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Re-enable flexible constraints with DD
2016-09-05
Berk Hess
Re-en
a
ble flexible constrai
n
ts wi
t
h DD
commit
|
commitdiff
|
tree
2016-09-02
Berk H
e
s
s
Me
r
ge br
a
nch
r
el
e
ase-5-1
into release-2016
commit
|
commitdiff
|
tree
2016-09-02
B
erk
Hess
Fix Parrine
l
lo-Rahman
with nst
p
c
o
uple>1
commit
|
commitdiff
|
tree
2016-08-30
Berk Hess
M
a
ke v
i
rial
r
eproducible
commit
|
commitdiff
|
tree
2016-08-24
Berk Hess
Fix Ewald surface+3DC
corrections
commit
|
commitdiff
|
tree
2016-08-24
B
e
rk Hes
s
Merge branch release-
5
-1
i
nto release-20
1
6
commit
|
commitdiff
|
tree
2016-08-23
B
erk H
e
ss
Remove
varia
b
le prec
i
sion gro writing
commit
|
commitdiff
|
tree
2016-08-17
Be
r
k H
e
ss
Fixe
d
opening of wall tab
l
e
f
ile
s
commit
|
commitdiff
|
tree
2016-08-15
Berk Hes
s
Reduce FE p
a
ir-list memory
u
sage
commit
|
commitdiff
|
tree
2016-08-10
Ber
k
H
e
ss
F
i
x dead
l
ock with
threa
d
-MPI
commit
|
commitdiff
|
tree
2016-08-09
B
erk Hess
Fix
twin-c
u
toff for GP
U
LJ pot-swi
t
ch
commit
|
commitdiff
|
tree
2016-07-07
B
erk Hess
Relax pull PB
C
chec
k
commit
|
commitdiff
|
tree
2016-07-05
Ber
k
H
e
s
s
A
dd c
h
ecks for too much
m
emory in g_nmeig
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add gr
o
m
p
p check fo
r
pull gr
o
up
commit
|
commitdiff
|
tree
2016-06-28
Berk Hess
P
r
o
p
erly reset C
U
DA application
c
lo
c
ks
commit
|
commitdiff
|
tree
2016-06-27
Berk Hess
Use
s
ys
c
onf(_SC_
N
PROCESS
O
RS_ONLN
)
commit
|
commitdiff
|
tree
2016-06-26
Berk He
s
s
Fix vsite bu
g
with MP
I
+OpenMP
commit
|
commitdiff
|
tree
2016-06-24
Berk Hess
Fix Verlet buff
e
r
calculation w
i
th nstlist=1
commit
|
commitdiff
|
tree
2016-06-23
Berk
H
ess
M
o
re a
c
c
ur
a
te
GPU list splitting
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Updated OpenCLTODOList
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Be
r
k Hess
A
dd nbnxn pair-list rebalancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Remove OpenMP overhe
a
d
at high paral
l
elizati
o
n
commit
|
commitdiff
|
tree
2016-06-22
Berk H
e
ss
C
or
r
ect GPU pair es
t
imate f
o
r list
s
plitt
i
ng
commit
|
commitdiff
|
tree
2016-06-21
Be
r
k Hes
s
Fix
b
ug wit
h
fbposre
s
+MPI+OpenMP
commit
|
commitdiff
|
tree
2016-06-19
B
e
rk Hess
Remove warn
i
n
g
s on checkpoint mismatch
commit
|
commitdiff
|
tree
2016-06-17
Berk Hess
Re
m
ove std::
t
hread::h
a
rdware_con
c
urren
c
y
(
)
commit
|
commitdiff
|
tree
2016-06-14
Berk Hess
F
i
x O
p
enCL error with empty dom
a
ins
commit
|
commitdiff
|
tree
2016-06-13
B
erk H
e
ss
Handle cons
t
raint e
r
r
o
rs with EM
commit
|
commitdiff
|
tree
2016-06-07
Be
r
k Hess
Fix data race in
h
w
i
nfo
w
ith thread-MPI
commit
|
commitdiff
|
tree
2016-06-03
B
erk Hess
Handle partially fro
z
en
a
nd con
s
t
rained a
t
oms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Repositio
n
nbnxn filler particles
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
A
void
n
umerical overflow with overlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Add chec
k
fo
r
finite energies
commit
|
