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Add flags for optional t_atoms entries
2016-09-29
B
e
rk Hess
Add flags for optional t_atoms entries
commit
|
commitdiff
|
tree
2016-09-22
Be
r
k Hess
Fix gcc
w
a
rning in AlignedAl
l
ocator
commit
|
commitdiff
|
tree
2016-09-20
Berk Hess
Remove
sta
t
e
du
p
li
c
ation i
n
serial r
u
ns
commit
|
commitdiff
|
tree
2016-09-16
Berk He
s
s
Merge branch release-2016
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
Made distan
c
e r
e
stra
i
nts work with thre
a
ds and DD
commit
|
commitdiff
|
tree
2016-09-13
Berk Hess
Moved e
x
panded
e
n
sem
b
le history to
point
e
r
i
n t_
s
t
a
te
commit
|
commitdiff
|
tree
2016-09-13
Berk Hess
Change ED and swapstate to pointers in t
_
state
commit
|
commitdiff
|
tree
2016-09-12
Be
r
k Hess
A
dd con
s
t to
t
h
rea
d
-MPI func
t
ions
commit
|
commitdiff
|
tree
2016-09-10
Berk He
s
s
Remove continuat
i
on from convert_tpr
commit
|
commitdiff
|
tree
2016-09-06
Berk Hess
Fix bug
w
ith
conjugate-gradien
t
and OpenMP
commit
|
commitdiff
|
tree
2016-09-06
Berk Hess
Co
n
solidate MD algorit
h
m atom setup
commit
|
commitdiff
|
tree
2016-09-05
B
e
r
k He
s
s
R
e
-enable flexible constrain
t
s wit
h
DD
commit
|
commitdiff
|
tree
2016-09-04
B
erk Hess
Mer
g
e branch release-
2
016
commit
|
commitdiff
|
tree
2016-09-03
Berk Hess
C
lean up PME flag
s
varia
b
le use
commit
|
commitdiff
|
tree
2016-09-02
Berk H
e
ss
M
e
r
ge bran
c
h release-5-
1
into
r
el
e
ase-2016
commit
|
commitdiff
|
tree
2016-09-02
Be
r
k Hess
Fix Parrinell
o
-Rah
m
an
w
i
t
h nstpcouple>1
commit
|
commitdiff
|
tree
2016-08-30
Berk H
e
ss
Make virial repr
o
d
u
cible
commit
|
commitdiff
|
tree
2016-08-27
Berk Hess
Reduce
rou
n
ding errors i
n
SETTLE
commit
|
commitdiff
|
tree
2016-08-24
Berk Hess
Fix Ew
a
ld s
u
rface+3DC c
o
r
r
ecti
o
n
s
commit
|
commitdiff
|
tree
2016-08-24
Be
r
k He
s
s
Merge branc
h
release-5-1 int
o
releas
e
-
2
016
commit
|
commitdiff
|
tree
2016-08-23
Ber
k
Hess
Rem
o
v
e
variabl
e
precision gro writing
commit
|
commitdiff
|
tree
2016-08-17
Berk Hess
F
i
xed
opening o
f
wall table files
commit
|
commitdiff
|
tree
2016-08-15
Berk Hess
R
educe FE pair-list memory usa
g
e
commit
|
commitdiff
|
tree
2016-08-10
Ber
k
Hess
Fix deadloc
k
with thread
-
M
PI
commit
|
commitdiff
|
tree
2016-08-09
B
e
rk Hess
F
i
x
twi
n
-
c
u
t
off
f
or GPU LJ pot-s
w
itch
commit
|
commitdiff
|
tree
2016-07-07
Berk Hess
R
elax p
u
ll PBC check
commit
|
commitdiff
|
tree
2016-07-05
Berk Hess
A
d
d
c
h
ecks for too much me
m
o
r
y i
n
g
_nmeig
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add grompp check
f
o
r
p
u
ll group
commit
|
commitdiff
|
tree
2016-06-28
Berk
Hess
Properly
r
e
s
et C
U
DA application clock
s
commit
|
commitdiff
|
tree
2016-06-27
Berk H
e
ss
Use s
y
sconf(
_
SC_NPROCESSORS_ON
L
N
)
commit
|
commitdiff
|
tree
2016-06-26
Berk Hess
Fix vsite b
u
g with
M
PI+OpenMP
commit
|
commitdiff
|
tree
2016-06-24
Ber
k
He
s
s
Fi
x
Verlet buffe
r
cal
c
ula
t
ion with nstlist=1
commit
|
commitdiff
|
tree
2016-06-23
B
er
k
Hess
More
a
ccur
a
te G
P
U list splitt
i
ng
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Updated Open
C
LTODOList
.
