n
sure IMD include de
p
endencies work
commit
|
commitdiff
|
tree
2016-05-29
Mark
A
braham
Si
m
pli
f
ied an
d
up
d
at
e
d OpenCL compil
a
tion
commit
|
commitdiff
|
tree
2016-05-23
B
e
rk Hess
Fi
x
bug in
v
-
r
e
scale thermostat & replica e
x
cha
n
ge
commit
|
commitdiff
|
tree
2016-05-10
E
r
i
k Li
n
d
ahl
F
i
xed
l
arge
file i
s
sue on 32-bi
t
pl
a
tfor
m
s
commit
|
commitdiff
|
tree
2016-05-08
B
e
rk
H
ess
Update m
d
ru
n
t
e
r
m
ination info
commit
|
commitdiff
|
tree
2016-04-03
Be
r
k Hess
Corre
c
t nr
d
f for 1D/2D
s
ystems
commit
|
commitdiff
|
tree
2015-12-24
Erik
Lindahl
Extended S
I
M
D, implemen
t
ation for IBM Po
w
e
r
7
/8
V
SX
commit
|
commitdiff
|
tree
2015-12-21
E
r
ik
L
indahl
Extende
d
SIMD,
i
mplementation for BlueG
e
ne/Q
commit
|
commitdiff
|
tree
2015-12-21
Erik Lindahl
Extended SIMD
implementation for 256-bit
AVX and
A
VX2
commit
|
commitdiff
|
tree
2015-12-16
E
r
ik Lin
d
ahl
Next-generation SIMD module, referenc
e
im
p
leme
n
ta
t
ion
commit
|
commitdiff
|
tree
2015-10-30
Er
i
k Lind
a
hl
Bre
a
k depen
d
e
n
ce
o
f
group kernels on simd module
commit
|
commitdiff
|
tree
2015-09-30
Roland Schulz
Require C++11
commit
|
commitdiff
|
tree
2015-08-13
M
a
rk Abraham
Re-enable
multi-GP
U
suppo
r
t
in OpenCL for thr
e
ad MPI
commit
|
commitdiff
|
tree
2015-08-05
Erik Lindahl
F
ix
PGI co
m
p
ile
r
f
lag
commit
|
commitdiff
|
tree
2015-07-27
Erik Lin
d
ahl
M
o
ve
d
additional gmx
l
ib
sources to C++
commit
|
commitdiff
|
tree
2015-07-26
Mark A
b
r
a
ham
Convert some mdrun utilit
y
co
d
e to C++
commit
|
commitdiff
|
tree
2015-07-26
Erik Lindahl
M
e
r
g
e
branch r
e
lea
s
e-5-1
commit
|
commitdiff
|
tree
2015-07-07
Erik Lindahl
Move QMM
M
source to C++
commit
|
commitdiff
|
tree
2015-07-05
Ber
k
He
s
s
Fi
x
DD DLB state issue
commit
|
commitdiff
|
tree
2015-06-27
Erik Lindahl
Fix si
n
gle-pr
e
c
.
s
o
ftcore
issue in 4
.
6 branch
commit
|
commitdiff
|
tree
2015-02-20
Eri
k
Lindahl
Famo
u
s q
u
ote
f
rom Colleen McCu
l
lough
commit
|
commitdiff
|
tree
2015-02-20
E
rik Lindahl
Added two pop-
c
ultu
r
e
q
uote
s
from
Andy Warhol
.
commit
|
commitdiff
|
tree
2014-09-20
Erik
Lin
d
ahl
Fix Re
l
Wit
h
DebInfo name bug
s
, a
n
d u
s
e full
o
ptimization
.
commit
|
commitdiff
|
tree
2014-09-02
Erik
Lindahl
Fixed st
r
ing var e
x
pa
n
sion in CMake due
t
o
CMP0053
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindah
l
M
ak
e
internal BLAS/LAPA
C
K
m
essa
g
es l
e
ss noisy
commit
|
commitdiff
|
tree
2014-07-28
Roland Schu
l
z
Add u
n
it tes
t
for
r
andom/Threefry
commit
|
commitdiff
|
tree
2014-07-27
Erik Lindahl
Fix selection of x
t
c group
s
not s
t
arting at index 0
commit
|
commitdiff
|
tree
2014-07-11
Erik Lindahl
Make AVX
2
check more
r
o
bust
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Fixed rece
n
t bug with disp
.
