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Add grompp check for pull group
2016-07-03
Berk Hess
Add
g
rom
p
p check
f
or pull
group
commit
|
commitdiff
|
tree
2016-06-28
Ber
k
Hes
s
Properly reset C
U
D
A appl
i
c
ation cloc
k
s
commit
|
commitdiff
|
tree
2016-06-27
Berk H
e
ss
Use sysconf(_SC_N
P
ROCESS
O
RS_ONLN)
commit
|
commitdiff
|
tree
2016-06-26
B
e
r
k
Hess
Fix vsite bug wi
t
h
M
P
I+OpenMP
commit
|
commitdiff
|
tree
2016-06-24
B
e
rk Hess
Fix V
e
r
let
b
uffer calculation wit
h
nstlis
t
=1
commit
|
commitdiff
|
tree
2016-06-23
Berk Hess
Mo
r
e acc
u
rate GPU li
s
t splittin
g
commit
|
commitdiff
|
tree
2016-06-22
Ber
k
Hess
Updated OpenC
L
TODOList
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Berk Hes
s
Add nbnxn
pair-l
i
st reb
a
lancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hes
s
Remove OpenMP
ove
r
h
ead at high paralleliz
a
tion
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Correct G
P
U pair esti
m
ate for list s
p
litting
commit
|
commitdiff
|
tree
2016-06-21
Berk Hess
F
i
x bug with fbp
o
sres+MPI+O
p
e
nMP
commit
|
commitdiff
|
tree
2016-06-19
Ber
k
Hess
Remove w
a
rnings on checkpoint mismatch
commit
|
commitdiff
|
tree
2016-06-17
Berk
H
ess
Remov
e
std::thread::hardware_co
n
currency()
commit
|
commitdiff
|
tree
2016-06-14
Berk
Hes
s
Fix
O
penC
L
err
o
r with emp
t
y domai
n
s
commit
|
commitdiff
|
tree
2016-06-13
Berk Hes
s
Hand
l
e const
r
aint
errors with
E
M
commit
|
commitdiff
|
tree
2016-06-07
B
e
rk Hess
F
ix data r
a
ce i
n
hwinfo wit
h
thread-MPI
commit
|
commitdiff
|
tree
2016-06-03
Be
r
k Hess
Handle partia
l
ly froze
n
and constrain
e
d
atoms
commit
|
commitdiff
|
tree
2016-05-31
B
e
rk Hess
R
e
posit
i
o
n nbnxn filler parti
c
les
commit
|
commitdiff
|
tree
2016-05-31
Be
r
k
H
ess
Av
o
id numerica
l
o
verflow with overlapping a
t
om
s
commit
|
commitdiff
|
tree
2016-05-31
B
erk Hess
A
d
d
c
heck for
f
i
nite energies
commit
|
commitdiff
|
tree
2016-05-30
Berk H
e
ss
Add grompp che
c
k
f
or unboun
d
atoms
commit
|
commitdiff
|
tree
2016-05-23
Be
r
k Hess
Fix bug in
v-res
c
al
e
thermostat & replic
a
exchange
commit
|
commitdiff
|
tree
2016-05-10
B
e
rk Hess
Optimized
the
v
site threading
commit
|
commitdiff
|
tree
2016-05-10
Berk Hes
s
Fix CUDA shmem
b
ug
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
S
u
pport cm
a
p with Q
M
MM
commit
|
commitdiff
|
tree
2016-05-08
Be
r
k
Hess
Update mdrun
termination info
commit
|
commitdiff
|
tree
2016-05-06
Berk
Hess
OpenMP
paralleli
z
ati
o
n
f
o
r
p
u
l
l
commit
|
commitdiff
|
tree
2016-04-20
Ber
k
Hess
Fix pul
l
leg
e
nd with external
p
otential
commit
|
commitdiff
|
tree
2016-04-19
B
e
rk
Hess
Allow rcoulomb>
r
vdw
with PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hes
s
Broadcast
pull external potential provider string
commit
|
commitdiff
|
tree
2016-04-19
B
e
rk H
e
ss
Fix gmx hbond gr
o
up overlap check
commit
|
commitdiff
|
tree
2016-04-14
Berk He
s
s
Add QMM
M
chec
k
s
commit
|
commitdiff
|
tree
2016-04-03
Berk
H
es
s
Correc
t
nrdf for 1D
/
2D systems
commit
|
commitdiff
|
tree
2016-03-31
Ber
k
Hes
s
F
ix i
