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Fix COM pulling with external potential with #ranks>32
2018-03-14
Be
r
k
Hess
Fix COM p
u
lling with
external potent
i
a
l with #ranks>
3
2
commit
|
commitdiff
|
tree
2018-03-14
Berk
Hess
F
ix pull
bug w
i
th g
e
ome
t
ry=di
r
ection-pe
r
iodic
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
Add AWH fixes to relea
s
e notes
commit
|
commitdiff
|
tree
2018-03-13
Berk H
e
ss
Fix AWH
e
nsemb
l
e c
h
eckpo
i
n
ting
commit
|
commitdiff
|
tree
2018-03-13
Berk He
s
s
Fix AWH deconvolu
t
io
n
whe
n
shar
i
n
g a bias
commit
|
commitdiff
|
tree
2018-03-09
B
e
rk Hes
s
Correct pd
b
2gmx -missing
o
pt
i
on
commit
|
commitdiff
|
tree
2018-03-06
B
e
rk Hess
Make mult
i
-a
t
om TPI reproduc
i
ble
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Work around gc
c
bug
w
ith group ker
n
el t
a
ble
s
commit
|
commitdiff
|
tree
2018-03-02
Berk H
e
ss
Fix AWH bi
a
s-sha
r
ing with parallel
simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk
Hess
Detect AMD SMT
to
p
ology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
F
ix mdrun multi
s
im with se
p
a
r
ate PME rank
s
commit
|
commitdiff
|
tree
2018-02-23
Ber
k
H
e
s
s
F
ix md inte
g
rator with No
s
e-Hoover coup
l
ing
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Correct multisim MPI
b
a
rrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
Fi
x
ran
g
e
b
u
g in a
d
d_selection_groups in
tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Ber
k
Hess
Fix grompp net ch
a
rge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net ch
a
rge
c
heck
commit
|
commitdiff
|
tree
2018-02-08
Be
r
k
Hess
Use SIMD
b
ondeds without perturbe
d
interacti
o
ns
commit
|
commitdiff
|
tree
2018-02-08
Be
r
k
H
e
s
s
Allow
bonds
w
ith distance=0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Set cut
o
f
f modifiers in fo
r
cerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix a
s
sert
i
on
f
ailure in TPI
commit
|
commitdiff
|
tree
2018-01-18
Berk Hes
s
Fix COM
M
re
m
oval on
part o
f
the syste
m
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add ch
e
c
k
i
n grompp
to avoid assertion failure
commit
|
commitdiff
|
tree
2018-01-17
Ber
k
Hess
Re-enable GPU with walls
a
nd 1 energy gr
o
up
commit
|
commitdiff
|
tree
2018-01-16
Ber
k
Hess
Remove
tumbling ice-cube
w
arning with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Avoid md
r
un ec
h
oing "No o
p
tion -multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Reword
CPU/
G
PU
i
mba
l
a
n
ce notes
commit
|
commitdiff
|
tree
2018-01-09
B
e
r
k He
s
s
Do not
t
u
r
n on DL
B
at replica exchang
e
commit
|
commitdiff
|
tree
2018-01-08
Be
r
k
H
ess
Fix triclinic d
o
main deco
m
position bug
commit
|
commitdiff
|
tree
2017-12-19
B
e
r
k
Hess
Make acceleration
c
orre
c
tion VCM
mode work
commit
|
commitdiff
|
tree
2017-12-19
B
e
rk
H
ess
Make oversu
b
scriptio
n
warning consis
t
ent
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Require -ntmpi with sett
i
ng -
n
to
m
p with GPUs
commit
|
commitdiff
|
tree
2017-12-12
B
e
rk Hess
Check for large ene
r
gy at
f
i
r
s
t s
t
ep
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
A
void yelling a
b
out thread pinnin
g
tw
i
ce
commit
|
commitdiff
|
tree
2017-12-11
Be
r
k
Hess
Add gr
o
m
pp
note for PR pcouple
+ positio
n
r
estraint
s
commit
|
commitdiff
|
tree
2017-12-10
Berk He
s
s
Remove SIMD war
n
ing for AMD
Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk He
s
s
Tone down
n
ote abo
u
t not pi
n
ning threads
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Correct
S
hake test
tolerances
commit
|
commitdiff
|
tree
2017-12-08
B
erk
Hess
Ad
d
Viveca Lindahl a
s
contributor
commit
|
commitdiff
|
