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fix OpenMP detection on Mac OS broken by a6fee0b
2013-01-16
Erik Lindahl
Fixed GB interactions
for
release-4-6
commit
|
commitdiff
|
tree
2013-01-11
Er
i
k
Lindah
l
Merge "m
a
d
e SHAKE w
o
r
k again wi
t
h pa
r
ticle
d
eco
m
po
s
tion
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Eri
k
Lindahl
Adde
d
basic CPU topology infor
m
ation to cpuid co
d
e
commit
|
commitdiff
|
tree
2013-01-11
E
r
i
k Li
n
da
h
l
Merg
e
"fixed nbnxn n
o
L
J
comb
.
r
ule AVX
2
56 PME kernel
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Erik
L
i
ndahl
Fi
x
e
d flop
-
account
i
ng for periodic improp
e
r
dihed
r
als
commit
|
commitdiff
|
tree
2013-01-10
E
rik
L
indahl
Disallow
t
he u
s
e of Clan
g
to co
m
pile AVX_128_F
M
A
commit
|
commitdiff
|
tree
2013-01-10
Erik L
i
nd
a
hl
Remove br
o
ken
g_dih tool
commit
|
commitdiff
|
tree
2013-01-10
E
r
i
k Lindah
l
Revert default
rl
i
s
t
/
r
vdw
/
rcoulomb to valid values
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
Fixes SSE
/
AVX
comp
i
lation
unde
r
Windows
commit
|
commitdiff
|
tree
2013-01-09
Eri
k
L
indahl
Merge "Corrected g
m
xchec
k
output f
o
r Gro
m
os96 bonds
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Erik Lindahl
Added work-around for
gcc bug in AVX i
n
trinsincs form
a
l
.
.
.
commit
|
commitdiff
|
tree
2013-01-08
Erik
Lindahl
A
dd check to
r
emove zero
C
harmm dihedrals
commit
|
commitdiff
|
tree
2013-01-08
E
rik Lindahl
D
o not always a
d
d -msse2 to release flag
s
fo
r
ic
c
commit
|
commitdiff
|
tree
2012-12-30
Erik Lin
d
ahl
Fi
x
ed GM
X
RC so we are not polluting standard shell
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
Erik Lindahl
Merg
e
"Thread-
M
PI fixes
for
i38
6
llvm &
s
i
mplification
.
.
.
commit
|
commitdiff
|
tree
2012-12-27
Eri
k
Li
n
dahl
Fixed error message for zwitterion residues
commit
|
commitdiff
|
tree
2012-12-21
Erik
Lindahl
Fixed gm
x
_cpuid not worki
n
g
on non
-
x86
commit
|
commitdiff
|
tree
2012-12-20
Erik
L
in
d
ahl
Me
r
ge "c
m
ak
e
: added o
p
ti
o
n to d
i
s
a
ble quotes
"
into
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
E
r
ik L
i
nda
h
l
Merge "
S
mall fix
fo
r
g
_
tune_pme" in
t
o relea
s
e
-
4-6
commit
|
commitdiff
|
tree
2012-12-20
Erik Lindahl
M
e
rge
"
Fixes for anders
e
n
temperature cont
r
ol"
into
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Erik Lindahl
M
e
rge "Fixes for
e
xpanded ensemble and
H
REPEX
"
i
nt
o
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
E
rik Lindah
l
Fixed AVX256 doub
l
e-precision
kernels
f
or gcc
commit
|
commitdiff
|
tree
2012-11-29
Erik Lin
d
ahl
Double precisi
o
n AVX-256
k
ernels
commit
|
commitdiff
|
tree
2012-11-29
Erik Lindah
l
D
o
uble p
r
ecision AVX_12
8
_
FMA kernels
commit
|
commitdiff
|
tree
2012-11-28
Erik Linda
h
l
SSE4
.
1 double precisio
n
k
e
rnels
commit
|
commitdiff
|
tree
2012-11-28
Erik Lindahl
Double preci
s
ion SSE2 kern
e
ls
commit
|
commitdiff
|
tree
2012-11-28
Er
i
k Lindahl
Ported back so
m
e AVX256 optimizations to SSE2/SSE4
.
.
.
commit
|
commitdiff
|
tree
2012-11-28
Erik Li
n
dahl
1
2
8
-
bit AVX kernels,
w
ith FMA in
s
tructions for Opteron
.
.
.
commit
|
commitdiff
|
tree
2012-11-27
Erik Lindahl
N
o
nbonded group kernels
for 256-b
i
t AVX (
I
ntel CPUs)
commit
|
commitdiff
|
tree
2012-11-27
Erik Lind
a
h
l
Merge "Add
e
d affinity
s
upport
ch
e
ck, vis
i
b
il
i
ty ma
c
r
o
s
.
.
.
commit
|
commitdiff
|
tree
2012-11-27
Erik Lin
d
ahl
M
e
rge
"
fixed bug in nb
n
xn OpenMP
n
o
n-bonded force re
d
u
c
tion
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
E
rik Lindahl
Merge "U
s
e stat
fo
r
gmx_is_file
.