t
x
t
commit
|
commitdiff
|
tree
2016-06-22
B
e
rk He
s
s
Add n
b
nxn pair-li
s
t rebalan
c
in
g
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
R
e
move OpenMP
overhead at high pa
r
allelization
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Cor
r
e
c
t
GPU pair estimate
for list splitting
commit
|
commitdiff
|
tree
2016-06-21
Berk Hess
F
ix bu
g
with fbposres+MPI+
O
pe
n
MP
commit
|
commitdiff
|
tree
2016-06-20
Berk
Hes
s
Increased tpx_incom
p
atibl
e
_version to 30
commit
|
commitdiff
|
tree
2016-06-19
Berk Hess
Rem
o
v
e warnings
on checkpoint mismatch
commit
|
commitdiff
|
tree
2016-06-17
Berk Hess
Remove std::thre
a
d::hardware_concurrency()
commit
|
commitdiff
|
tree
2016-06-14
Berk Hes
s
Fix OpenC
L
err
o
r
w
it
h
e
m
pty
d
o
m
a
ins
commit
|
commitdiff
|
tree
2016-06-13
B
e
rk Hess
Handle const
r
aint errors with EM
commit
|
commitdiff
|
tree
2016-06-07
Berk
H
ess
Fi
x
data race in hwi
n
f
o
w
ith thread-MP
I
commit
|
commitdiff
|
tree
2016-06-03
Berk
Hess
Handl
e
partially fro
z
en and c
o
nstrained atoms
commit
|
commitdiff
|
tree
2016-05-31
Be
r
k Hess
Repositi
o
n nbnxn fi
l
le
r
p
articles
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
A
v
oi
d
nu
m
erical overflow
w
i
t
h overlapping at
o
ms
commit
|
commitdiff
|
tree
2016-05-31
Berk H
e
ss
Add che
c
k
for
f
i
n
ite energies
commit
|
commitdiff
|
tree
2016-05-30
Berk Hes
s
Add grompp check for u
n
b
o
und at
o
ms
commit
|
commitdiff
|
tree
2016-05-23
Ber
k
Hess
Fix
bug in v
-
resc
a
le th
e
rmostat & replica excha
n
ge
commit
|
commitdiff
|
tree
2016-05-10
Berk He
s
s
Op
t
imized the vsite threading
commit
|
commitdiff
|
tree
2016-05-10
Berk Hes
s
Fi
x
CUDA
shmem b
u
g
commit
|
commitdiff
|
tree
2016-05-10
Berk He
s
s
Support
c
m
ap
w
ith QMMM
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Update mdrun termi
n
ation info
commit
|
commitdiff
|
tree
2016-05-06
Berk He
s
s
OpenMP parall
e
lization for
pull
commit
|
commitdiff
|
tree
2016-04-20
Berk Hess
Fix pull legend w
i
t
h
external potential
commit
|
commitdiff
|
tree
2016-04-19
Berk He
s
s
All
o
w rcoulomb>rvdw with PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Broadcas
t
pull
e
xternal potential provider
stri
n
g
commit
|
commitdiff
|
tree
2016-04-19
Berk Hes
s
Fix
g
mx hbond group overlap check
commit
|
commitdiff
|
tree
2016-04-14
B
erk Hess
Add QMMM
c
hec
k
s
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
Correct
n
rdf for
1
D
/2D s
y
stems
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
F
i
x
includes in
rea
d
pull
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Add
opt
i
on for e
x
te
r
n
al
pul
l
potential
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
C
o
rre
c
t
m
d
r
u
n
tMPI (
n
on-)para
l
lel er
r
or
message
commit
|
commitdiff
|
tree
2016-03-26
B
erk Hess
A
dd real/SIMD
template for LJ-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Ber
k
H
e
ss
Avoid asser
t
i
on failure i
n
pme_load
b
al_do
commit
|
commitdiff
|
tree
2016-03-22
Berk
H
ess
M
ake gm
x
vanhove work wit
h
out PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
L
J
c