tree
2017-12-07
B
e
rk H
e
ss
C
h
oose fast
e
r
nbnxn S
I
MD kernels on AMD
Z
en
commit
|
commitdiff
|
tree
2017-12-05
Berk H
e
s
s
Fix DD exact
c
on
t
inuation bug
commit
|
commitdiff
|
tree
2017-12-04
B
erk Hess
Fix pme ga
t
her
in d
o
uble with AVX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Merge
"M
e
rge
b
ranch
r
e
l
e
a
se-2016 into release-
2
018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fi
x
ed initial t
e
mpe
r
a
ture reportin
g
commit
|
commitdiff
|
tree
2017-12-04
Berk Hes
s
Update mdrun signal h
e
lp t
e
xt
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Only
st
o
p at
n
s
t
list
s
teps wi
t
h -
r
eprod
commit
|
commitdiff
|
tree
2017-12-03
Berk Hes
s
Clear
v
site vel
o
ci
t
ies for simple integrators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Tighten
B
-spline moduli single
precis
i
on test tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoid asse
r
ti
o
n failure in AW
H
commit
|
commitdiff
|
tree
2017-11-29
B
erk Hess
Change the GPU S
M
T cut-off
t
o quadratic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Update docume
n
t
i
o
n
o
f Nose-Ho
o
ver
o
utpu
t
commit
|
commitdiff
|
tree
2017-11-28
Be
r
k Hess
Ref
a
ctor nbnxn exclu
s
ion setting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend gro
m
pp
m
issing e
n
ergy ter
m
mess
a
ge
commit
|
commitdiff
|
tree
2017-11-27
B
erk Hess
Enable auto
thread pinning wi
t
h thre
a
d
l
imiting
commit
|
commitdiff
|
tree
2017-11-27
B
e
rk Hess
Fix PME GPU with
w
al
l
s
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
Fix
c
o
mpiler wa
r
ning without MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk He
s
s
D
i
sabled CUD
A
timings
commit
|
commitdiff
|
tree
2017-11-24
B
erk H
e
ss
Speed
u
p nb
n
xn buffer cl
e
a
r
ing
commit
|
commitdiff
|
tree
2017-11-24
Ber
k
Hess
L
i
mit S
M
T wit
h
PME on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk
Hess
Update note in manual o
n
S
D
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Correc
t
PME
G
PU timi
n
g na
m
i
ng
commit
|
commitdiff
|
tree
2017-11-20
Berk H
e
s
s
Prevent PME tu
n
ing
e
xcess
i
ve
grid scali
n
g
commit
|
commitdiff
|
tree
2017-11-19
Berk Hess
Add SIM
D
for AWH
commit
|
commitdiff
|
tree
2017-11-16
B
e
rk Hess
Also
print 1x1 pair
-
list setup t
o
log
commit
|
commitdiff
|
tree
2017-11-10
Be
r
k Hess
F
ix genion charge summati
o
n accuracy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hes
s
Fix Ekin a
t
ste
p
0 with
C
OM remo
v
a
l
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Add
m
i
s
s
ing Ew
a
ld
c
orrection
f
or pme-user
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove unused sign par
a
met
e
r
fro
m
dih_angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
Remove
i
n
correct
comment
f
or
C
HARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
B
erk H
e
ss
F
i
x
gmx check
for tp
r
s with
d
i
fferent #atoms
commit
|
commitdiff
|
tree
2017-10-23
Berk Hess
Fix incorrect dV/dlambda for walls
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
Merge "
M
erge br
a
nch release-2016"
commit
|
commitdiff
|
tree
2017-10-20
B
e
r
k
Hess
Fix warning
f
or
c
onfout with per
i
odic mole
c
ul
e
s
commit
|
commitdiff
|
tree
2017-10-18
Berk
Hess
Made CUDA PME textu
r
e refer
e
nce c
o
nd
i
tional
commit
|
commitdiff
|
tree
2017-10-15
Berk H
e
ss
Impr
o
v
e vsite parallel checking
commit
|
commitdiff
|
tree
2017-10-12
Ber
k
H
ess
Simplify virial handlin
g
commit
|
commitdiff
|
tree
2017-10-11
Berk He
s
s
D
i
sable ARM Neon native
rsqrt iter
a
tion
commit
|
commitdiff
|
tree
2017-10-06
Berk
H
ess
Add accel
e
ra
t
i
o
n correction VCM mode
commit
|
commitdiff
|
tree
2017-10-06
Berk
H
ess
Fix max
_
size() in allo
c
ator
.