Fix get_li
b
dir with
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
Erik Li
n
dahl
Merge "Extend
e
d b
u
ild information
o
u
t
put and reference
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
Er
i
k
Linda
h
l
F
i
x for icc 13 optim
i
zation-relat
e
d i
s
s
ue and TIP4P
.
.
.
commit
|
commitdiff
|
tree
2012-11-22
Erik
L
in
d
a
hl
Implem
e
nted RMS-based force tolera
n
ce in gmxcheck
commit
|
commitdiff
|
tree
2012-11-22
Erik Li
n
da
h
l
F
i
xed
L
J-14
e
r
r
or in
f
ree ener
g
y
commit
|
commitdiff
|
tree
2012-11-19
Er
i
k Lin
d
ahl
SSE4
.
1 single-precision ke
r
n
e
ls
commit
|
commitdiff
|
tree
2012-11-16
Erik L
i
ndahl
SSE2 singl
e
-precision ke
r
nels
commit
|
commitdiff
|
tree
2012-11-13
E
r
i
k Linda
h
l
Remove
d
some unnecessary instruct
i
ons, and fix
e
d a
.
.
.
commit
|
commitdiff
|
tree
2012-11-09
E
r
ik Li
n
d
a
h
l
R
e
mo
v
e
d o
l
d
(n
o
w unused) bl
u
egene kernels
.
commit
|
commitdiff
|
tree
2012-11-09
Eri
k
L
i
ndahl
Re
m
oved
u
nuse
d
old kernel genera
t
or
commit
|
commitdiff
|
tree
2012-11-09
Erik Lindahl
Removal of
s
tale Fortran/Power6 kerne
l
s
commit
|
commitdiff
|
tree
2012-11-09
E
r
ik Li
n
dahl
Removal of s
t
ale
F
ortran kernels
commit
|
commitdiff
|
tree
2012-11-08
Er
i
k Lin
d
ahl
Fixed
b
ug
i
n
t
h
e
n
e
w switch-mo
d
ified intera
c
tions in
.
.
.
commit
|
commitdiff
|
tree
2012-11-08
E
r
ik Lindah
l
Allow rcoul
o
mb=rlis
t
l
o
ng for PME
w
i
t
h
nstcalcl
r
=1
commit
|
commitdiff
|
tree
2012-11-08
E
r
i
k
L
i
n
d
a
hl
Infrastruct
u
re for new group kerne
l
s, and n
e
w C
k
er
n
els
commit
|
commitdiff
|
tree
2012-06-21
Erik Lindahl
Fixed gcc in
l
ine assembly issue wit
h
P
I
C
and
o
lder
.
.
.
commit
|
commitdiff
|
tree
2012-06-16
Erik Lindahl
New CPU
d
etection &
A
VX/SS
E
code, r
e
moved raw assembly
.
.
.
commit
|
commitdiff
|
tree
2011-09-16
Erik Lindahl
Me
r
ge "made allo
c
a
t
ion for LI
N
CS w
i
th
p
a
r
ticle de
c
o
mpo
s
ition
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
E
r
ik Linda
h
l
Introduced differen
t
options fo
r
pdb2gmx termini introduct
i
o
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
Er
i
k Lindahl
Fixed inco
r
rection
AmberGS force
f
ield (redmine #728)
commit
|
commitdiff
|
tree
2011-05-05
Erik Lind
a
hl
M
e
r
g
e branch
'rele
a
se
-
4-
5
-p
a
tches' of
git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2011-05-05
Erik Li
n
dah
l
Update
doc to clarify
t
hat Amber nucleic params a
r
e
.
.
.
commit
|
commitdiff
|
tree
2011-01-30
Erik Lindahl
Improved
PBC han
d
li
n
g
for large molecules dur
i
ng
cluster PB
C
commit
|
commitdiff
|
tree
2011-01-30
Erik Lindahl
Fixed the pbc clus
t
er option of trjc
o
nv by
s
wit
c
hing
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Eri
k
Li
n
d
ahl
Me
r
ge
b
ranch 'release
-
4-5-pat
c
hes' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-10-09
Erik Lindahl
Fixed uninitialized
variab
l
e
warning in grompp
.
c
commit
|
commitdiff
|
tree
2010-09-01
Eri
k
Lindahl
Removed lots of unn
e
cessa
r
y messages t
o
stdout from
.
.
.
commit
|
commitdiff
|
tree
2010-09-01
Er
i
k Linda
h
l
Added Ge
r
rit to the list
o
f
a
uthors
.
