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Fix ref error in constraint pull code
2014-06-19
Rol
a
nd Schulz
Fix ref
e
rror in constraint pu
l
l co
d
e
commit
|
commitdiff
|
tree
2014-06-18
Erik Lindahl
F
ixed CMake 2
.
8
.
12+ CUDA
d
ylib
b
u
g
s and warnings
on
.
.
.
commit
|
commitdiff
|
tree
2014-06-18
Berk Hess
Fixed sign error in posr
e
s dvdl
commit
|
commitdiff
|
tree
2014-06-17
Car
l
o Camilloni
F
ix a Replic
a
Exchange out
p
u
t
problem
commit
|
commitdiff
|
tree
2014-06-17
Roland Sc
h
ulz
F
i
x that s
k
ip
p
i
n
g fa
i
l
s if ta
r
g
e
t is 2nd frame
commit
|
commitdiff
|
tree
2014-06-17
Berk Hes
s
Removed rounding is
s
ue
i
n n
b
nxn Ewald table
commit
|
commitdiff
|
tree
2014-06-14
Ber
k
Hess
Fixed
P
M
E bug with
#
Op
e
nMP-threads a
l
a
rge prime
commit
|
commitdiff
|
tree
2014-06-14
Erik Lindahl
Make su
r
e figure legends are a
d
apted to xmgr/xmgrace
commit
|
commitdiff
|
tree
2014-06-13
Berk He
s
s
Ch
a
nged a
p
pendi
n
g file
n
ame error
message
commit
|
commitdiff
|
tree
2014-06-13
D
a
vid van der
Spoel
F
ix memory-usa
g
e error i
n
g
_chi
commit
|
commitdiff
|
tree
2014-06-13
Eri
k
L
indahl
Fo
r
ce g_bond
t
o us
e
s
t
ructure file
commit
|
commitdiff
|
tree
2014-06-12
Erik Lin
d
ahl
Added du
m
m
y
ma
s
s for c
h
armm TYR ar
o
matic vsites
commit
|
commitdiff
|
tree
2014-06-12
B
erk Hess
F
ixed perturbe
d
wall inter
a
ctions
commit
|
commitdiff
|
tree
2014-06-11
R
ossen Apostolov
Mapped
H
IS1 to HSD in charmm
2
7
.
commit
|
commitdiff
|
tree
2014-06-11
Erik Linda
h
l
Avoid writing
x
vgr formattin
g
with -xvg
n
o
ne
commit
|
commitdiff
|
tree
2014-06-10
Er
i
k
L
in
d
ahl
Process negative s
i
g
m
a correctly with combrule 2
o
r 3
commit
|
commitdiff
|
tree
2014-06-09
Rosse
n
Apostolov
I
ssue a warn
i
ng for us
i
ng
gm
x
_rms -
p
rev with la
r
g
e
.
.
.
commit
|
commitdiff
|
tree
2014-06-09
Rosse
n
Ap
o
s
tolov
Fix
e
d typo in description of con
v
ersion factors
.
commit
|
commitdiff
|
tree
2014-06-05
Berk Hess
Fix
c
onstraint vi
r
i
al
wit
h
multiple time stepping
commit
|
commitdiff
|
tree
2014-06-04
Rossen
Aposto
l
o
v
Updated C-/N-
t
ermin
a
l pa
r
tial charges in
A
m
ber03
.
ff
.
commit
|
commitdiff
|
tree
2014-05-22
R
o
ssen Apostolo
v
Normal modes
don't work c
u
rrently with virt
u
al si
t
es
.
.
.
commit
|
commitdiff
|
tree
2014-05-22
Mark Ab
r
aham
Add fat
a
l errors
fo
r
VV and twin-range MTS
commit
|
commitdiff
|
tree
2014-05-20
Justi
n
Lemkul
Improvements to
t
he g_lie help descri
p
tion
.
commit
|
commitdiff
|
tree
2014-05-20
R
o
sse
n
Apostolo
v
Added a note about
using
direct
i
o
n-periodic
p
ulling
.
commit
|
commitdiff
|
tree
2014-05-20
Rossen Apost
o
lov
A
dded a
n
ote about
unsupported Verlet cut
o
ff + Buckin
g
ham
.
commit
|
commitdiff
|
tree
2014-05-09
Alexey Shv
e
tsov
Fi
x
clang 3
.