h
commit
|
commitdiff
|
tree
2017-10-06
B
e
rk Hess
Add SI
M
D intrin
s
ic
s
version
of simple update
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Improve Pa
d
dedRVecVector resizing
commit
|
commitdiff
|
tree
2017-10-05
Ber
k
Hess
Make S
I
MD ambiguou
s
test
w
ork with float/dou
b
le only
commit
|
commitdiff
|
tree
2017-10-04
B
e
rk
H
ess
Rem
o
ve a for
c
e buffer arg
u
ment fr
o
m IForcePro
v
id
e
r
commit
|
commitdiff
|
tree
2017-10-03
Ber
k
Hess
Move calling of s
p
ecial force f
u
nctions
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Remove hybr
i
d
g
pu+
c
pu nonbonded mode
commit
|
commitdiff
|
tree
2017-09-25
Berk He
s
s
Put rerun stat
e
p
r
epa
r
ation in a function
commit
|
commitdiff
|
tree
2017-09-25
Berk Hess
Set
glo
b
al state on master rank only
commit
|
commitdiff
|
tree
2017-09-23
B
e
rk H
e
ss
Fix grompp with Ander
s
en massiv
e
and n
o
C
O
M remov
a
l
commit
|
commitdiff
|
tree
2017-09-20
B
e
rk Hess
Change n
b
nxn in
d
exing t
o
te
m
plates
commit
|
commitdiff
|
tree
2017-09-15
Berk Hess
Remove nb-parameters from t_fo
r
cere
c
commit
|
commitdiff
|
tree
2017-09-14
Berk Hess
Fix n
b
nxn SIMD 2xNN
P
M
E
tabulated kernel
commit
|
commitdiff
|
tree
2017-09-12
B
e
rk Hess
Fix
e
xceptio
n
in SIMD LJ
PME solv
e
commit
|
commitdiff
|
tree
2017-09-12
Berk
H
ess
Do not
pass state to init_replica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Ber
k
He
s
s
Fix PBC
b
ugs in
the swa
p
code
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
Avoi
d
inf
in SIMD double sq
r
t()
commit
|
commitdiff
|
tree
2017-09-07
Berk Hess
Fix
FEP
sta
t
e w
i
th r
e
run
commit
|
commitdiff
|
tree
2017-09-04
Be
r
k Hess
F
i
x t
w
o nb
n
xn se
a
rch
i
ndex
i
ng bugs
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Consolidate ar
c
hitect
u
re b
o
oleans
commit
|
commitdiff
|
tree
2017-09-03
Berk Hess
Put
mdru
n
option
s
in str
u
cts
commit
|
commitdiff
|
tree
2017-09-02
Be
r
k Hess
P
ut
a
ll
dom
d
ec o
p
tions in a struct
commit
|
commitdiff
|
tree
2017-09-02
B
erk Hess
Fix mdrun -nb option pointer
commit
|
commitdiff
|
tree
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