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Update to prepare for 2018.4 point release
2018-08-22
Berk Hess
Fix missing interac
t
i
o
n
s
w
i
th GPU an
d
DD
commit
|
commitdiff
|
tree
2018-08-21
Berk Hess
En
s
ure domains are large
e
noug
h
for atom
m
ot
i
on
commit
|
commitdiff
|
tree
2018-08-21
Berk
H
ess
Fixe
d
mdrun seg
v
with QM/MM ONIOM
s
c
heme
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
Refactor calc_ve
r
l
et
_
buff
e
r_size()
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix Verlet buffer
estima
t
e with BD
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fix assertion fail
u
re in CG
commit
|
commitdiff
|
tree
2018-08-20
Berk
H
ess
R
e
ally fix C
G
with
m
u
ltipl
e
domains
commit
|
commitdiff
|
tree
2018-08-18
Berk Hess
Add c
h
eck for pull gro
u
p PBC
t
o gr
o
mp
p
commit
|
commitdiff
|
tree
2018-06-12
B
erk Hess
Add AWH
c
ont
i
nuation c
o
nsi
s
tenc
y
c
h
e
c
ki
n
g
commit
|
commitdiff
|
tree
2018-06-12
B
er
k
H
e
ss
Add fatal error fo
r
i
n
con
s
istent grap
h
commit
|
commitdiff
|
tree
2018-06-12
B
erk Hess
Avoid COM removal
m
oving froz
e
n
atoms
commit
|
commitdiff
|
tree
2018-06-12
Berk Hess
R
e
move c
o
nstraint v c
o
r
r
e
ction
for frozen
atoms
commit
|
commitdiff
|
tree
2018-06-06
B
e
rk Hes
s
Fix MPI incons
i
stency in EM a
f
ter c
o
ns
t
r
a
int failur
e
commit
|
commitdiff
|
tree
2018-06-04
Be
r
k Hess
Fix
s
e
g
v i
n
AWH error
message
commit
|
commitdiff
|
tree
2018-05-03
Berk
H
ess
Enab
l
e
SIMD version of upda
t
e
commit
|
commitdiff
|
tree
2018-04-24
Berk Hess
Fi
x
i
ndex
i
ng issue in the pull code
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Change warninp filenm
to std::string
commit
|
commitdiff
|
tree
2018-03-20
Berk
H
ess
Fix gmx dump AWH fo
r
matt
i
ng issue
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
D
isallow
single simulat
i
o
n with
m
ultisim
commit
|
commitdiff
|
tree
2018-03-16
Berk
H
ess
Correct PMF sign erro
r
in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Fix re
c
e
nt
m
drun signaling bug
commit
|
commitdiff
|
tree
2018-03-15
Berk H
e
ss
Fi
x
virial
w
ith
ex
t
er
n
al pull p
o
tentia
l
and MPI
commit
|
commitdiff
|
tree
2018-03-14
B
erk Hess
Impro
v
e inter-simulation
s
ignaling
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
F
ix mdrun signa
l
ling
with AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk He
s
s
Fix COM pu
l
ling with exte
r
na
l
potent
i
al w
i
th
#
r
an
k
s>32
commit
|
commitdiff
|
tree
2018-03-14
Be
r
k Hess
Fix pul
l
bug wit
h
geometry=direction-periodic
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add AWH fi
x
es
to release notes
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
Fix A
W
H e
n
semble checkpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
F
ix AWH de
c
onvolution w
h
en sharin
g
a bia
s
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
C
o
r
rect pdb2
g
m
x
-missing option
commit
|
commitdiff
|
tree
2018-03-06
B
e
rk Hess
Make multi-
a
tom TPI reproduci
b
le
commit
|
commitdiff
|
tree
2018-03-05
Be
r
k Hess
Work around gcc bu
g
w
ith g
r
oup kernel tables
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AWH b
i
as-sharing with parallel simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk
He
s
s
Detect AMD S
M
T
t
opology
commit
|
commitdiff
|
tree
2018-03-01
B
erk Hess
Fix mdru
n
multisim with
s
e
p
arate PME ranks
commit
|
commitdiff
|
tree
2018-02-23
Ber
k
Hess
Fix
md inte
g
rat
o
r
wit
h
Nose-Hoover c
o
u
p
l
ing
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Correct m
u
l
t
i
sim MP
I
bar
r
i
e
r
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk Hess
Fix range bu
g
in add_selection_g
r
oups in
tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk Hess
F
ix
g
rompp net ch
a
rge c
h
e
c
k
commit
|
commitdiff
|
tree
2018-02-14
Ber
k
Hess
F
ix grom
p
p
n
e
t
charge che
c
k
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
Use SIMD bondeds withou
t
perturbed i
n
teract
i
ons
commit
|
commitdiff
|
tree
2018-02-08
B
erk Hess
Allow bonds with d
i
stance=0
commit
|
commitdiff
|
tree
2018-02-05
B
er
k
H
es
s
Set
cutoff modifiers in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Be
r
k He
s
s
Fix assertion failure i
n
TPI
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix COMM re
m
ov
a
l on
p
art of the
s
y
stem
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add check in gr
o
mpp to
a
v
oid a
s
serti
o
n failure
commit
|
commitdiff
|
tree
2018-01-17
B
e
rk Hess
Re
-
en
a
bl
e
GPU wi
t
h walls
a
nd 1 energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Remove
tumbling ice-c
u
be warning with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk H
e
ss
Avoid mdrun echo
i
ng "No opti
o
n -m
u
lti"
commit
|
commitdiff
|
tree
2018-01-09
Berk
Hess
Reword CPU/GPU imbal
a
nce note
s