5 w
a
rn
i
ngs
r
egarding *abs*
commit
|
commitdiff
|
tree
2014-04-29
Berk Hess
Removed truncati
o
n
of nrdf
in v-rescale therm
o
s
t
at
commit
|
commitdiff
|
tree
2014-04-21
Michael Shirts
Issue warnings for po
t
e
n
tial switc
h
w/o
d
efini
n
g
s
witch
.
.
.
commit
|
commitdiff
|
tree
2014-04-07
Mark Abraham
Fix inva
l
id dereference in g_tu
n
e_pme
commit
|
commitdiff
|
tree
2014-04-07
Erik Lind
a
hl
Make sure wat
e
r optimizat
i
o
n
is d
i
sable
d
for es
o
te
r
ic
.
.
.
commit
|
commitdiff
|
tree
2014-03-23
Berk Hes
s
Fixed bug in paral
l
el v/f
c
ons
t
r
aining
commit
|
commitdiff
|
tree
2014-03-14
Carsten Ku
t
zner
A
void
cross product
w
ith zer
o
vector in rotational
.
.
.
commit
|
commitdiff
|
tree
2014-03-02
Teemu Murtola
Fix incorrect
g
rid cell size
i
n
g
_sas -nopbc
commit
|
commitdiff
|
tree
2014-03-01
Mark Abraham
Add fa
t
al error
for Ande
r
sen+con
s
t
rai
n
ts+DD
commit
|
commitdiff
|
tree
2014-02-24
Mark Ab
r
ah
a
m
P
e
rmit
warning-free use of Andersen th
e
r
mostat
commit
|
commitdiff
|
tree
2014-02-20
Christoph J
u
ngh
a
ns
added gmx_is_{sin
g
le,double}_precision
commit
|
commitdiff
|
tree
2014-02-20
Roland Sc
h
ulz
Fix alig
n
ed store to una
l
igned me
m
o
ry
commit
|
commitdiff
|
tree
2014-02-20
Mark Abraham
avoid md
r
un crash
w
hen
r
dtscp
i
s not supported
commit
|
commitdiff
|
tree
2014-02-08
Mark Abraham
Issue fat
a
l errors rather than use
b
r
o
k
en shell code
commit
|
commitdiff
|
tree
2014-01-28
Christoph Junghans
cmake: added FF
T
W_UR
L
to allow e
a
sy offline build
commit
|
commitdiff
|
tree
2014-01-28
Mark A
b
raham
Unify logic for
t
imi
n
g
c
ount
s
commit
|
commitdiff
|
tree
2014-01-28
Szilárd Páll
clarified OpenMP-related things in m
d
run help/man
commit
|
commitdiff
|
tree
2014-01-09
Dav
i
d van der Spoel
Fixed precision
i
n
thermal e
x
p
an
s
io
n
coeffic
i
ent calc
.
commit
|
commitdiff
|
tree
2013-12-26
Ca
r
s
t
e
n
Ku
t
z
ner
Pass on default value of r
a
dstep in
m
ake_edi
commit
|
commitdiff
|
tree
2013-12-25
Carste
n
Kutzner
Essen
t
ial dynamics: move bN
e
ed
D
oEd
s
am evaluation
to
.
.
.
commit
|
commitdiff
|
tree
2013-12-23
C
arst
e
n Kut
z
ner
Fixe
d
essential dynamics (ED) cont
i
nuati
o
n from
.
cpt
.
.
