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Convert nbnxn_search to C++
2018-05-23
Berk Hess
Convert
nbnxn_search t
o
C++
commit
|
commitdiff
|
tree
2018-05-22
Berk
H
e
s
s
Change nbnxn grid r
e
allocati
o
n
commit
|
commitdiff
|
tree
2018-05-22
B
erk Hess
Use std::ve
c
tor
i
n nbnxn_
s
earch
_
t
commit
|
commitdiff
|
tree
2018-05-22
B
e
r
k Hess
Use std::vect
o
r in nbnxn_gri
d
_t
commit
|
commitdiff
|
tree
2018-05-18
Ber
k
Hess
Clean up in nbnxn_grid
.
c
pp
commit
|
commitdiff
|
tree
2018-05-17
Berk
H
ess
Split off domdec di
s
tribution and cellsizes
commit
|
commitdiff
|
tree
2018-05-17
B
e
rk Hess
Split
atom redistri
b
ution o
f
f from domd
e
c
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Remove commre
c
from set_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
Berk He
s
s
Clean up PME domain
c
ount pa
s
sing
commit
|
commitdiff
|
tree
2018-05-03
Be
r
k H
e
ss
Ena
b
le SI
M
D ve
r
si
o
n
of u
p
date
commit
|
commitdiff
|
tree
2018-04-27
Ber
k
Hess
R
e
move
pull MPI cod
e
duplication
commit
|
commitdiff
|
tree
2018-04-24
Berk H
e
ss
Fix indexing issue in the
pull code
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Move
n
atoms_mol out of gmx_m
o
lblock_t
commit
|
commitdiff
|
tree
2018-04-09
Berk
Hess
Convert gmx_
m
olbl
o
c
k
_
t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Convert gmx_mtop_t to
C
++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Change warninp filenm to std::strin
g
commit
|
commitdiff
|
tree
2018-04-03
B
erk Hess
Do not calcul
a
te COM for pul
l
group 0
commit
|
commitdiff
|
tree
2018-03-29
B
e
rk Hess
Move
fi
l
e o
p
enin
g
out
o
f
i
n
it_pul
l
()
commit
|
commitdiff
|
tree
2018-03-29
B
erk Hes
s
Modularize
pull_coord_
w
ork_t
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
R
e
m
o
v
e mols from
gmx_m
t
o
p_t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fix g
m
x dump AWH formatting issue
commit
|
commitdiff
|
tree
2018-03-20
B
e
rk Hess
Disallo
w
sin
g
le simulation with
m
ultisim
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Co
r
rect P
M
F sign err
o
r
in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Fix recent mdrun signaling
b
ug
commit
|
commitdiff
|
tree
2018-03-15
Berk Hess
Fix virial with ex
t
e
rn
a
l pull potential
a
nd MPI
commit
|
commitdiff
|
tree
2018-03-14
Be
r
k
Hess
Impr
o
v
e
inter-simulat
i
o
n si
g
n
aling
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix mdrun sign
a
lling with A
W
H
bia
s
sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix COM pullin
g
with external p
o
ten
t
i
a
l
w
ith #rank
s
>32
commit
|
commitdiff
|
tree
2018-03-14
Berk
Hess
F
ix pull bug with geometry=d
i
rection-periodic
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add
A
WH
f
ixes to release notes
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensemble checkpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk
H
e
ss
Fix AWH
d
econ
v
o
l
ution when sharing a bia
s
commit
|
commitdiff
|
tree
2018-03-09
Ber
k
Hess
Correct
p
db2gmx -missing opti
o
n
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix
m
emory leak in PME
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Convert t_filenm to C
+
+
commit
|
commitdiff
|
tree
2018-03-06
Be
r
k Hess
Make
m
u
l
ti-atom TPI reprodu
c
ible
commit
|
commitdiff
|
tree
2018-03-05
Be
r
k Hess
Work ar
o
und gcc bug
w
i
t
h group kernel
t
a
bles
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Leave nullptr opt
in t_filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk
Hess
Fix
c
pp
c
heck warning
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AWH bias-sharing with parall
e
l
simulat
i
on
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect AMD SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
F
ix mdrun multisim wi
t
h separate PM
E
r
a
nk
s
commit
|
commitdiff
|
tree
2018-02-23
Ber
k
Hess
Fix md int
e
g
ra
t
or with Nose-H
o
over coupli
n
g
commit
|
commitdiff
|
tree
2018-02-22
B
erk Hess
S
implify mdrun tMPI
thr
e
ad spa
w
ning
commit
|
commitdiff
|
tree
2018-02-16
B
erk
H
es
s
Correct
m
ultisim
M
PI barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Remove
s
upport
for tpx
vers
i
on before 58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix range bug
in
a
dd_s
e
lection_groups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
B
e
r
k
Hess
Fix grompp net
c
harge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net charge
c
he
c
k
commit
|
commitdiff
|
tree
2018-02-08
B
e
rk
H
ess
Use
S
I
M
D bo
n
de
d
s
w
i
t
hout per
t
u
rbe
d
interact
i
ons
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
A
llow bonds with distance=0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Se
t
cutoff modifi
e
rs
i
n forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk H
e
ss
Fi
x
a
sse
r
tion fa
i
lure in TPI
commit
|
commitdiff
|
tree
2018-01-30
Be
r
k Hess
Removed unused flag
P
C
A_CAN_RE
A
D
_N
O
DE
commit
|
commitdiff
|
tree
2018-01-18
Berk
Hes
s
Fix
COMM
r
emoval on part o
f
the
system
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add chec
k
in grompp to avoid assertion fail
u
re
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Replace stderr
prints in file
n
m
.
