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Fix duplicate warning
2017-12-19
Berk Hess
Ma
k
e
accelerat
i
on
c
o
rrecti
o
n VCM mode w
o
r
k
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make
o
versubscription warni
n
g
c
o
n
s
i
s
t
ent
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Requi
r
e -
n
tmpi with
s
etting -ntomp with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Check f
o
r
la
r
ge energ
y
at first step
commit
|
commitdiff
|
tree
2017-12-12
Berk Hes
s
Avoid y
e
lling about thr
e
a
d
p
inning t
w
ice
commit
|
commitdiff
|
tree
2017-12-11
Berk
H
ess
A
dd gro
m
pp note for PR pcouple + position r
e
strai
n
ts
commit
|
commitdiff
|
tree
2017-12-10
Ber
k
Hess
Rem
o
ve SIMD warning for AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
B
e
rk He
s
s
T
one down note about not pinning threads
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Correct Shake test to
l
erances
commit
|
commitdiff
|
tree
2017-12-08
Ber
k
Hess
Add
Viv
e
ca Lind
a
hl as contributo
r
commit
|
commitdiff
|
tree
2017-12-07
B
e
rk He
s
s
Cho
o
s
e fas
t
er nbnxn SIMD ker
n
e
l
s o
n
AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
F
ix
D
D exact continuation bug
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k Hess
Fix pme
g
a
th
e
r in double with AVX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
B
erk He
s
s
Merge "Merge bra
n
ch r
e
lea
s
e-201
6
into releas
e
-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fixe
d
initi
a
l
tempera
t
ure reporting
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Update mdrun
s
ignal help
text
commit
|
commitdiff
|
tree
2017-12-04
B
erk Hess
O
n
ly stop at nstlist steps with -
r
ep
r
od
commit
|
commitdiff
|
tree
2017-12-03
Berk
H
ess
Cle
a
r vsite velocities for
s
imple integrators
commit
|
commitdiff
|
tree
2017-12-03
Berk H
e
ss
Tighten B-spli
n
e moduli single precis
i
on tes
t
to
l
e
r
a
n
c
e
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
B
erk Hess
Avoid assertion
failure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Be
r
k
H
ess
Cha
n
g
e the GPU SMT
cut-off to quadratic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Up
d
a
t
e
do
c
ument
i
on of
N
ose
-
Hoo
v
er output
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Refa
c
tor nbnxn excl
u
sion
setting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hes
s
Extend
grom
p
p missing energ
y
term m
e
ssag
e
commit
|
commitdiff
|
tree
2017-11-27
B
e
rk
H
ess
Enabl
e
auto thread
pinnin
g
w
i
th t
h
read l
i
miti
n
g
commit
|
commitdiff
|
tree
2017-11-27
Berk He
s
s
F
i
x PME
GP
U
with walls
commit
|
commitdiff
|
tree
2017-11-25
Be
r
k Hess
F
i
x compi
l
er warni
n
g without
MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Disabled
CUDA timings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Speed
up nbnxn buffer clearing
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
L
i
mit SMT with PME on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Update note in
m
anual
on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk
Hes
s
Cor
r
ect PME GPU ti
m
i
n
g naming
commit
|
commitdiff
|
tree
2017-11-20
Ber
k
Hess
Preve
n
t PME tuning excess
i
v
e grid scaling
commit
|
commitdiff
|
tree
2017-11-19
B
erk
Hess
A
d
d SIMD
fo
r
AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk
He
s
s
Also p
r
int 1x1 pair-list setup
to log
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
Fix g
e
n
i
o
n
charge
s
umm
a
tion a
c
curacy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix Ekin at s
t
ep 0 with COM removal
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Add missing
E
wald correction f
o
r pme-u
s
e
r
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remo
v
e unuse
d
si
g
n
para
m
eter fro
m
d
i
h_ang
l
e()
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
Remove incorrect comment for CHARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Ber
k
Hess
Fix gmx check for tp
r
s w
i
th
diff
e
rent #
a
t
o
ms
commit
|
commitdiff
|
tree
2017-10-23
B
erk Hess
Fix incorrect dV/dla
m
bda for walls
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
Merge "Merge branch re
l
ease-2016"
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
F
ix warni
n
g fo
r
confout with period
i
c m
o
lecules
commit
|
commitdiff
|
tree
2017-10-18
Berk Hess
M
ade
C
UDA PME texture refere
n
ce condi
t
i
onal
commit
|
commitdiff
|
tree
2017-10-15
B
e
rk
H
es
s
Improve vsite
parallel chec
k
ing
commit
|
commitdiff
|
tree
2017-10-12
Berk
H
ess
Simplif
y
virial hand
l
ing
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Dis
a
ble ARM Neon nat
i
ve rsqrt
i
te
r
ati
o
n
commit
|
commitdiff
|
tree
2017-10-06
B
erk Hess
Add acceleratio
n
correc
t
ion VC
M
m
ode
commit
|
commitdiff
|
tree
2017-10-06
B
e
rk Hess
Fix
max_size() in allo
c
at
o
r
.