commit
|
commitdiff
|
tree
2018-01-09
B
e
rk Hess
Do
not turn on DLB
a
t
r
eplica exchange
commit
|
commitdiff
|
tree
2018-01-08
Be
r
k He
s
s
Fix
t
riclinic domain deco
m
p
o
s
ition bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make
a
ccelerati
o
n correction VCM mod
e
work
commit
|
commitdiff
|
tree
2017-12-19
Berk H
e
ss
M
ake oversu
b
scripti
o
n warning consis
t
e
n
t
commit
|
commitdiff
|
tree
2017-12-14
Be
r
k Hess
R
equire
-
ntmpi wi
t
h setting -ntom
p
with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Ber
k
Hess
C
h
eck for large energy
at firs
t
s
te
p
commit
|
commitdiff
|
tree
2017-12-12
B
e
rk Hess
Av
o
id ye
l
l
i
n
g about
t
hread pinning
t
w
ice
commit
|
commitdiff
|
tree
2017-12-11
Berk He
s
s
Add grompp note
f
o
r
PR
p
c
o
uple + pos
i
t
i
on rest
r
aints
commit
|
commitdiff
|
tree
2017-12-10
Berk
H
ess
Rem
o
ve SI
M
D
warni
n
g for AMD
Ze
n
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Tone down note about not pinning threads
commit
|
commitdiff
|
tree
2017-12-08
B
e
rk Hess
Correct Shake test tole
r
a
n
ces
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add
Vivec
a
L
indahl as contributor
commit
|
commitdiff
|
tree
2017-12-07
Be
r
k He
s
s
Choose fast
e
r
nb
n
xn SIMD ker
n
els on A
M
D Zen
commit
|
commitdiff
|
tree
2017-12-05
B
erk
H
ess
Fix DD exact continuatio
n
bug
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
ess
Fix
p
me gather in doubl
e
with
A
V
X(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Merge "Merge
branch
r
elease
-
2016 i
n
to releas
e
-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fixed i
n
itial tempe
r
at
u
re rep
o
r
t
ing
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
U
p
date mdrun si
g
nal h
e
lp tex
t
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk H
e
ss
O
nly stop
a
t
nstlist ste
p
s with -reprod
commit
|
commitdiff
|
tree
2017-12-03
B
erk Hess
Clea
r
vsite velocities
f
or sim
p
le integ
r
ators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Tighten
B-spline modu
l
i si
n
g
l
e precision t
e
st toleran
c
e
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
B
e
r
k Hess
Avo
i
d a
s
sertion failure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
Change the GP
U
SMT cut-off t
o
qu
a
dratic
commit
|
commitdiff
|
tree
2017-11-28
Berk
Hess
U
pdate docume
n
ti
o
n of Nose-Hoover output
commit
|
commitdiff
|
tree
2017-11-28
B
e
rk
Hess
Refactor nbnxn exclusion setting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend grompp miss
i
n
g energy term message
commit
|
commitdiff
|
tree
2017-11-27
Be
r
k Hess
Enable auto thr
e
ad pinning with threa
d
limiting
commit
|
commitdiff
|
tree
2017-11-27
B
erk Hess
Fix PM
E
GPU
w
ith walls
commit
|
commitdiff
|
tree
2017-11-25
Ber
k
Hess
Fi
x
com
p
i
l
e
r
warning wi
t
hout MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Disa
b
led CUDA ti
m
i
ngs
commit
|
commitdiff
|
tree
2017-11-24
B
erk
H
e
ss
S
pe
e
d
up nbnxn
b
u
ffer c
l
e
a
rin
g
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
L
imit SMT with P
M
E on
GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk He
s
s
Upd
a
te note in manu
a
l on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk He
s
s
Correct PME G
P
U t
i
ming naming
commit
|
commitdiff
|
tree
2017-11-20
Be
r
k He
s
s
P
revent
P
ME tuning excessive grid scaling
commit
|
commitdiff
|
tree
2017-11-19
Berk He
s
s
A
dd SIMD for
A
WH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Also
print 1x1
p
air
-
list setu
p
to log
commit
|
commitdiff
|
tree
2017-11-10
Berk He
s
s
Fix genion charge summation accura
c
y
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix Eki
n
at
step 0 wi
t
h COM removal
commit
|
commitdiff
|
tree
2017-11-02
Berk
H
e
ss
A
d
d
mi
s
s
i
ng
Ewald co
r
recti
o
n for pme-user
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove unused sign p
a
ram
e
te
r
from
dih_angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
R
e
move
i
ncorre
c
t comme
n
t for CHARMM ti
p
s3p
commit
|
commitdiff
|
tree
2017-10-24
Berk Hess
Fix
gmx check
f
or tprs with
d
ifferent #atoms
commit
|
commitdiff
|
tree
2017-10-23
Berk H
e
ss
Fix incorrect
d
V
/dl
a
mbda for walls
commit
|
commitdiff
|
tree
2017-10-21
Be
r
k Hess
M
e
rge "M
e
rge bra
n
c
h
relea
s
e-20
1
6"
commit
|
commitdiff
|
tree
2017-10-20
B
erk Hess
Fix warnin
g
fo
r
c
onfout wi
t
h periodic mole
c
ules
commit
|
commitdiff
|
tree
2017-10-18
Ber
k
Hess
Made CUDA PM
E
t
e
x
ture reference
conditional
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Improve vsite parallel ch
e
cking
commit
|
commitdiff
|
tree
2017-10-12
Berk H
e
ss
Simplify viria
l
handling
commit
|
commitdiff
|
tree
2017-10-11
Ber
k
Hess
Di
s
able AR
M
Neon native rsqrt iteration
commit
|
commitdiff
|
tree
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