commitdiff
|
tree
2016-05-30
Berk He
s
s
A
d
d g
r
o
m
pp check for
unbound a
t
oms
commit
|
commitdiff
|
tree
2016-05-23
Be
r
k Hess
Fix bug i
n
v-rescale ther
m
o
s
tat
&
replica exchange
commit
|
commitdiff
|
tree
2016-05-10
Berk Hes
s
Optimized the
v
site threading
commit
|
commitdiff
|
tree
2016-05-10
B
e
r
k
Hess
Fix CUDA shmem b
u
g
commit
|
commitdiff
|
tree
2016-05-10
B
erk Hess
Support cmap with
Q
MMM
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Update md
r
un t
e
rmination info
commit
|
commitdiff
|
tree
2016-05-06
Berk Hess
OpenMP parall
e
lization for pull
commit
|
commitdiff
|
tree
2016-04-20
Berk
H
e
ss
Fix
p
ull legend wit
h
external potential
commit
|
commitdiff
|
tree
2016-04-19
Berk
H
ess
Allow rcoulomb>rvdw wit
h
PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Broadcast pull external potential provider string
commit
|
commitdiff
|
tree
2016-04-19
Berk H
e
ss
Fix
g
mx
h
bond group ov
e
r
l
a
p
check
commit
|
commitdiff
|
tree
2016-04-14
B
erk H
e
ss
Add
Q
MMM checks
commit
|
commitdiff
|
tree
2016-04-03
Berk H
e
ss
Correct
nrdf for 1D/
2
D s
y
stems
commit
|
commitdiff
|
tree
2016-03-31
Berk H
e
ss
F
i
x includes i
n
readpull
.
c
pp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Add opti
o
n f
o
r external pu
l
l potential
commit
|
commitdiff
|
tree
2016-03-30
Berk H
e
s
s
Correct
mdrun tMPI (non
-
)parallel
error messag
e
commit
|
commitdiff
|
tree
2016-03-26
Berk Hess
Add real/
S
I
M
D
templat
e
for LJ
-
14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Avoid ass
e
rtion fa
i
lure in
p
m
e
_loadbal_do
commit
|
commitdiff
|
tree
2016-03-22
B
e
r
k Hess
Mak
e
gmx
v
a
nhove work
w
ithou
t
PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ combin
a
tion rule kernels fo
r
CUDA
commit
|
commitdiff
|
tree
2016-03-21
Berk
H
ess
Mo
v
ed pull initializ
a
t
i
on back
to mdrunner
commit
|
commitdiff
|
tree
2016-03-18
B
e
rk H
e
ss
Fix
non-normali
z
ation of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
Berk Hess
Remove restriction
on dihdraltypes or
d
e
r
commit
|
commitdiff
|
tree
2016-03-12
Berk Hess
Split
off Fermi ker
n
el
f
rom CUD
A
k
e
rnel
commit
|
commitdiff
|
tree
2016-03-09
Berk Hess
Fix Ewal
d
3
D
C
d
ipo
l
e
wit
h
Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk Hess
Co
n
verted cset
t
le()
t
o
us
e
real/Si
m
dRea
l
template
commit
|
commitdiff
|
tree
2016-03-03
Berk He
s
s
Use
S
IMD
t
ransp
o
s
e
sc
a
t
t
e
r in bondeds
commit
|
commitdiff
|
tree
2016-03-03
B
e
r
k Hess
Use rvec4
f
or lis
t
ed force buffer
commit
|
commitdiff
|
tree
2016-02-27
Be
r
k Hess
R
e
move epsfac from
G
P
U
k
ernel inner-loops
commit
|
commitdiff
|
tree
2016-02-27
Berk Hess
Mino
r
c
ode
r
eo
r
dering in GPU ker
n
els
commit
|
commitdiff
|
tree
2016-02-26
Berk Hess
Fix compilation
with
S
imd4Float, without Sim
d
4
D
ouble
commit
|
commitdiff
|
tree
2016-02-19
Berk He
s
s
Fix exces
s
ive list
s
plitting
commit
|
commitdiff
|
tree
2016-02-17
Berk Hess
Re
n
amed nbnxn static const ints
commit
|
commitdiff
|
tree
2016-02-11
Berk Hess
Ad
d
SIMD
v
ersion of pbc_dx
_
aiuc
commit
|
commitdiff
|
tree
2016-02-09
