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New and reorganized documentation
2014-02-11
Mark
A
braham
Update stuf
f
for old
BlueGene
commit
|
commitdiff
|
tree
2014-02-09
T
eemu
M
u
r
to
l
a
Mak
e
'gmx -h'
i
nvariant
w
rt
.
provided
opt
i
ons
commit
|
commitdiff
|
tree
2014-02-09
T
e
e
m
u Murtola
Rem
o
ve old hel
p
fo
r
matting code
commit
|
commitdiff
|
tree
2014-02-09
Teemu Mu
r
to
l
a
Make FileName
O
pti
o
n behave more l
i
ke
o
ld
f
ilenm parser
commit
|
commitdiff
|
tree
2014-02-09
T
e
emu Murtola
Implement synopsis for help output
commit
|
commitdiff
|
tree
2014-02-04
Mark Abraha
m
Use
f
e
a
tur
e
to explain t
h
at tpbconv
h
as moved
commit
|
commitdiff
|
tree
2014-02-01
Er
i
k
Lind
a
hl
Added AVX2 d
e
tection to cmake
a
nd created CPU
a
c
c
e
leration
.
.
.
commit
|
commitdiff
|
tree
2014-01-29
Mark Abraham
Kee
p
clan
g
Address Sanitizer h
a
ppy
commit
|
commitdiff
|
tree
2014-01-28
Mark Abraham
M
e
rge branch 'rel
e
ase
-
4-6
'
commit
|
commitdiff
|
tree
2014-01-28
Ma
r
k Abr
a
ham
Remove u
n
u
sed fplog
commit
|
commitdiff
|
tree
2014-01-27
Mark Abraham
D
on't number a list
m
an
u
a
lly
commit
|
commitdiff
|
tree
2014-01-21
Mark Abraham
Remove hidden o
p
tion
t
o
g
m
x
dump
commit
|
commitdiff
|
tree
2014-01-20
M
ark Abraham
R
e
move
var
i
o
u
s outdated things from the repo
commit
|
commitdiff
|
tree
2014-01-20
M
a
rk Abrah
a
m
Renam
e
'
g
mx tpbconv'
t
o 'gmx conve
r
t-tpr'
commit
|
commitdiff
|
tree
2014-01-20
Magnus
Lundborg
Add TNG
w
riting and reading support
commit
|
commitdiff
|
tree
2014-01-09
Rol
a
n
d
Schulz
Remove remaining u
s
age of SI
Z
EOF*
commit
|
commitdiff
|
tree
2014-01-08
M
ark
Abr
a
ham
Creat
e
math module
commit
|
commitdiff
|
tree
2013-12-05
Ma
r
k Abraham
Vers
i
on bump
af
t
er 5
.
0
-
beta1
relea
s
e
commit
|
commitdiff
|
tree
2013-12-05
Mark Abraham
Fix administr
i
via
commit
|
commitdiff
|
tree
2013-12-02
Mark Abraham
Version bump af
t
er
4
.
6
.
5 r
e
lea
s
e
commit
|
commitdiff
|
tree
2013-12-02
Berk Hess
Made c
u
to
f
f-sch
e
me=
V
erlet the default
commit
|
commitdiff
|
tree
2013-12-02
B
erk Hess
R
enamed verl
e
t-b
u
ffer-drift
t
o
verlet
-
buf
f
er-t
o
lerance
commit
|
commitdiff
|
tree
2013-12-02
M
ark Abraham
Version
b
umps before releas
e
commit
|
commitdiff
|
tree
2013-12-02
M
ark Abraham
Me
r
ge branc
h
'release
-
4-6'
commit
|
commitdiff
|
tree
2013-11-28
T
eemu Murtola
Fix some #include problems
.
commit
|
commitdiff
|
tree
2013-11-27
Mark Abraham
Fi
x
s
trange char
a
cter i
n
ma
n
u
a
l
commit
|
commitdiff
|
tree
2013-11-26
Berk
H
ess
F
i
xed return value o
f
gmx_
m
to
p
_bondeds
_
f
ree_energy
commit
|
commitdiff
|
tree
2013-11-19
Mark Abra
h
am
F
i
x
i
ncor
r
ec
t
v
ar
i
able name
i
n
d
oc
u
m
ent
a
tion
commit
|
commitdiff
|
tree
2013-11-15
Mar
k
Abraham
Merge branch re
l
ease-4
-
6
commit
|
commitdiff
|
tree
2013-11-13
Mar
k
Abraham
B
um
p
v
e
rsio
n
a
f
ter
4
.
6
.
4
release
commit
|
commitdiff
|
tree
2013-11-08
M
a
rk Abraham
Fix m
a
lformed CMake
commit
|
commitdiff
|
tree
2013-10-26
Roland Schulz
Fix
N
BNxN
S
IMD refere
n
ce kerne
l
s
commit
|
commitdiff
|
tree
2013-10-26
Mark Abraham
Encapsulat
e
gmx_wallclock_account
i
ng_t int
o
new timing
.
.