Sorry for
forgetting
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik
Li
n
dahl
Made the options program for the latex manua
l
comp
i
le
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Fixed typ
o
in
src
/
co
n
trib/Makefile
.
am
commit
|
commitdiff
|
tree
2010-08-31
Eri
k
Li
n
dahl
Fixe
d
i
n
correc
t
call to
gmx_finalize() in gm
x
_pme_err
o
r()
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Added final newli
n
e to avoid compiler w
a
rning i
n
sf
a
ctor
.
h
commit
|
commitdiff
|
tree
2010-08-31
Erik L
i
n
da
h
l
Merge
b
ranch 'rele
a
se-4-5-p
a
tches' of g
i
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Added Cpack support
commit
|
commitdiff
|
tree
2010-08-31
Eri
k
Li
n
dahl
Added labe
l
writing cap
a
b
ility
t
o editcon
f
when used
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik
Lind
a
hl
Add
e
d c
h
eck for <2 frames
w
hen autocorr
e
latio
n
is requ
e
sted
.
.
.
commit
|
commitdiff
|
tree
2010-08-31
Erik Lindahl
Moved buggy and unsupported g_sdf to contrib directory
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
Erik
L
i
n
da
h
l
Improved handling of include paths i
n
gmxc
p
p from T
e
emu
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Added lon
g
e
r
l
ist of autho
r
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
M
erge b
r
a
n
ch 'release-4-5-patches'
o
f git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
Lindahl
A
dded check fo
r
SSE
2
support to
u
s
e
generali
z
ed born
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Eri
k
L
i
n
d
ahl
Adde
d
trj
c
onv check f
o
r topology prescence, s
e
e
bugzill
a
526
commit
|
commitdiff
|
tree
2010-08-27
Erik Lin
d
ahl
Merge
b
ranch 'release-4-5-patches
'
of git
.
gro
m
acs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Fixed gmxcpp to always use unix
p
ath sep
a
rators in
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Me
r
ge branch 'release-4
-
5-
p
atches' o
f
git
.
g
r
omacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Fixed anoth
e
r uninit
i
alized vari
a
ble warning in gmx_
e
nergy
.
c
commit
|
commitdiff
|
tree
2010-08-27
Erik Lindahl
Add cu
r
rent path
(
.
/) to topol
.
top include when force
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
E
r
i
k Linda
h
l
Dont write EOF warn
i
ngs to stdout ev
e
r
y
time we che
c
kpoint
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik Li
n
dahl
Merge branch 'release-4-
5
-patch
e
s'
o
f git
.
grom
a
c
s
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-27
Erik
Lindahl
Fixed first st
a
tem
e
me
n
t occur
i
n
g
b
e
f
o
re variable declara
t
ion
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Eri
k
Lindahl
M
e
rge branch 'release-4
-
5-patc
h
es' of gi
t
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
M
o
dified pdb
2
g
m
x to automatically pick the force field
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lindah
l
Fix
e
d pointer typ
o
in patch from Alexey Shv
e
tsov
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
A
d
ded PBC check
i
ng patch to g_cluste
r
from Alex
e
y Shvetsov
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lindahl
Me
r
ge br
a
n
ch '
r
elease-4
-
5-patche
s
' of
g
it
.
grom
a
cs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
i
k L
i
ndahl
Modified p
d
b
2gmx
t
o not ac
c
e
p
t extra hydr
o
gen atoms
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
rik Lin
d
ahl
Merge branch 'r
e
l
e
a
se
-
4-5-patches' of
g
it
.
g
romacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
dahl
true/false
i
np
u
t setting
s
should be cal
l
ed bo
o
l
i
n
s
tead
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Linda
h
l
Merge
branch 'release-4
-
5
-patche
s
' of git
.
g
romacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Linda
h
l
Revert
"
Made pd
b
2gmx be
s
l
ightly mo
r
e help
f
ul when
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik
Lindahl
Updated completions
fo
r
4
.
5
r
elea
s
e
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik Lindahl
Made
/usr/l
o
cal/gro
m
acs default installatio
n
path in
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
Erik Lind
a
hl
Upda
t
ed html do
c
umentation for release
4
.
5
commit
|
commitdiff
|
tree
2010-08-26
Erik Lind
a
h
l
Updated
m
anua
l
pages
,
now with correct ver
s
i
o
n (4
.
5
.
.
.
commit
|
commitdiff
|
tree
2010-08-26
E
r
ik
Lindahl
Fix
f
or warning in
n
gmx
m
akefile
commit
|
commitdiff
|
tree
2010-08-26
E
rik
Lindahl
Changed version to b
e
ta4
commit
|
commitdiff
|
tree
2010-08-26
Er
i
k Lindahl
Updated scripts to pr
o
duce 4
.
5 man pages
commit
|
commitdiff
|
tree
2010-08-26
Erik
Lindahl
U
pdated manpage
s
f
o
r 4
.
5 rele
a
s
e
commit
|
commitdiff
|
tree
2010-08-26
Erik Li
n
d
ahl
R
emo
v
ed usel
e
s
s g_logo
a
nd g_hi
g
hwa
y
p
rogram
s
fro
m
.
.
.
commit
|
commitdiff
|
tree
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