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Use std::vector in nbnxn_search_t
2018-05-22
Berk Hess
Use
std::vect
o
r in nbnxn_search_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use std::vector in nbnx
n
_
gr
i
d_t
commit
|
commitdiff
|
tree
2018-05-18
Ber
k
Hess
Clean up in n
b
nxn_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Ber
k
Hess
Split off domdec distribution and cellsize
s
commit
|
commitdiff
|
tree
2018-05-17
Berk
H
e
s
s
Split atom redistrib
u
t
i
o
n
off
f
rom domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk He
s
s
Remove commrec
from
s
et_dd
b
ox
(
)
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Clea
n
up PME domain count passing
commit
|
commitdiff
|
tree
2018-05-03
B
erk Hess
E
nable S
I
MD version o
f
update
commit
|
commitdiff
|
tree
2018-04-27
Ber
k
He
s
s
Remove pull MPI code dupl
i
c
a
tion
commit
|
commitdiff
|
tree
2018-04-24
Berk Hess
Fix indexi
n
g i
s
s
ue in the pull code
commit
|
commitdiff
|
tree
2018-04-16
Berk
H
e
s
s
Mov
e
natoms_
m
o
l
ou
t
o
f
gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-09
B
erk Hess
Convert gmx_m
o
lblo
c
k
_
t to C++
commit
|
commitdiff
|
tree
2018-04-03
B
erk Hess
Con
v
er
t
gmx_mto
p
_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Change wa
r
ninp filenm
t
o
std::string
commit
|
commitdiff
|
tree
2018-04-03
Be
r
k Hess
Do
not calculate COM for p
u
ll group 0
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move file
opening ou
t
of in
i
t_pull(
)
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
M
odu
l
ariz
e
p
ul
l
_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Berk H
e
ss
Remove mols f
r
om
gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-20
Berk
H
e
s
s
Fix
g
mx
dump AWH formatting i
s
sue
commit
|
commitdiff
|
tree
2018-03-20
Berk He
s
s
Disallo
w
single simu
l
at
i
o
n
with multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk
H
e
ss
C
o
r
rect PMF
s
i
g
n err
o
r i
n
AWH bias sh
a
ring
commit
|
commitdiff
|
tree
2018-03-16
B
e
rk Hess
Fix recen
t
m
d
run
s
ign
a
ling
b
ug
commit
|
commitdiff
|
tree
2018-03-15
Berk He
s
s
Fix vi
r
ial with e
x
ternal p
u
ll pote
n
tial and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Impro
v
e inter-simulat
i
on s
i
gn
a
l
i
n
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix mdrun si
g
nallin
g
with AWH bias sha
r
ing
commit
|
commitdiff
|
tree
2018-03-14
B
e
r
k
Hess
Fix COM pul
l
ing wi
t
h external potential with #ranks
>
3
2
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk Hess
Fix pull bug with geome
t
ry
=
direction
-
p
e
ri
o
dic
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add
A
WH fixes to release notes
commit
|
commitdiff
|
tree
2018-03-13
Berk
H
es
s
Fi
x
AWH ensemb
l
e
c
h
eck
p
ointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH
d
e
co
n
volution
w
hen
s
h
aring a bias
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Correct pd
b
2gmx -missing op
t
ion
commit
|
commitdiff
|
tree
2018-03-07
Ber
k
Hess
F
ix memory
l
eak in PME
commit
|
commitdiff
|
tree
2018-03-06
Berk
Hes
s
C
o
nvert t_fil
e
nm to C++
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Make multi-ato
m
TPI reproducible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Work a
r
ound gcc bug wi
t
h g
r
ou
p
k
ernel tables
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Leave nu
l
lptr op
t
in t_f
i
lenm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix c
p
pcheck warn
i
ng
commit
|
commitdiff
|
tree
2018-03-02
B
erk Hess
Fix AWH bias-shar
i
ng
w
i
t
h
p
arallel simu
l
ation
commit
|
commitdiff
|
tree
2018-03-01
B
e
rk Hess
Detect AMD SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Be
r
k H
e
ss
Fix mdru
n
multis
i
m
w
ith separate PME ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix md integrator with Nose-Hoover co
u
pling
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simpli
f
y mdrun
tMPI th
r
ead spawning
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Corr
e
ct m
u
ltisim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk He
s
s
Remove support for tpx ver
s
i
o
n before 58/g
m
x4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix range bug in a
d
d
_
selection_grou
p
s in
tngio
.
c
p
p
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp n
e
t
c
harge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix gr
o
m
pp
net ch
a
rge
chec
k
commit
|
commitdiff
|
tree
2018-02-08
Berk Hes
s
U
se SIMD bondeds without p
e
rt
u
rbed intera
c
tions
commit
|
commitdiff
|
tree
2018-02-08
Ber
k
Hess
Allow bonds wi
t
h
distance=0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Set
cut
o
ff mo
d
ifiers in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk
Hess
Fix assertion failur
e
in TP
I
commit
|
commitdiff
|
tree
2018-01-30
B
erk Hess
R
e
moved unuse
d
f
lag PCA_CAN_RE
A
D
_
NOD
E
commit
|
commitdiff
|
tree
2018-01-18
Be
r
k Hess
Fix CO
M
M r
e
moval on
part o
f
the syste
m
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Ad
d
ch
e
ck in grom
p
p
t
o a
v
oid
assertio
n
failure
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
R
e
p
l
ace stderr prints in filenm
.
