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Merge branch release-2016
2016-09-16
Berk
H
e
ss
Me
r
ge
b
r
anch release-2016
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
M
ad
e
distance r
e
straints
w
ork with t
h
re
a
ds
a
nd
DD
commit
|
commitdiff
|
tree
2016-09-13
Be
r
k Hess
Moved expa
n
ded en
s
emble history to pointer
i
n
t_state
commit
|
commitdiff
|
tree
2016-09-13
Berk He
s
s
Change ED and swapsta
t
e
t
o pointe
r
s in t_state
commit
|
commitdiff
|
tree
2016-09-12
Be
r
k Hess
Add
c
onst
to thre
a
d-MPI f
u
nction
s
commit
|
commitdiff
|
tree
2016-09-10
Ber
k
Hess
R
e
move continuation from c
o
nvert_tpr
commit
|
commitdiff
|
tree
2016-09-06
Berk H
e
ss
Fix bug with conjugate-gradient an
d
Ope
n
MP
commit
|
commitdiff
|
tree
2016-09-06
Berk Hess
C
o
nsolidat
e
MD algorithm atom se
t
up
commit
|
commitdiff
|
tree
2016-09-05
Be
r
k Hess
Re-enable flexible constrai
n
t
s
with DD
commit
|
commitdiff
|
tree
2016-09-04
Berk Hess
Merge branch release-2016
commit
|
commitdiff
|
tree
2016-09-03
Ber
k
H
e
ss
Clean
u
p PME flag
s
v
ari
a
ble u
s
e
commit
|
commitdiff
|
tree
2016-09-02
Berk
H
ess
Merge bra
n
c
h
r
e
l
ease
-
5-1
i
n
t
o r
e
lease-
2
01
6
commit
|
commitdiff
|
tree
2016-09-02
Berk Hess
Fix Parr
i
nello-
R
a
h
man wit
h
nstpcou
p
le>1
commit
|
commitdiff
|
tree
2016-08-30
Berk
H
ess
Make virial reproducib
l
e
commit
|
commitdiff
|
tree
2016-08-27
B
e
rk
H
ess
Red
u
ce ro
u
nding
e
rror
s
i
n
SETTLE
commit
|
commitdiff
|
tree
2016-08-24
Berk
H
e
ss
Fix Ewald surface+3DC
c
o
r
rections
commit
|
commitdiff
|
tree
2016-08-24
Berk Hess
Merge branch relea
s
e-5-1 into rel
e
a
se-
2
016
commit
|
commitdiff
|
tree
2016-08-23
B
erk H
e
s
s
Remove var
i
abl
e
prec
i
sion gro writing
commit
|
commitdiff
|
tree
2016-08-17
Berk Hess
F
i
xed open
i
ng of wall
tabl
e
files
commit
|
commitdiff
|
tree
2016-08-15
B
e
rk Hess
Reduc
e
FE pair-
l
ist memory usage
commit
|
commitdiff
|
tree
2016-08-10
Be
r
k H
e
ss
Fix d
e
adlock with thread-MPI
commit
|
commitdiff
|
tree
2016-08-09
Berk
H
ess
Fix
t
win-cutof
f
for GPU
L
J pot-switch
commit
|
commitdiff
|
tree
2016-07-07
Berk Hess
Relax
p
u
ll
P
BC check
commit
|
commitdiff
|
tree
2016-07-05
Berk
Hess
Add checks
for
too much memory in g_nmeig
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add g
r
omp
p
check for pull
g
roup
commit
|
commitdiff
|
tree
2016-06-28
Berk Hess
Pro
p
erly
r
e
s
et CUDA appli
c
ation clocks
commit
|
commitdiff
|
tree
2016-06-27
Berk He
s
s
Use
s
ysconf(_
S
C
_NPROCESSORS_O
N
LN)
commit
|
commitdiff
|
tree
2016-06-26
Berk Hess
Fix vsite bu
g
with M
P
I
+
Open
M
P
commit
|
commitdiff
|
tree
2016-06-24
Be
r
k Hess
Fi
x
Verle
t
buffer calculation
with nstlist
=
1
commit
|
commitdiff
|
tree
2016-06-23
Ber
k
Hess
More
a
ccurate G
P
U list splitting
commit
|
commitdiff
|
tree
2016-06-22
Berk
H
e
ss
Upda
t
ed OpenCLTODOList
.