ombination rule ke
r
nels for CUDA
commit
|
commitdiff
|
tree
2016-03-21
B
e
rk Hess
M
o
ved p
u
ll initializat
i
on back
t
o
m
drun
n
er
commit
|
commitdiff
|
tree
2016-03-18
Be
r
k Hess
Fix
non-normalization of FFT
a
u
t
o
corr
commit
|
commitdiff
|
tree
2016-03-14
Berk
H
ess
Remove
restriction on
d
ihdral
t
ype
s
orde
r
commit
|
commitdiff
|
tree
2016-03-12
Berk Hess
Split off Fe
r
m
i
kernel f
r
om CUDA
ker
n
e
l
commit
|
commitdiff
|
tree
2016-03-09
B
erk H
e
ss
Fix Ewald
3DC
dipole
with Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk
H
ess
Converted csettle() to
use real/SimdReal template
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use
SIMD
transpose s
c
atter in bondeds
commit
|
commitdiff
|
tree
2016-03-03
Berk H
e
ss
Use rve
c
4 for liste
d
forc
e
buffer
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Re
m
ov
e
epsfa
c
from GP
U
ke
r
nel inn
e
r
-
loops
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Mino
r
code reordering in GP
U
kern
e
ls
commit
|
commitdiff
|
tree
2016-02-26
Berk Hess
Fix compilation with
Simd4Float, without Simd4Double
commit
|
commitdiff
|
tree
2016-02-19
Berk
H
ess
Fix
e
xcessive list
s
plitting
commit
|
commitdiff
|
tree
2016-02-17
Be
r
k
Hess
Renamed n
b
nxn static
c
onst ints
commit
|
commitdiff
|
tree
2016-02-11
Berk Hes
s
Add SIMD version of pbc_dx_aiuc
commit
|
commitdiff
|
tree
2016-02-09
Berk
Hess
R
e
plac
e
d nbnxn
search+grid simd mac
r
os
commit
|
commitdiff
|
tree
2016-02-07
Berk Hess
Fix incorrect
c
map pa
r
sing
commit
|
commitdiff
|
tree
2016-02-05
Berk
H
ess
Fix incorr
e
c
t
cma
p
parsing
commit
|
commitdiff
|
tree
2016-02-03
Be
r
k Hess
Replace
d
l
i
terals in nb
n
xn lists
b
y ints
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fi
x
mdrun removing Verlet buf
f
er with
E
M
commit
|
commitdiff
|
tree
2016-02-03
B
e
r
k
He
s
s
Fix SE
T
T
LE error han
d
l
ing
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Added
docume
n
tation
for pme
g
r
i
d
i
ndexi
n
g
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
F
i
x
TPI
ignor
i
ng PME
m
esh contributions
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Update -ntomp_pme -n
p
m
e
chec
k
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Add ch
e
c
k for double
p
ert
u
rbatio
n
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix
LINCS
t
r
i
angle
c
o
n
st
r
a
int
t
h
read issue
commit
|
commitdiff
|
tree
2016-01-28
Berk Hess
Update
pair-list buffer manual
commit
|
commitdiff
|
tree
2016-01-24
Berk H
e
s
s
Fi
x
exa
c
t
cont
i
nuation
fro
m
non-energy
s
teps
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
F
ix energy file
con
t
inuation with
md-
v
v
commit
|
commitdiff
|
tree
2016-01-24
B
e
r
k Hess
Fi
x
ener
g
y average with continuation
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
F
i
x
PME l
o
a
d ba
l
anci
n
g skipp
i
ng
a
setup
commit
|
commitdiff
|
tree
2015-12-29
B
erk H
e
ss
Correct
vector chec
k
of g
m
x check
commit
|
commitdiff
|
tree
2015-12-27
Berk Hes
s
Reorga
n
ized domde
c
initialization
commit
|
commitdiff
|
tree
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