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Allow empty lines in hdb files
2017-12-19
Berk H
e
s
s
Make
accelerati
o
n
c
orr
e
ctio
n
V
C
M
mode
work
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Mak
e
oversub
s
cr
i
ption warning consistent
commit
|
commitdiff
|
tree
2017-12-14
B
e
r
k Hess
Requi
r
e
-ntmpi with sett
i
ng -nto
m
p with
G
PUs
commit
|
commitdiff
|
tree
2017-12-12
Berk
Hess
Chec
k
f
or lar
g
e energy at first step
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
A
v
oid yelling about thr
e
ad pi
n
ni
n
g
twice
commit
|
commitdiff
|
tree
2017-12-11
Berk
Hes
s
A
dd gr
o
mp
p
n
o
te
f
or PR pcouple + posit
i
on restraints
commit
|
commitdiff
|
tree
2017-12-10
B
e
rk H
e
ss
Remove SIMD warning f
o
r AMD
Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
T
one
down
n
ote about not pinning threads
commit
|
commitdiff
|
tree
2017-12-08
Berk H
e
s
s
Co
r
r
e
ct Sha
k
e test tolera
n
c
es
commit
|
commitdiff
|
tree
2017-12-08
B
erk
H
e
ss
Add Vivec
a
Lindahl as co
n
t
r
ib
u
tor
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Choose fas
t
er
nbn
x
n SIMD
kernels on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
B
e
r
k Hess
Fix DD
e
xact continuation bug
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fix
pme gather in double with AVX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
M
e
rge
"
Merge
branch
r
ele
a
se-2016 into
release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k Hess
F
i
xed initial temperature
r
eport
i
ng
commit
|
commitdiff
|
tree
2017-12-04
Berk Hes
s
Update mdrun signal help text
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk
H
es
s
Only s
t
op at nstlist steps with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Be
r
k Hess
Clear v
s
ite veloci
t
ies
f
o
r
s
impl
e
int
e
gr
a
tors
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
T
ighten
B
-splin
e
m
o
d
uli single preci
s
i
on test tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk
H
e
s
s
A
void asser
t
i
on f
a
ilure in
AWH
commit
|
commitdiff
|
tree
2017-11-29
Be
r
k Hess
C
hange the GPU
S
M
T
cut
-
o
f
f to q
u
a
drat
i
c
commit
|
commitdiff
|
tree
2017-11-28
B
e
rk Hess
U
p
d
a
te do
c
ument
i
on of Nos
e
-Hoo
v
er o
u
tput
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Refactor nbn
x
n
exclusion setting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend
g
rompp missing ener
g
y ter
m
mess
a
g
e
commit
|
commitdiff
|
tree
2017-11-27
Ber
k
Hess
Enable auto thread pin
n
ing w
i
th threa
d
limiting
commit
|
commitdiff
|
tree
2017-11-27
Be
r
k
Hes
s
F
i
x
P
M
E GPU
w
i
th w
a
lls
commit
|
commitdiff
|
tree
2017-11-25
Berk He
s
s
Fix compile
r
warn
i
ng wi
t
hout
M
P
I
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
D
i
s
abled
CU
D
A
t
i
mings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Speed up n
b
nxn b
u
ff
e
r clearing
commit
|
commitdiff
|
tree
2017-11-24
B
erk Hess
L
i
mit
S
MT with
PME
o
n GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Upd
a
te note in manual on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
C
o
r
rect PME GP
U
timing n
a
min
g
commit
|
commitdiff
|
tree
2017-11-20
Berk H
e
ss
Preven
t