t
x
t
commit
|
commitdiff
|
tree
2016-06-22
Be
r
k Hess
Add nbnxn pair-
l
i
st
r
e
balancing
commit
|
commitdiff
|
tree
2016-06-22
Berk H
e
ss
Re
m
o
ve OpenMP
ov
e
r
head at
h
igh paralleli
z
atio
n
commit
|
commitdiff
|
tree
2016-06-22
Berk He
s
s
Corr
e
ct GPU
p
a
ir e
s
timate for l
i
st split
t
ing
commit
|
commitdiff
|
tree
2016-06-21
Berk Hess
F
i
x bug wit
h
fbposres+MPI+OpenMP
commit
|
commitdiff
|
tree
2016-06-20
Berk H
e
ss
I
n
creased tpx_incompati
b
le_version to 30
commit
|
commitdiff
|
tree
2016-06-19
Be
r
k
Hess
R
e
move warnings on ch
e
ckpoint mismatch
commit
|
commitdiff
|
tree
2016-06-17
B
e
rk Hes
s
Remov
e
std::thread::hardw
a
re
_
concurre
n
cy
(
)
commit
|
commitdiff
|
tree
2016-06-14
Berk Hess
Fix OpenCL err
o
r
w
i
th empty domains
commit
|
commitdiff
|
tree
2016-06-13
Berk Hess
Handle
constrai
n
t errors with EM
commit
|
commitdiff
|
tree
2016-06-07
Berk
Hess
F
ix
data r
a
ce in hwinfo wit
h
thr
e
ad-
M
PI
commit
|
commitdiff
|
tree
2016-06-03
B
e
r
k
Hess
Hand
l
e pa
r
t
i
ally frozen and c
o
nstrained atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk
Hess
Repos
i
tion
n
bnxn f
i
ller pa
r
ticles
commit
|
commitdiff
|
tree
2016-05-31
Berk H
e
ss
Avoid n
u
merical overflo
w
with overlapping
atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Add check for f
i
nite ene
r
gie
s
commit
|
commitdiff
|
tree
2016-05-30
Ber
k
Hess
Ad
d
gromp
p
check for unboun
d
at
o
ms
commit
|
commitdiff
|
tree
2016-05-23
Ber
k
Hess
F
i
x bug in v-re
s
cale thermo
s
tat
& rep
l
ica
exchange
commit
|
commitdiff
|
tree
2016-05-10
B
erk
H
ess
O
ptimized
the vsite t
h
r
e
ading
commit
|
commitdiff
|
tree
2016-05-10
Be
r
k Hess
Fix CUDA shmem bu
g
commit
|
commitdiff
|
tree
2016-05-10
Berk
H
ess
Support cmap
w
ith QMMM
commit
|
commitdiff
|
tree
2016-05-08
Ber
k
Hess
U
p
date
m
drun termination info
commit
|
commitdiff
|
tree
2016-05-06
B
e
r
k
Hess
OpenMP
parallelizati
o
n for pull
commit
|
commitdiff
|
tree
2016-04-20
Berk He
s
s
Fix pull legend
w
ith external potential
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Allow rcoulomb>rv
d
w with
PME
commit
|
commitdiff
|
tree
2016-04-19
Berk
H
ess
B
r
oadcas
t
pull external po
t
ential
provid
e
r str
i
n
g
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Fix gm
x
hbond group over
l
a
p
chec
k
commit
|
commitdiff
|
tree
2016-04-14
Berk
H
ess
Add QMMM
ch
e
cks
commit
|
commitdiff
|
tree
2016-04-03
Ber
k
Hess
Correct
n
rdf for
1
D/2D systems
commit
|
commitdiff
|
tree
2016-03-31
B
e
rk Hess
Fix i
n
cludes
in
r
e
adpull
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
B
erk Hes
s
Add optio
n
f
or exte
r
nal pull p
o
t
e
nti
a
l
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
C
o
rrect mdrun tMPI (non-)parallel error me
s
s
a
ge
commit
|
commitdiff
|
tree
2016-03-26
Berk Hess
Add r
e
al/SIMD
t
emplate for LJ-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk Hes
s
Avoid asserti
o
n failure
i
n
pme
_
load
b
al_
d
o
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Ma
k
e
g
mx van
h
ov
e
work without PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ combinatio
n
r
u
le kerne
l
s for CUDA
commit
|
commitdiff
|
tree
2016-03-21
Berk Hess
Moved
p
ull initial
i
z
a