.
commit
|
commitdiff
|
tree
2013-12-19
Mark Abr
a
ham
Fix non
-
criti
c
al typ
o
i
n
#
ifdef GMX_OMP
E
N
_
MP
commit
|
commitdiff
|
tree
2013-11-19
Szi
l
árd P
á
ll
Fix
D
D
load balancing
b
u
g
with GPU sharing
commit
|
commitdiff
|
tree
2013-11-13
Mark Abrah
a
m
Fix
m
inor things bef
o
re
r
e
l
ease
commit
|
commitdiff
|
tree
2013-11-13
Szilard P
a
ll
Cl
a
rified GP
U
se
l
ec
t
ion output and
mdrun help
commit
|
commitdiff
|
tree
2013-11-07
Berk Hess
correc
t
ed
dynamic load balan
c
i
n
g
w
he
n
s
h
aring GPUs
commit
|
commitdiff
|
tree
2013-11-05
Berk
Hess
GPU detection is done once per physical node
commit
|
commitdiff
|
tree
2013-11-05
B
erk Hess
remove
d
(harmless
)
left-ove
r
i
n
nbn
x
n S
I
MD
k
e
rnels
commit
|
commitdiff
|
tree
2013-10-31
M
ark Abra
h
a
m
Rename GMX_IS_* to G
M
X_TARGET
_
*
commit
|
commitdiff
|
tree
2013-10-29
Berk He
s
s
cor
r
ect
e
d volum
e
with
s
e
r
ial
N
PT
r
ep
l
ica exchange
commit
|
commitdiff
|
tree
2013-10-28
Berk
Hess
imp
r
oved the nbnxn buffer size estimate with G
P
U
s
commit
|
commitdiff
|
tree
2013-10-18
Mark
Abr
a
ham
BlueGe
n
e/Q Verlet
c
ut-
o
ff scheme kernels
commit
|
commitdiff
|
tree
2013-10-18
M
ark
A
braham
Call at
o
m
i
cs from TestAtomic
.
c
commit
|
commitdiff
|
tree
2013-10-18
Roland Schulz
Fix tMPI_Atomic_
m
e
mory
_
barrier for MIC
commit
|
commitdiff
|
tree
2013-10-17
Ma
r
k Abraham
Fix typo in g_membed docume
n
tation
commit
|
commitdiff
|
tree
2013-10-17
R
o
land
S
chulz
Fix SIMD C refere
n
ce
n
bnxn kernels
commit
|
commitdiff
|
tree
2013-10-17
Michael Shirts
R
e
starting from checkpoint no longer reinitia
l
izes
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Be
r
k Hess
a
v
oid divis
i
o
n
by ze
r
o
in SIMD angles a
n
d dihedrals
commit
|
commitdiff
|
tree
2013-10-16
Micha
e
l
S
hirts
turni
n
g off
expanded ensemble for all integrator
s
but
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Berk Hes
s
fixed a half bin misalignment i
n
g
m
x_vanhove -or
commit
|
commitdiff
|
tree
2013-10-16
Michael Shirts
Fi
x
es a proble
m
with pair type
2 int
e
ractions with
.
.
.
commit
|
commitdiff
|
tree
2013-10-15
Szilard Pal
l
m
ake use of CUDA strea
m
p
r
iorities
commit
|
commitdiff
|
tree
2013-10-11
Berk
Hess
introd
u
ced general 4-wide SIMD support
commit
|
commitdiff
|
tree
2013-10-02
Berk H
e
ss
Fixes reaction fie
l
d fr
e
e energy
b
u
g
commit
|
commitdiff
|
tree
2013-10-01
Mark Abraham
Silence clang wa
r
n
i
ngs
commit
|
commitdiff
|
tree
2013-09-29
Sz
i
la
r
d Pa
l
l
allow c
o
mpi
l
ation to
o
ptimize
f
o
r
CUDA compute c
a
p
.
.
.
commit
|
commitdiff
|
tree
2013-09-29
Jarvi
s
t Moore Fr
o
st
C
o
r
r
ec
t
ed info text
.
-ce
n
ter --> -bo
x
cen
t
er
commit
|
commitdiff
|
tree
2013-09-27
Manuel
Luitz
F
ixed limit
a
tions in g_clus
t
er
commit
|
commitdiff
|
tree
2013-09-26
Michael
S
hirts
log
i
c fix for free energies wi
t
h
mdrun -re
r
un
commit
|
commitdiff
|
tree
2013-09-26
Chr
i
stoph
Junghans
Drop
md5sum chec
k
for
GMX_BUILD_OWN_FFT
W
commit
|
commitdiff
|
tree
2013-09-25
Erik Lindahl
Fix
bug in (l
o
ng)
n
e
ighborlist SIM
D
padding wh
e
n adding
.