.
commit
|
commitdiff
|
tree
2013-10-23
M
a
rk Abraham
M
erge
branch
r
elease-4
-
6
into master
commit
|
commitdiff
|
tree
2013-10-20
Mark Abraham
Remov
e
h
t
ml target f
r
om and excessive PDFs for man
u
al
commit
|
commitdiff
|
tree
2013-10-14
Szilard Pall
use C
U
DA
tex
t
ure obj
e
c
t
s
w
hen support
e
d
commit
|
commitdiff
|
tree
2013-10-08
Mark Abra
h
am
Remove som
e
unused
variables fr
o
m
MD loop
commit
|
commitdiff
|
tree
2013-10-06
Mark Abraham
Fixed triggering of CPU
acc
e
leration-
s
cheme detection
commit
|
commitdiff
|
tree
2013-10-04
Teemu Murtola
Clean up CT
e
st u
s
a
ge
.
commit
|
commitdiff
|
tree
2013-10-03
Christ
o
ph Junghans
Fix parallel build for
G
M
X
_BUILD_OWN_FFT
W
commit
|
commitdiff
|
tree
2013-09-26
Mark Abr
a
ham
Merge b
r
a
nch release
-
4-6
commit
|
commitdiff
|
tree
2013-09-26
Ma
r
k
A
braham
Remove Genera
l
C
oupling Theory
stuff
commit
|
commitdiff
|
tree
2013-09-20
Mark
Abraham
Merge
bran
c
h 'releas
e
-4
-
6'
commit
|
commitdiff
|
tree
2013-08-15
Mark Ab
r
a
h
am
Produ
c
tive aftern
o
on of meetings
.
.
.
more quot
e
s!
commit
|
commitdiff
|
tree
2013-08-09
Mark Abraham
Reordered FFT
W
fat
a
l e
r
ror
;
a
v
oids using unset
variables
commit
|
commitdiff
|
tree
2013-07-26
Mark
Abraham
Merg
e
branch release
-
4-6 i
n
to ma
s
t
e
r
commit
|
commitdiff
|
tree
2013-07-24
Ma
r
k
Abraham
Me
r
ge
b
r
an
c
h
re
l
ease-4
-
6 i
n
to master
commit
|
commitdiff
|
tree
2013-06-27
Roland Schulz
Merge branch
'
rele
a
se-4-6' into master
commit
|
commitdiff
|
tree
2013-06-16
Jeff Ha
m
m
o
nd
D
e
fine
b
oth C and
C
++ compilers in BGQ
tool
c
h
a
i
n
s;
.
.
.
commit
|
commitdiff
|
tree
2013-06-16
Jeff Hammond
Us
e
m
o
re obvious
n
ame of
BGQ
c
ompi
l
er MPI wrappers
commit
|
commitdiff
|
tree
2013-06-16
Jeff H
a
mm
o
nd
fix CMak
e
bug relate
d
t
o
T
e
stQ
P
X
.
c loca
t
ion
commit
|
commitdiff
|
tree
2013-06-16
Jeff Hamm
o
nd
fi
x
ed a
t
ypo (
u
nclosed
b
racket) that cau
s
e CM
a
ke to
.
.
.
commit
|
commitdiff
|
tree
2013-05-30
Mark
A
b
rah
a
m
New patch rele
a
se 4
.
6
.
2
commit
|
commitdiff
|
tree
2013-05-26
Mich
a
el Shirts
Fi
x
of memory leak
commit
|
commitdiff
|
tree
2013-05-07
Mark Abra
h
am
Fix ex
t
ant re
f
erences to form
e
r
G
PL licen
s
ing
commit
|
commitdiff
|
tree
2013-04-26
Michael
S
h
irts
Fixing a problem
w
ith dh/dl 1
-
4
interactions
commit
|
commitdiff
|
tree
2013-04-26
Mark Abraham
U
pdate l
i
nking t
o
MKL an
d
d
ocument
s
a
me
commit
|
commitdiff
|
tree
2013-04-19
Mark A
b
raham
v-r
e
scale works with t
a
u
-
t >= 0
commit
|
commitdiff
|
tree
2013-03-11
Mark
Abraham
Added install guide section for BLAS/
L
A
PACK
commit
|
commitdiff
|
tree
2013-03-05
Mark A
b
r
aham
Warn
i
f X1
1
wa
s
not
fo
u
nd
and t
h
e
use
r
wanted it
commit
|
commitdiff
|
tree
2013-03-05
M
a
rk Ab
r
aham
fix broken things in mkhtml
commit
|
commitdiff
|
tree
2013-02-26
Ma
r
k
Abraham
Un
c
rustified code
changes since
4
.
6
commit
|
commitdiff
|
tree
2013-02-20
Mark Abrah
a
m
M
e
rge release-4-5-patches into release-4-6
commit
|
commitdiff
|
tree
2013-02-18
Rolan
d
Sch
u
lz
Issue errors/wa
r
ning
s
for IC
C
befo
r
e 12
.
0
.