tion back to mdrunner
commit
|
commitdiff
|
tree
2016-03-18
Be
r
k Hess
Fix
n
o
n-
n
ormaliz
a
tion of FF
T
autocorr
commit
|
commitdiff
|
tree
2016-03-14
B
e
rk Hess
Remove re
s
tricti
o
n on dihdraltypes
o
rder
commit
|
commitdiff
|
tree
2016-03-12
Berk Hess
Split
off Fermi
k
e
r
n
e
l fro
m
C
U
D
A kernel
commit
|
commitdiff
|
tree
2016-03-09
Berk Hess
F
i
x Ewald
3
DC dipole
w
it
h
Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk H
e
s
s
Co
n
verted csettle
(
) to use real/SimdReal te
m
plate
commit
|
commitdiff
|
tree
2016-03-03
Berk H
e
ss
Use SIMD transpose
scatter in
bondeds
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
U
s
e rvec4 f
o
r
listed force buffer
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
R
e
move epsfa
c
from GP
U
ker
n
el
i
nner-loops
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Minor code reord
e
ring in GPU kernels
commit
|
commitdiff
|
tree
2016-02-26
Berk Hess
F
i
x compilation with
Simd
4
Float, without Simd
4
D
oubl
e
commit
|
commitdiff
|
tree
2016-02-19
Berk Hess
Fix
exc
e
s
sive list spli
t
ting
commit
|
commitdiff
|
tree
2016-02-17
Berk
H
e
ss
Rename
d
nbnxn static co
n
st ints
commit
|
commitdiff
|
tree
2016-02-11
Be
r
k Hess
Add SIMD ver
s
io
n
of pbc_dx_aiuc
commit
|
commitdiff
|
tree
2016-02-09
Berk Hess
Replaced nb
n
xn search+
g
rid simd macros
commit
|
commitdiff
|
tree
2016-02-07
Berk
H
e
ss
Fix incorrect cmap
parsing
commit
|
commitdiff
|
tree
2016-02-05
Berk Hess
Fix inc
o
rrect c
m
ap parsing
commit
|
commitdiff
|
tree
2016-02-03
Berk Hes
s
Re
p
laced lite
r
als i
n
nbnxn lists by ints
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
F
ix mdrun re
m
oving Verlet buffe
r
with EM
commit
|
commitdiff
|
tree
2016-02-03
B
e
r
k Hess
F
i
x SET
T
LE error
handling
commit
|
commitdiff
|
tree
2016-01-29
B
e
rk
H
ess
Ad
d
ed docu
m
entatio
n
for pme grid indexing
commit
|
commitdiff
|
tree
2016-01-29
Ber
k
H
ess
F
i
x TPI
i
g
n
oring PME m
e
sh c
o
ntrib
u
tion
s
.
commit
|
commitdiff
|
tree
2016-01-29
B
e
rk Hes
s
Upda
t
e -ntom
p
_p
m
e -n
p
me check
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Add check for double pertur
b
ation
commit
|
commitdiff
|
tree
2016-01-29
Ber
k
Hes
s
Fix
LIN
C
S triangle cons
t
raint thread
issu
e
commit
|
commitdiff
|
tree
2016-01-28
Berk
H
e
s
s
Update pair-
l
ist buffer man
u
al
commit
|
commitdiff
|
tree
2016-01-24
Berk
He
s
s
Fix exact continuation from non-en
e
r
gy steps
commit
|
commitdiff
|
tree
2016-01-24
Berk
H
ess
F
i
x
energy file continu
a
tion wi
t
h
md-vv
commit
|
commitdiff
|
tree
2016-01-24
Berk H
e
ss
Fix energy averag
e
wit
h
c
o
nti
n
u
ati
o
n
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
Fix P
M
E lo
a
d balan
c
in
g
skipp
i
ng a s
e
tup
commit
|
commitdiff
|
tree
2015-12-29
Be
r
k Hess
Correct
v
e
ctor
c
heck o
f
gm
x
check
commit
|
commitdiff
|
tree
2015-12-27
Berk H
e
s
s
Re
o
rg
a
nized
d
o
mdec
i
nitializatio
n
commit
|
commitdiff
|
tree
2015-12-20
Be
r
k H
e
s
s
Merg
e
re
l
ease-5-1 into master
commit
|
commitdiff
|
tree
2015-12-19
Berk
H
e
ss
Br
i
n
g
p
erforma
n
ce e
s
timat
i
on up
to date
commit
|
commitdiff
|
tree
2015-12-17
Berk Hess
Remo
v
ed
t
o
p
ology pointers from DD str
u
ct
commit
|
commitdiff
|
tree
next