co
r
r
.
a
n
d
vdwtyp
e
=shift
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Enable termin
u
s-specific atom
t
ranslation
commit
|
commitdiff
|
tree
2014-06-22
Erik Li
n
dahl
M
a
k
e log file option listing sim
i
lar to mdp names
commit
|
commitdiff
|
tree
2014-06-21
E
rik
L
inda
h
l
Make
s
ure masses a
r
e copied from termini
da
t
a
b
ases
commit
|
commitdiff
|
tree
2014-03-31
Teemu Mu
r
tola
Move some math heade
r
s away fro
m
legacyh
e
a
d
e
r
s/
commit
|
commitdiff
|
tree
2014-03-16
Erik Lindahl
U
se
a constant instead
of sizeof(int) for SSE2 imm
e
d
iate
.
.
.
commit
|
commitdiff
|
tree
2014-02-01
E
r
i
k Lin
d
a
hl
Use pseudo-ran
d
om inste
a
d of random strea
m
s to i
n
t
i
alize
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland Schulz
Remove unnecessa
r
y
I
CC flags aff
e
cting perf
o
rmance
commit
|
commitdiff
|
tree
2013-01-10
E
r
ik
L
indahl
Fixes
S
SE/AV
X
compilation und
e
r Windows
commit
|
commitdiff
|
tree
2013-01-09
Erik Lindahl
Added work-around for gcc bu
g
i
n
AVX in
t
rin
s
incs
f
ormal
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
Eri
k
Lindahl
Fixed GMXRC so
w
e are not
p
olluting standard she
l
l
.
.
.
commit
|
commitdiff
|
tree
2012-12-27
Erik
L
i
n
dahl
F
ixed error message for zwitterion residues
commit
|
commitdiff
|
tree
2012-12-20
E
rik L
i
ndahl
Fixed AVX256 doubl
e
-pre
c
i
sion kern
e
ls for gc
c
commit
|
commitdiff
|
tree
2012-11-22
Erik Lindahl
F
i
x fo
r
icc 13 optimization-related issue a
n
d TIP4P
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
Erik Linda
h
l
Im
p
lemented RMS-based
forc
e
t
o
leran
c
e i
n
gmxcheck
commit
|
commitdiff
|
tree
2012-11-22
Eri
k
Lindahl
Fixed
LJ-14 e
r
ror in free
energ
y
commit
|
commitdiff
|
tree
2012-11-09
Erik Li
n
dahl
Removed old (now u
n
us
e
d) bl
u
e
g
ene
ke
r
n
e
ls
.
commit
|
commitdiff
|
tree
2012-11-09
Erik Lindahl
Removed unused old kerne
l
gen
e
rato
r
commit
|
commitdiff
|
tree
2012-11-09
Erik
Lindahl
Re
m
oval of s
t
ale For
t
ran
/
Power
6
kerne
l
s
commit
|
commitdiff
|
tree
2012-11-09
Erik Li
n
dahl
Removal
of stale Fortran kernels
commit
|
commitdiff
|
tree
2012-11-08
E
r
ik Lin
d
ahl
Fixed bug in the new s
w
itc
h
-modified
i
nteractions in
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
Erik Li
n
da
h
l
Allow
r
c
o
ulomb=rlistlong
for PME with nstc
a
l
c
lr=1
commit
|
commitdiff
|
tree
2012-06-21
Erik Lindahl
Fix
e
d gcc inli
n
e assembly issue
w
ith P
I
C a
n
d o
l
d
e
r
.
.
.
commit
|
commitdiff
|
tree
2012-06-16
Erik
L
i
n
dahl
N
e
w
CPU
de
t
ection & AVX/SSE code
,
removed raw ass
e
mbly
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Erik Lindahl
Introduced different option
s
for pdb2gmx
t
e
rmini introductio
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
E
rik
L
i
n
dahl
F
ix
e
d incorrection
A
mberGS force fi
e
ld (re
d
mine #72
8
)
commit
|
commitdiff
|
tree
2011-05-05
Erik
L
indahl
M
e
rg
e
bran
c
h '
r
elease-4-
5
-patc
h
es' of
git
.
g
romacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
E
rik Linda
h
l
Upd
a
t
e doc to
c
l
arify that Amber nucleic
par
a
ms ar
e
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
Erik Lindahl
M
erge branch
'
master
'
of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2011-05-05
Erik Lindahl
Update doc to clarify that Am
b
er
n
uc
l
eic params are
.