h
commit
|
commitdiff
|
tree
2017-10-06
Ber
k
Hess
A
d
d
S
IMD intrinsics version of si
m
ple updat
e
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Improve Pad
d
edRVecVect
o
r
resizing
commit
|
commitdiff
|
tree
2017-10-05
Berk H
e
ss
M
a
k
e
SIMD ambiguous
test wo
r
k with float/double only
commit
|
commitdiff
|
tree
2017-10-04
B
e
rk H
e
ss
Remove a f
o
rce buffer argumen
t
fr
o
m IForcePr
o
vider
commit
|
commitdiff
|
tree
2017-10-03
Be
r
k Hess
Move call
i
n
g of
special fo
r
ce functions
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Remove hybrid
gpu+cpu nonb
o
nded mode
commit
|
commitdiff
|
tree
2017-09-25
Berk
H
e
s
s
P
ut re
r
un st
a
te
p
rep
a
r
a
t
i
o
n in
a
func
t
ion
commit
|
commitdiff
|
tree
2017-09-25
Be
r
k Hess
Set global
state on ma
s
ter rank only
commit
|
commitdiff
|
tree
2017-09-23
Berk
Hes
s
F
ix
g
r
ompp with
Andersen
massive and
n
o COM removal
commit
|
commitdiff
|
tree
2017-09-20
Berk
Hess
Change nbnxn ind
e
xing to
t
empl
a
tes
commit
|
commitdiff
|
tree
2017-09-15
Ber
k
Hess
Rem
o
ve
nb-par
a
meters f
r
o
m t_forcerec
commit
|
commitdiff
|
tree
2017-09-14
Berk
H
ess
Fix nbnxn SIMD 2xNN PME t
a
bulated
k
e
rnel
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Fix excep
t
ion i
n
SIMD LJ
P
ME solv
e
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Do not pass state to i
n
it_replica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Berk Hess
Fix PBC bugs i
n
the swap
code
commit
|
commitdiff
|
tree
2017-09-09
Be
r
k
H
ess
Avoid i
n
f
in SIMD double
sqrt()
commit
|
commitdiff
|
tree
2017-09-07
Berk Hes
s
Fix FEP st
a
te with
re
r
un
commit
|
commitdiff
|
tree
2017-09-04
Berk He
s
s
Fix
two nbnxn search indexing bugs
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Consolidate architecture b
o
olean
s
commit
|
commitdiff
|
tree
2017-09-03
Berk Hess
Put mdrun options in
structs
commit
|
commitdiff
|
tree
2017-09-02
B
e
r
k
Hess
P
u
t
al
l
d
om
d
e
c
options
i
n a stru
c
t
commit
|
commitdiff
|
tree
2017-09-02
Berk
H
ess
F
i
x
mdrun
-n
b
optio
n
poin
t
er
commit
|
commitdiff
|
tree
2017-09-01
B
e
r
k Hess
F
i
x mdrun -nb op
t
i
on pointe
r
commit
|
commitdiff
|
tree
2017-08-29
Berk He
s
s
M
ake pull
poten
t
ial regis
t
ration th
r
ead-safe
commit
|
commitdiff
|
tree
2017-08-29
B
e
rk Hess
S
et default GM
X
_OPEN
M
P
_MAX_THREADS
t
o
64
commit
|
commitdiff
|
tree
2017-08-28
Be
r
k Hess
Avoid bonded
f
orces loops/t
i
mers
on
i
n
p
uts wi
t
h no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Berk Hess
Enable dyn
a
mic
p
air
l
ist
pruning
commit
|
commitdiff
|
tree
2017-08-18
Berk Hess
Ad
d
CPU reference and SIMD pruning kernels
commit
|
commitdiff
|
tree
2017-08-16
Berk
H
ess
A
d
d dy
n
amic
pair-list pr
u
ning f
r
ame
w
or
k
commit
|
commitdiff
|
tree
2017-08-16
B
e
r
k
Hess
Clean up nbnx
n
cluster pair a
d
dition code
commit
|
commitdiff
|
tree
2017-08-15
Berk Hess
A
d
d OpenMP for orient
a
tion re
s
traints
commit
|
commitdiff
|
tree
2017-08-15
Berk Hess
Us
e
graph with orientation
r
e
s
t
raints
commit
|
commitdiff
|
tree
2017-08-12
Berk He
s
s
Remove loo
p
over all atoms in in
i
t_mdatoms
commit
|
commitdiff
|
tree
2017-08-03
Berk
H
ess
Fix
o
rientation res
t
raint reference
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Add check f
o
r nr of orientation
r
e
straints
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fi
x
bugs with
o
rientation re
s
t
r
aints
commit
|
commitdiff
|
tree
2017-08-02
Be
r
k He
s
s
Clean up matrix inversion
commit
|
commitdiff
|
tree
2017-08-02
Ber
k
Hess
F
i
x orientation r
e
straint referenc
e
commit
|
commitdiff
|
tree
2017-08-02
Ber
k
H
e
ss
M
a
ke
l
o
op variab
l
es in orires
.
c
p
p local
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Ad
d
c
h
eck fo
r
nr of or
i
entati
o
n rest
r
ain
t
s
commit
|
commitdiff
|
tree
2017-07-25
Berk Hess
F
ix
b
u
g
s with ori
e
ntation restraints
commit
|
commitdiff
|
tree
2017-07-09
Ber
k
Hess
R
estructure the lo
a
d
balanci
n
g ti
m
ing
commit
|
commitdiff
|
tree
2017-07-04
Berk Hess
Uni
f
y nbnxn kernel di
s
patche
r
s
commit
|
commitdiff
|
tree
2017-07-03
B
erk
Hess
Remo
v
e gmx_conste
x
pr
commit
|
commitdiff
|
tree
2017-06-17
Berk Hess
Ad
d
tolerance to calc_verl
e
tbuf test
commit
|
commitdiff
|
tree
2017-06-12
B
e
r
k Hess
Disab
l
e PME t
u
ning
with the group s
c
heme
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
Fix null pointer print in DD
commit
|
commitdiff
|
tree
2017-06-10
Berk Hess
Put replica exc
h
ange paramet
e
rs in a struct
commit
|
commitdiff
|
tree
2017-06-09
Be
r
k He
s
s
R
e
p
lace iso by instead of
commit
|
commitdiff
|
tree
2017-06-08
Berk Hess
Fix COM pull
f
o
rc
e
with
S
D
commit
|
commitdiff
|
tree
next