cpp by ass
e
rts
commit
|
commitdiff
|
tree
2018-01-17
B
erk Hess
Re-
e
nable GPU
w
ith walls
a
nd 1 energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk H
e
ss
Remove
t
u
mbling ice-cube war
n
ing with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Avoid
m
d
r
un echoing "No option -multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk
Hess
Re
w
ord C
P
U/
G
PU i
m
balan
c
e not
e
s
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do
n
o
t turn on DLB at repl
i
ca exchange
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
F
i
x tric
l
inic domain d
e
comp
o
s
i
t
ion bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Ma
k
e accelera
t
ion
c
orrecti
o
n VCM m
o
de
w
ork
commit
|
commitdiff
|
tree
2017-12-19
Berk
Hess
Make oversu
b
s
cription warning con
s
istent
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Re
q
uire -ntmpi with setting -ntomp with GPU
s
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Check for large energy at fi
r
st step
commit
|
commitdiff
|
tree
2017-12-12
Berk
H
ess
A
v
oid yel
l
i
ng about thread
pi
n
nin
g
twice
commit
|
commitdiff
|
tree
2017-12-11
Be
r
k Hess
Add grom
p
p note
f
or PR pcouple + posi
t
ion restr
a
ints
commit
|
commitdiff
|
tree
2017-12-10
Be
r
k Hess
Remove SIMD
w
a
r
ni
n
g for A
M
D Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Tone
down note about not
p
inni
n
g thr
e
ads
commit
|
commitdiff
|
tree
2017-12-08
Berk
H
e
s
s
C
orre
c
t Shake tes
t
tolerances
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add
V
iveca Lindahl as contributor
commit
|
commitdiff
|
tree
2017-12-07
B
e
rk Hess
Choose faste
r
nbn
x
n SIMD
k
ernel
s
on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk
Hess
Fix DD exa
c
t
cont
i
n
uatio
n
b
ug
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk
H
e
ss
Fi
x
pme gather in dou
b
le
with AVX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
e
ss
Merge
"
Merge
b
r
a
nch
rele
a
se-2016
i
nto release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fixed init
i
a
l tem
p
e
r
ature r
e
p
o
rting
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Update mdrun signal help tex
t
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
ess
Onl
y
stop a
t
nstlis
t
ste
p
s with -rep
r
od
commit
|
commitdiff
|
tree
2017-12-03
Berk H
e
ss
Clear vsite vel
o
citi
e
s f
o
r simple
integrators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Tighten B
-
spli
n
e moduli
single precis
i
on test tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk H
e
ss
Avoid ass
e
rtion failure in
AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
C
h
ange the
GPU SMT cut-o
f
f to quadr
a
tic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Update document
i
on
o
f N
o
se-Hoov
e
r
o
u
t
put
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Refactor
n
bnxn excl
u
sion set
t
i
n
g
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend grompp missing
e
n
er
g
y term
m
e
ssage
commit
|
commitdiff
|
tree
2017-11-27
Berk
Hess
E
nable au
t
o thread pin
n
ing with t
h
read limit
i
ng
commit
|
commitdiff
|
tree
2017-11-27
Ber
k
Hess
Fix PME G
P
U with wall
s
commit
|
commitdiff
|
tree
2017-11-25
B
e
rk Hess
Fi
x
compiler warning without MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hes
s
Dis
a
bled
CUDA timings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Speed up
nbnxn bu
f
fer
clearing
commit
|
commitdiff
|
tree
2017-11-24
B
erk Hess
L
i
mit SMT with PM
E
on GPU
commit
|
commitdiff
|
tree
2017-11-23
B
e
r
k
H
ess
U
pdate note in m
a
nu
a
l on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Corr
e
ct PME GPU timin
g
naming
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
Preven
t
P
M
E
tunin
g
excess
i
ve gr
i
d scali
n
g
commit
|
commitdiff
|
tree
2017-11-19
Berk
H
es
s
A
dd SIMD for AWH
commit
|
commitdiff
|
tree
2017-11-16
Be
r
k Hess
Also print 1x1 pair-list set
u
p
t
o
l
og
commit
|
commitdiff
|
tree
2017-11-10
Berk Hes
s
F
ix g
e
nion
cha
r
g
e
summ
a
t
io
n
accuracy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hes
s
Fix E
k
i
n a
t
step 0 with
C
OM removal
commit
|
commitdiff
|
tree
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