Berk Hess
Repl
a
ced
nbnxn s
e
arch+gr
i
d simd m
a
cro
s
commit
|
commitdiff
|
tree
2016-02-07
Berk
H
ess
Fix incorrect cmap parsing
commit
|
commitdiff
|
tree
2016-02-05
Berk Hes
s
Fix incor
r
ect cmap pa
r
sin
g
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Rep
l
aced l
i
ter
a
ls in
n
b
n
x
n
l
ists by ints
commit
|
commitdiff
|
tree
2016-02-03
B
e
r
k
Hess
Fix mdr
u
n removing Verlet buffer with
EM
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix SETTLE error handling
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Added documenta
t
ion for pme grid
i
nd
e
xing
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix TPI ignoring PM
E
me
s
h
contribu
t
i
o
n
s
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Update -ntomp_pme -npme chec
k
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Add check for double per
t
urbation
commit
|
commitdiff
|
tree
2016-01-29
B
erk Hess
Fix LINCS triang
l
e constr
a
i
n
t
thread issue
commit
|
commitdiff
|
tree
2016-01-28
Berk Hess
Updat
e
pair-list buffer ma
n
ual
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix exact
c
o
n
tin
u
ation
from non-energy
steps
commit
|
commitdiff
|
tree
2016-01-24
Berk H
e
s
s
Fix en
e
rg
y
file continuation with md-vv
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
F
i
x energy averag
e
with
con
t
inuation
commit
|
commitdiff
|
tree
2016-01-08
Ber
k
Hess
Fi
x
PM
E
load balancing
s
kipp
i
ng
a
setup
commit
|
commitdiff
|
tree
2015-12-29
Be
r
k
Hess
Correct
v
ect
o
r check of g
m
x c
h
eck
commit
|
commitdiff
|
tree
2015-12-27
Berk
H
ess
R
e
organi
z
ed domd
e
c in
i
tialization
commit
|
commitdiff
|
tree
2015-12-20
Berk Hess
M
e
r
ge
r
e
l
eas
e
-5-1
i
nto master
commit
|
commitdiff
|
tree
2015-12-19
Ber
k
Hess
Br
i
ng performance
e
s
timat
i
o
n up to date
commit
|
commitdiff
|
tree
2015-12-17
Ber
k
He
s
s
Re
m
o
ved top
o
log
y
pointe
r
s from DD struct
commit
|
commitdiff
|
tree
2015-12-16
Ber
k
Hes
s
Add one
element to
s
ta
t
e rvec arrays
commit
|
commitdiff
|
tree
2015-12-12
B
erk Hess
Rem
o
ved unused mdrun option -dn
commit
|
commitdiff
|
tree
2015-12-11
Ber
k
Hess
F
i
x bug with
pul
l
g
roup weigh
t
s
commit
|
commitdiff
|
tree
2015-12-07
B
erk
Hess
M
o
ved pul
l
p
a
r
a
m
s to m
d
type
s
/pull-param
s
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Increase pd
b
cha
i
n ids to
6
2 i
n
output
commit
|
commitdiff
|
tree
2015-12-02
Berk He
s
s
Refacto
r
ed se
t
_pbc_dd
commit
|
commitdiff
|
tree
2015-12-02
Be
r
k Hess
Made t
_
inputrec const in PME load balancing
commit
|
commitdiff
|
tree
2015-12-01
Berk Hes
s
Pu
l
l
g
roup count for coords stored in tpr
commit
|
commitdiff
|
tree
2015-11-19
Ber
k
H
e
ss
Removed mdrun
f
atal_error
with P3M-AD
commit
|
commitdiff
|
tree
2015-11-18
Berk Hess
Remo
v
ed Rea
c
t
ion-Field-
n
e
c
commit
|
commitdiff
|
tree
2015-11-14
Berk Hess
Optimized the
bonded t
h
read force reductio
n
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
Fixed (ha
r
mless)
fp excepti
o
n
i
n w
a
l
lcy
c
l
e
_
s
u
m
commit
|
commitdiff
|
tree
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