0
commit
|
commitdiff
|
tree
2013-02-15
Mi
c
hael Shirts
bugfix f
o
r md-vv + nose-ho
o
ve
r
+ (nstcalcenergy
>
n
st
t
cou
p
le)
commit
|
commitdiff
|
tree
2013-02-15
M
a
rk Abraham
U
s
e explicit kernel poi
n
ter ty
p
ecasts
commit
|
commitdiff
|
tree
2013-02-15
Mark Abraha
m
B
um
p
s
hared object
v
er
s
ion to 7
commit
|
commitdiff
|
tree
2013-02-15
Peter Kass
o
n
Unwinds
f
l
ag dependenci
e
s
i
n g_or
d
er
.
commit
|
commitdiff
|
tree
2013-02-13
Mark Abraham
Fi
x
code bug with thread
-
MPI o
n
PowerPC
w
it
h
xlc
commit
|
commitdiff
|
tree
2013-02-13
Mark Ab
r
ah
a
m
More de
s
criptive Verlet kernel
macro parameter nam
e
s
commit
|
commitdiff
|
tree
2013-02-13
Mark Abraham
Fix
and add Verle
t
k
ernel error messages
commit
|
commitdiff
|
tree
2013-02-13
Ma
r
k Abrah
a
m
Re-
g
en
e
rated group kernels
commit
|
commitdiff
|
tree
2013-02-09
Mark Abr
a
ham
T
y
po fix
commit
|
commitdiff
|
tree
2013-02-05
M
ark Abraham
Documented what GM
X
_CPU_AC
C
E
L
ERATION really means
commit
|
commitdiff
|
tree
2013-01-17
Mar
k
Abrah
a
m
Updating the
shell com
p
letion fi
l
es
commit
|
commitdiff
|
tree
2013-01-17
Mark
A
braha
m
Gromacs install guide upda
t
es
.
commit
|
commitdiff
|
tree
2013-01-17
Mark
A
braham
Merge bra
n
ch 'release-4-5-
p
a
t
ches' into
r
elea
s
e-4-6
commit
|
commitdiff
|
tree
2013-01-16
Roland Schulz
Don't cach
e
${F
F
T
W}_HAVE_(S
I
MD|
A
VX)
commit
|
commitdiff
|
tree
2013-01-16
Erik
Lindahl
Fixed G
B
interactions for r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-01-16
Berk Hess
split off pi
c
k_nbnxn_resource fr
o
m nbnx
n
_
p
ic
k
_
n
bnxn
commit
|
commitdiff
|
tree
2013-01-16
M
ark Abraham
Quiet stderr o
u
tput, particu
l
arly for
multi-simula
t
ion
s
commit
|
commitdiff
|
tree
2013-01-16
Michael Shirts
fixes issu
e
s with p
r
essu
r
e control
a
nd i
n
f
r
e
quent evaluation
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
Added check for valid wall_atomtype in
.
mdp
commit
|
commitdiff
|
tree
2013-01-14
Ma
r
k Ab
r
aham
Added fa
t
al er
r
or for con
s
traints + L-BFGS minimizer
commit
|
commitdiff
|
tree
2013-01-14
M
a
rk Abrah
a
m
Hid nbnxn kernel name
s
behind a
l
o
okup function
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
Updated code checks
w
it
h
dista
n
ce restrain
t
s
commit
|
commitdiff
|
tree
2013-01-13
M
a
rk Abraham
Fixing trj
c
o
n
v -
s
ub
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
No
t
i
ng
t
hat a
n
d
w
hy gmxdump -s -sys is broken
commit
|
commitdiff
|
tree
2013-01-13
Mark Abraham
Man
a
ge BlueGene/Q c
o
nfigura
t
ion
commit
|
commitdiff
|
tree
2013-01-13
Mark
Abrah
a
m
Re-organize BlueGene toolcha
i
n
f
iles
commit
|
commitdiff
|
tree
2013-01-13
Mark
A
brah
a
m
C
h
anged defa
u
lts fo
r
bui
l
d
ing shared libraries
commit
|
commitdiff
|
tree
2012-12-20
Michael Shirts
F
ix for
t
h
e
pressure in MTTK with constraints +
d
i
spers
i
on
commit
|
commitdiff
|
tree
2012-12-19
Mark Abraham
Rem
o
v
e
d orphan file
commit
|
commitdiff
|
tree
2012-12-19
Mark A
b
r
aham
Avoid u
s
ing
u
ndefin
e
d C
M
ake variables
commit
|
commitdiff
|
tree
2012-12-13
Mark Abr
a
ham
Fix typo
commit
|
commitdiff
|
tree
2012-12-06
Mark Abrah
a
m
Apply LGPL lic
e
nse to new fi
l
es
commit
|
commitdiff
|
tree
2012-12-06
Mark Abraham
Updates for insta
l
l gui
d
e
commit
|
commitdiff
|
tree
2012-12-06
M
i
chael
Shirts
Removing (inaccurat
e
)
virial temperature c
a
lc
.
commit
|
commitdiff
|
tree
2012-12-06
Mark Abraham
Eliminate confusio
n
fr
o
m pkgco
n
fig FFTW detecti
o
n
commit
|
commitdiff
|
tree
2012-12-05
Christo
p
h Jungha
n
s
fixed obsolete
gmx_fata
l
in OpenMM
bu
i
ld
commit
|
commitdiff
|
tree
next