.
.
commit
|
commitdiff
|
tree
2013-09-24
Berk Hess
o
ptimized generic SIMD i
n
vsqrt
commit
|
commitdiff
|
tree
2013-09-21
Berk Hess
fix
e
d mult
i
ple distanc
e
re
s
t
rai
n
ts
wi
t
h OpenMP
commit
|
commitdiff
|
tree
2013-09-20
Mark Abra
h
am
Described another way
g
_t
u
n
e_pme m
i
ght reasonably fail
commit
|
commitdiff
|
tree
2013-09-20
Mark Ab
r
aham
Fix
to
t
a
l
tim
e
m
e
asureme
n
t with separate
P
ME nodes
commit
|
commitdiff
|
tree
2013-09-19
Mark Abrah
a
m
Fixed reading history_t
f
ro
m
checkpoin
t
commit
|
commitdiff
|
tree
2013-09-19
Mark
Abraham
Fixed g_tune_pme assum
p
t
io
n
t
ha
t
MPI is a
v
ailable
commit
|
commitdiff
|
tree
2013-09-18
Be
r
k He
s
s
made
f
ree
e
nergy PME ke
r
nel 40% faster
commit
|
commitdiff
|
tree
2013-09-16
Michael S
h
irts
Fixing manual for sc-
c
ou
l
d
escription
.
commit
|
commitdiff
|
tree
2013-09-16
Berk H
e
s
s
m
d
run
w
ithout OpenMP wit
h
threa
d
-MPI no
w
uses a
l
l
c
or
e
s
commit
|
commitdiff
|
tree
2013-09-13
Be
r
k
H
ess
corrected grompp
c
onstraint/
D
OF warning with vsites
commit
|
commitdiff
|
tree
2013-08-25
M
ark Ab
r
a
h
am
Split
u
p
Verlet S
I
MD kernels for faster compi
l
ation
commit
|
commitdiff
|
tree
2013-08-25
M
ark Abraham
Fix detection a
n
d suggestion
in
g
mx_cpuid fo
r
IBM QPX
commit
|
commitdiff
|
tree
2013-08-25
Berk Hess
introdu
c
e
d nbnxn da
t
a
s
t
r
ucture fo
r
bound
i
ng boxes
commit
|
commitdiff
|
tree
2013-08-25
Mark Abraham
F
i
x
e
s f
o
r Bluegene/Q
commit
|
commitdiff
|
tree
2013-08-25
Mark
Abra
h
am
Consolida
t
ed NBNx
N
SIMD kerne
l
u
tility routines
commit
|
commitdiff
|
tree
2013-08-25
Mar
k
Abraham
Fix minor
w
allcycle ou
t
put is
s
ues
commit
|
commitdiff
|
tree
2013-08-25
Mark
A
b
raham
Fixed GMX_DD_DUMP_
G
RI
D
commit
|
commitdiff
|
tree
2013-08-20
B
e
rk Hess
fixed parallel normal
m
odes w
i
th
PME
commit
|
commitdiff
|
tree
2013-08-05
Ma
r
k
Abraham
F
i
x
ed reference SIM
D
code to work with MSVC
commit
|
commitdiff
|
tree
2013-08-01
Mark
A
br
a
ham
R
efactored preparati
o
n of
b
u
ffer fo
r
N
BNxN table loads
commit
|
commitdiff
|
tree
2013-08-01
C
a
rsten
K
utzner
Properly
f
inalize MPI on mdrun
-ver
s
ion
.
Fixes #1313
commit
|
commitdiff
|
tree
2013-07-25
Just
i
n
L
emkul
Updated
dlist
.
c to recognize more at
o
m names
.
commit
|
commitdiff
|
tree
2013-07-25
M
a
r
k
Ab
r
aham
Find m
k
l
.
h o
n
more icc versions
commit
|
commitdiff
|
tree
2013-07-25
Mark Abraham
Up
d
ate managem
e
nt of
l
i
near algebra librar
i
es
commit
|
commitdiff
|
tree
next