n
c
l
u
d
e
s in readpull
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Add opti
o
n
f
o
r
external pu
l
l p
o
tential
commit
|
commitdiff
|
tree
2016-03-30
Be
r
k Hess
C
o
r
r
ect
m
d
run tMPI (non-)paral
l
el error m
e
ssage
commit
|
commitdiff
|
tree
2016-03-26
Ber
k
Hess
Add real/SIMD t
e
mp
l
a
te for L
J
-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Avoid assertion failure in pme_lo
a
dbal_do
commit
|
commitdiff
|
tree
2016-03-22
B
e
rk Hes
s
M
ake gmx van
h
o
v
e
work
witho
u
t PBC
commit
|
commitdiff
|
tree
2016-03-22
Be
r
k Hess
LJ
combi
n
ation
rule kernels
for CU
D
A
commit
|
commitdiff
|
tree
2016-03-21
Berk H
e
ss
Moved
pull
i
n
i
tializat
i
on
bac
k
to
m
d
runner
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix non-normal
i
za
t
ion o
f
FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
Berk
H
es
s
Remove
r
estriction
on dihdraltypes order
commit
|
commitdiff
|
tree
2016-03-12
B
e
rk He
s
s
Spli
t
off Fermi kernel from
CUDA kernel
commit
|
commitdiff
|
tree
2016-03-09
B
e
rk Hess
F
ix Ewald 3DC dipo
l
e wi
t
h Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
Be
r
k
Hess
Conv
e
rted cset
t
le()
t
o
use rea
l
/Si
m
dR
e
al templat
e
commit
|
commitdiff
|
tree
2016-03-03
Berk
Hess
Use SIMD transpose
scatter in
b
ondeds
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Us
e
r
v
e
c
4 for listed f
o
r
c
e buffer
commit
|
commitdiff
|
tree
2016-02-27
Ber
k
H
ess
R
e
mo
v
e
e
p
sf
a
c from
G
PU kern
e
l
i
nner-loops
commit
|
commitdiff
|
tree
2016-02-27
Berk
Hess
Minor code reordering in GPU kernels
commit
|
commitdiff
|
tree
2016-02-26
Berk Hess
Fix compilation with Simd4Float,
without Simd4Double
commit
|
commitdiff
|
tree
2016-02-19
Ber
k
Hess
Fix ex
c
essive
l
ist
spl
i
t
ting
commit
|
commitdiff
|
tree
2016-02-17
Be
r
k He
s
s
R
enamed nbnxn static const ints
commit
|
commitdiff
|
tree
2016-02-11
Berk
H
ess
Ad
d
SIMD version of pbc_dx_aiuc
commit
|
commitdiff
|
tree
2016-02-09
Be
r
k
H
ess
Replace
d
nbnxn search+g
r
id
sim
d
mac
r
os
commit
|
commitdiff
|
tree
2016-02-07
Berk Hess
Fix incorrect cmap
p
ars
i
n
g
commit
|
commitdiff
|
tree
2016-02-05
Berk Hess
Fix incorrect
c
map pa
r
sing
commit
|
commitdiff
|
tree
2016-02-03
B
e
rk Hess
Replaced
literal
s
in
nbnxn lists
by ints
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix
m
drun removing
V
erlet buffer with EM
commit
|
commitdiff
|
tree
2016-02-03
Berk
Hess
Fix SETTLE e
r
ror hand
l
ing
commit
|
commitdiff
|
tree
2016-01-29
Be
r
k Hess
Adde
d
docum
e
ntation
f
or pme gr
i
d indexing
commit
|
commitdiff
|
tree
2016-01-29
Be
r
k Hes
s
Fi
x
TPI ignoring PME me
s
h
contributions
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Update -nt
o
mp_pm
e
-npme check
commit
|
commitdiff
|
tree
2016-01-29
Berk
He
s
s
A
d
d c
h
eck
f
or d
o
u
ble p
e
rturbatio
n
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
F
i
x
LINCS triangle const
r
aint thread issue
commit
|
commitdiff
|
tree
2016-01-28
Berk Hess
Update
p
ai
r
-list
buffer manua
l
commit
|
commitdiff
|
tree
2016-01-24
Berk
H
ess
Fix ex
a
c
t c
o
ntinuation
f
rom non
-