PME tuning excessive grid s
c
alin
g
commit
|
commitdiff
|
tree
2017-11-19
Berk
H
es
s
Add SIMD for
A
WH
commit
|
commitdiff
|
tree
2017-11-16
Berk H
e
ss
Also print 1x1 pair-
l
ist setup
t
o log
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
Fix genion charge sum
m
a
tion accu
r
acy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix
E
kin at step
0
wi
t
h COM r
e
moval
commit
|
commitdiff
|
tree
2017-11-02
B
e
r
k Hess
Add missin
g
Ewa
l
d correction f
o
r pme-user
commit
|
commitdiff
|
tree
2017-10-30
Berk Hes
s
Remove unused sign pa
r
ameter from dih_an
g
le()
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
Remov
e
incor
r
ect comment for CHA
R
M
M tips
3
p
commit
|
commitdiff
|
tree
2017-10-24
Berk
H
ess
Fix gmx check for tprs wi
t
h different
#
atoms
commit
|
commitdiff
|
tree
2017-10-23
Berk
He
s
s
Fix incorrect dV/dlambda
f
o
r
w
a
lls
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
Merg
e
"
Merge branch releas
e
-
2
0
1
6
"
commit
|
commitdiff
|
tree
2017-10-20
Berk He
s
s
Fix warning for confo
u
t
with
p
eriodic
m
olecu
l
es
commit
|
commitdiff
|
tree
2017-10-18
B
e
r
k
Hess
Made CUDA PME texture reference conditional
commit
|
commitdiff
|
tree
2017-10-15
B
erk He
s
s
Improve vsite parallel che
c
k
i
n
g
commit
|
commitdiff
|
tree
2017-10-12
Berk Hess
S
implify virial
h
a
n
d
lin
g
commit
|
commitdiff
|
tree
2017-10-11
B
e
rk H
e
s
s
Disable ARM Neon native rsqrt
it
e
r
a
tion
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Add ac
c
eler
a
t
ion correctio
n
VCM mod
e
commit
|
commitdiff
|
tree
2017-10-06
B
erk Hess
Fix max_size() in
a
llocato
r
.
h
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Add S
I
MD
i
n
t
rinsics version of simp
l
e update
commit
|
commitdiff
|
tree
2017-10-06
B
erk H
e
ss
Improve PaddedRVecVector resi
z
ing
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
Mak
e
SIMD ambiguous
t
e
st
w
or
k
with float
/
double
onl
y
commit
|
commitdiff
|
tree
2017-10-04
Berk H
e
ss
Remove a
f
o
rce buff
e
r
argu
m
e
n
t
f
r
o
m
IForceProvider
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
M
o
ve ca
l
l
i
ng of
s
pecial for
c
e functions
commit
|
commitdiff
|
tree
2017-10-02
Berk
H
ess
Remove hybrid
g
p
u
+
cpu nonbon
d
ed mode
commit
|
commitdiff
|
tree
2017-09-25
Berk
Hess
Put
r
e
r
un state prepa
r
a
t
ion in a funct
i
on
commit
|
commitdiff
|
tree
2017-09-25
Berk Hess
Set global st
a
te on mas
t
er rank only
commit
|
commitdiff
|
tree
2017-09-23
Berk Hess
Fix grompp
wi
t
h Anders
e
n massi
v
e and no COM re
m
ova
l
commit
|
commitdiff
|
tree
2017-09-20
Berk Hess
Chan
g
e nbnxn indexing to templates
commit
|
commitdiff
|
tree
2017-09-15
B
e
r
k Hess
Remove nb-paramete
r
s from t_forcerec
commit
|
commitdiff
|
tree
2017-09-14
Berk
H
ess
Fix
n
bnx
n
S
IMD 2xNN PME tabu
l
ated kernel
commit
|
commitdiff
|
tree
2017-09-12
Be
r
k Hess
Fix exception i
n
SIMD LJ P
M
E solve
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Do
not pass sta
t
e to
init_replica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Berk Hess
Fix PBC bugs
i
n the swap
code
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
A
v
oid inf in SIMD double
s
q
rt()
commit
|
commitdiff
|