.
.
commit
|
commitdiff
|
tree
2011-01-30
Erik Lind
a
h
l
Improved PBC handling for large
m
olecules dur
i
n
g
cluster PBC
commit
|
commitdiff
|
tree
2011-01-30
E
rik Linda
h
l
Fix
e
d
the pbc cluster option of
t
r
jconv by
s
witc
h
ing
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Erik L
i
ndah
l
M
e
rge
branch 'rel
e
ase-4-5-patche
s
' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Erik Lin
d
ahl
Fix
e
d unin
i
ti
a
l
iz
e
d variabl
e
war
n
ing in grompp
.
c
commit
|
commitdiff
|
tree
2010-09-01
Erik Lindahl
Removed lots of
u
nnec
e
s
s
a
ry m
e
ssages to stdou
t
f
rom
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Erik Lindahl
A
dded Gerrit to the
lis
t
o
f
authors
.
Sor
r
y for
f
orgetti
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik
L
indah
l
Mad
e
the options prog
r
am for
t
h
e
l
atex manual compile
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
F
i
x
ed
typ
o
in sr
c
/contrib/Makef
i
le
.
am
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Fixed inc
o
rr
e
ct call to
g
mx_f
i
na
l
iz
e
()
i
n gmx
_
pme_error()
commit
|
commitdiff
|
tree
2010-08-31
Eri
k
Lindahl
A
d
ded final
newlin
e
to avoi
d
c
omp
i
ler
w
arnin
g
in sfa
c
tor
.
h
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k
L
indahl
M
e
rge branch 'release-4-5
-
p
a
t
ches' of
g
i
t
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Er
i
k Lin
d
ahl
Added Cp
a
ck sup
p
or
t
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Added la
b
e
l
writi
n
g capability to editconf when
used
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik
Lindahl
Added c
h
ec
k
for <2 frames when auto
c
o
r
relati
o
n is requested
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lin
d
a
h
l
M
o
ved buggy a
n
d
uns
u
pported g_sdf to
c
ontrib d
i
rec
t
ory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik Lindahl
Imp
r
oved handli
n
g o
f
include paths in
gmxcpp from Teemu
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Li
n
dahl
M
erge branch
'release-4
-
5
-p
a
tches'
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
ahl
Added longer
l
ist of authors
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Er
i
k Lind
a
hl
Merge branch 'relea
s
e-4-5-patches' of git
.
gromacs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik
L
indahl
A
dded check for S
S
E2
s
u
p
port to
use g
e
neraliz
e
d born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
ahl
Resolved merge conf
l
ict in gmx_m
e
mbed
.
c
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lindahl
Merge b
r
an
c
h 'rel
e
ase-4-5-pa
t
ches' of
g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik Lindahl
Fixed gmxc
p
p to al
w
ays use unix path s
e
pa
r
ators
in
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
L
indahl
Merge branch
'release-4-5-patches' of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Fixed a
n
ot
h
e
r un
i
nitialized var
i
able warning in gm
x
_
energy
.
c
commit
|
commitdiff
|
tree
2010-08-27
E
r
ik
L
indahl
Add current path (
.
/) to topol
.
top include when f
o
r
c
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
L
indahl
Dont write EOF warnings to s
t
dout ev
e
ry time
w
e
checkpoi
n
t
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
a
h
l
Me
r
ge
b
r
anch 'release-4-5-patches' of git
.
gro
m
ac
s
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Fixed fir
s
t stat
e
m
ement
oc
c
uring before varia
b
le declarati
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Added tr
j
conv check for topolo
g
y presc
e
nce,
see bugzilla 526
commit
|
commitdiff
|
tree
2010-08-26
Erik L
i
n
dahl
Merg
e
branch
'
rele
a
se-
4
-5-patches' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lind
a
hl
Modifi
e
d
pdb2gmx to au
t
omatical
l
y
pick th
e
force
f
ield
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dahl
Fixed
p
oi
n
te
r
typo in pa
t
ch f
r
om Alex
e
y Shvet
s
o
v
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik L
i
ndahl
Ad
d
ed P
B
C checking pat
c
h
t
o g_clu
s
te
r
from
Alexe
y
Shvetsov
.
.
.
commit
|
commitdiff
|
tree
next