cpp by asser
t
s
commit
|
commitdiff
|
tree
2018-01-17
Be
r
k Hess
Re-
e
n
able GPU
w
i
th walls
and 1
energy group
commit
|
commitdiff
|
tree
2018-01-16
Ber
k
Hess
Re
m
ov
e
tumbling ice-cube warning with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk
H
ess
Avoid mdrun
echoin
g
"No option -mu
l
ti"
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Reword CP
U
/GPU imbalance no
t
es
commit
|
commitdiff
|
tree
2018-01-09
Ber
k
Hess
Do not
turn on DLB
at
r
ep
l
ica exchange
commit
|
commitdiff
|
tree
2018-01-08
Berk Hes
s
F
ix tricl
i
n
i
c domain de
c
omposition bug
commit
|
commitdiff
|
tree
2017-12-19
Ber
k
Hess
Make acce
l
eratio
n
correction VCM m
o
de wo
r
k
commit
|
commitdiff
|
tree
2017-12-19
Berk
H
ess
Mak
e
oversubscription warning
consist
e
nt
commit
|
commitdiff
|
tree
2017-12-14
B
e
r
k
He
s
s
Require -
n
tmp
i
w
i
th se
t
tin
g
-
n
t
om
p
w
i
t
h
G
PUs
commit
|
commitdiff
|
tree
2017-12-12
B
e
r
k Hess
C
h
eck for large ener
g
y
a
t first step
commit
|
commitdiff
|
tree
2017-12-12
Be
r
k He
s
s
Av
o
id yellin
g
abo
u
t
thread p
i
nning tw
i
ce
commit
|
commitdiff
|
tree
2017-12-11
B
erk Hess
Add grompp no
t
e f
o
r
PR
pcouple +
position res
t
rain
t
s
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remov
e
SIMD w
a
r
n
i
n
g
f
o
r
AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Ton
e
d
o
wn note
a
bou
t
not pin
n
i
n
g thr
e
a
d
s
commit
|
commitdiff
|
tree
2017-12-08
Be
r
k Hes
s
Correct Shak
e
t
e
st
tole
r
a
n
ces
commit
|
commitdiff
|
tree
2017-12-08
Ber
k
Hess
Add V
i
v
eca Lindahl as con
t
ributor
commit
|
commitdiff
|
tree
2017-12-07
Berk
Hess
Choose f
a
ster nbnxn
S
IMD kerne
l
s on A
M
D Zen
commit
|
commitdiff
|
tree
2017-12-05
B
erk H
e
s
s
Fix DD exact continuation bug
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fix
p
me g
a
t
h
er in double wit
h
A
V
X(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk
Hess
Merge "
M
erg
e
branch release-201
6
i
nto re
l
ease-201
8
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
Fixed init
i
al temperatur
e
rep
o
rtin
g
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k
Hes
s
Update m
d
run signal help text
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
ess
Onl
y
stop at nstli
s
t ste
p
s
with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Berk
H
ess
Clear v
s
ite
velo
c
ities fo
r
simple inte
g
r
ators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Tighten B-spline moduli single
preci
s
ion test tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoid assertion fail
u
re in
A
WH
commit
|
commitdiff
|
tree
2017-11-29
Be
r
k
H
ess
Chan
g
e the GP
U
S
MT cut-of
f
to quadratic
commit
|
commitdiff
|
tree
2017-11-28
B
e
rk Hes
s
Update docum
e
ntion of Nose-Hoover output
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
R
e
fa
c
tor nbnxn exclu
s
ion
setting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend gr
o
m
pp missin
g
e
nergy term me
s
sage
commit
|
commitdiff
|
tree
2017-11-27
B
erk
H
ess
Enable aut
o
thread pi
n
n
i
n
g
with
thr
e
ad limiting
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Fix P
M
E GPU with
w
alls
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
Fix compiler w
a
rnin
g
without
MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk
H
ess
Disabled CUDA timi
n
gs
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
S
p
e
e
d up nbnxn buff
e
r clearin
g
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Li
m
it SMT
w
ith PME on GPU
commit
|
commitdiff
|
tree
2017-11-23
Ber
k
H
ess
U
p
d
ate note in manu
a
l on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk He
s
s
Correct PM
E
GPU tim
i
n
g
naming
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
Preven
t
PME
tuning ex
c
essi
v
e grid scaling
commit
|
commitdiff
|
tree
2017-11-19
Be
r
k Hess
Add SIMD fo
r
AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hes
s
Also print 1x1 pair-l
i
st setup to lo
g
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
Fix genion charge summa
t
ion accurac
y
commit
|
commitdiff
|
tree
2017-11-02
Berk H
e
ss
Fix Ekin at step 0 with COM removal
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Add missing Ewald correction for p
m
e-user
commit
|
commitdiff
|
tree
2017-10-30
Ber
k
Hess
Remo
v
e
u
nused sign param
e
ter f
r
om dih_angle()
commit
|
commitdiff
|
tree
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