tree
2017-09-07
Berk Hes
s
Fix
FEP sta
t
e
wit
h
rerun
commit
|
commitdiff
|
tree
2017-09-04
B
e
rk Hess
Fix two
n
bnxn se
a
rch indexing
bugs
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Consol
i
d
ate ar
c
hitecture booleans
commit
|
commitdiff
|
tree
2017-09-03
Berk Hess
Put md
r
un options in
s
tru
c
ts
commit
|
commitdiff
|
tree
2017-09-02
Berk He
s
s
Put all domdec option
s
in a struct
commit
|
commitdiff
|
tree
2017-09-02
Be
r
k Hes
s
F
i
x mdrun -nb optio
n
poi
n
t
er
commit
|
commitdiff
|
tree
2017-09-01
Berk
H
ess
Fix mdrun -nb optio
n
poi
n
t
er
commit
|
commitdiff
|
tree
2017-08-29
Berk Hess
Make pull potential r
e
gistration thread-safe
commit
|
commitdiff
|
tree
2017-08-29
Ber
k
He
s
s
S
e
t default GMX_OPENMP_MAX_TH
R
EA
D
S to 64
commit
|
commitdiff
|
tree
2017-08-28
Berk Hess
Avoid bo
n
ded
f
orce
s
loop
s
/
t
imers o
n
inputs
with no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Berk Hess
E
n
abl
e
dynamic
pair li
s
t prun
i
ng
commit
|
commitdiff
|
tree
2017-08-18
Ber
k
He
s
s
Add CPU reference and SIMD prun
i
ng kernels
commit
|
commitdiff
|
tree
2017-08-16
B
e
rk Hess
A
dd dynamic
p
a
ir-list pruning framewo
r
k
commit
|
commitdiff
|
tree
2017-08-16
Berk Hess
Clean up nbnxn clu
s
ter pair addit
i
on co
d
e
commit
|
commitdiff
|
tree
2017-08-15
Ber
k
H
ess
Add OpenMP for orie
n
tation restraints
commit
|
commitdiff
|
tree
2017-08-15
Berk
H
ess
U
s
e graph
w
ith orientati
o
n re
s
traints
commit
|
commitdiff
|
tree
2017-08-12
Berk
He
s
s
Remov
e
loop ov
e
r all a
t
om
s
in init_m
d
atoms
commit
|
commitdiff
|
tree
2017-08-03
Berk H
e
ss
Fix orien
t
ation restr
a
i
n
t r
e
f
e
rence
commit
|
commitdiff
|
tree
2017-08-03
B
e
r
k H
e
ss
A
dd c
h
e
c
k for
n
r of
o
r
ientatio
n
restra
i
n
ts
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fix bugs with
o
r
ientat
i
on restrain
t
s
commit
|
commitdiff
|
tree
2017-08-02
Be
r
k Hess
C
l
e
a
n up
m
a
tr
i
x in
v
ersion
commit
|
commitdiff
|
tree
2017-08-02
Berk
H
ess
F
i
x orientation rest
r
aint referen
c
e
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Make loop v
a
riables
in orires
.
cpp local
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Add
check for nr of
o
r
ie
n
tation restra
i
nts
commit
|
commitdiff
|
tree
2017-07-25
Berk Hes
s
Fix
b
ugs with
or
i
entation
r
e
straints
commit
|
commitdiff
|
tree
2017-07-09
Berk Hess
Restru
c
ture
t
he load balancing timing
commit
|
commitdiff
|
tree
2017-07-04
Berk Hess
Uni
f
y
n
bnxn ker
n
el dispa
t
c
h
ers
commit
|
commitdiff
|
tree
2017-07-03
Berk Hess
Rem
o
ve gmx
_
cons
t
expr
commit
|
commitdiff
|
tree
2017-06-17
Berk Hess
Add tolerance to
calc_v
e
r
l
etbuf test
commit
|
commitdiff
|
tree
2017-06-12
Berk Hes
s
Disable PME tuning with th
e
g
r
oup
scheme
commit
|
commitdiff
|
tree
2017-06-12
Be
r
k Hess
Fix nu
l
l
p
oin
t
er pr
i
nt in DD
commit
|
commitdiff
|
tree
2017-06-10
Berk Hess
Put rep
l
ica exchange
p
arameters in
a
struct
commit
|
commitdiff
|
tree
2017-06-09
B
e
rk
Hess
Replace
i
so by
i
nstead of
commit
|
commitdiff
|
tree
2017-06-08
Be
r
k
Hess
F
ix COM pul
l
force
w
ith SD
commit
|
commitdiff
|
tree
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