energy steps
commit
|
commitdiff
|
tree
2016-01-24
Berk He
s
s
Fix ener
g
y file contin
u
at
i
on wi
t
h md-vv
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix
e
ne
r
gy
a
verag
e
with cont
i
nua
t
ion
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
F
i
x PME load ba
l
ancing skipping a
setup
commit
|
commitdiff
|
tree
2015-12-29
Be
r
k Hess
Correct vector
c
he
c
k of gmx
c
h
eck
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Reorganized
d
o
mdec ini
t
i
a
liz
a
t
ion
commit
|
commitdiff
|
tree
2015-12-20
Berk Hess
Merg
e
release-5-1 into
m
a
ster
commit
|
commitdiff
|
tree
2015-12-19
Berk
Hess
Bring p
e
rformance
e
stim
a
t
i
on up to da
t
e
commit
|
commitdiff
|
tree
2015-12-17
Ber
k
Hess
Removed topology po
i
n
t
er
s
from DD
s
t
ruct
commit
|
commitdiff
|
tree
2015-12-16
Berk Hess
Add
o
n
e
elemen
t
to state
rvec arrays
commit
|
commitdiff
|
tree
2015-12-12
Berk He
s
s
Remov
e
d
unused md
r
un option
-dn
commit
|
commitdiff
|
tree
2015-12-11
Berk Hess
Fix bug with pull group weights
commit
|
commitdiff
|
tree
2015-12-07
Berk Hess
Mov
e
d pull
p
aram
s
to mdty
p
es/pull
-
params
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk Hes
s
In
c
rease pdb c
h
ain ids to 62
in output
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
R
e
factored set_pbc_
d
d
commit
|
commitdiff
|
tree
2015-12-02
B
erk Hess
Made t_inputrec const in PME load balancing
commit
|
commitdiff
|
tree
2015-12-01
Berk Hess
Pull group cou
n
t
f
or coords stored in tpr
commit
|
commitdiff
|
tree
2015-11-19
Berk Hess
Removed mdrun f
a
tal_error wi
t
h P3M-AD
commit
|
commitdiff
|
tree
2015-11-18
B
e
r
k
Hess
R
e
m
o
ved Re
a
ction-
F
ie
l
d-nec
commit
|
commitdiff
|
tree
2015-11-14
Be
r
k Hess
O
pt
i
mized the bonded
t
hrea
d
force
r
educ
t
ion
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
Fi
x
ed (harmless) fp exce
p
tion in wa
l
lcycle_sum
commit
|
commitdiff
|
tree
2015-11-09
Berk
Hess
Correct LIN
C
S
d
Hdl contr
i
bution
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
F
ix no wallcycle sup
p
o
rt
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Removed
nbnxn kernel blen
d
v
o
pt
i
mization
commit
|
commitdiff
|
tree
2015-11-02
B
erk Hes
s
Fix
i
ntermolecular interaction
s
with
sma
l
l
mols
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
Fixed nbnxn_4xN performanc
e
regress
i
on
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
Fix bugs wi
t
h intermol inter
a
ctions and DD
commit
|
commitdiff
|
tree
2015-10-01
Berk
H
ess
Removed CUDA polling
w
ait
commit
|
commitdiff
|
tree
2015-09-27
Berk Hess
Move gmx_d
o
mdec_
c
omm_t definition
commit
|
commitdiff
|
tree
2015-09-22
B
erk
Hess
Remov
e
d us
e
less multiple
s
hifts i
n
pb
c
.
c
p
p
commit
|
commitdiff
|
tree
2015-09-16
Berk Hess
Split nbnxn_
g
rid
.
c off from nbnxn_
s
earch
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk Hess
De
t
ect incorrect cycle c
o
u
n
t
i
ng
commit
|
commitdiff
|
tree
2015-08-25
Berk
Hess
Simplify changing th
e
tpx_
v
ersi
o
n
commit
|
commitdiff
|
tree
2015-08-14
Berk Hess
Mak
e
m
drun -nt work
again
commit
|
commitdiff
|
tree
next