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Change nbnxn grid reallocation
2018-05-22
Berk He
s
s
Change nbnxn
g
r
id reallocat
i
on
commit
|
commitdiff
|
tree
2018-05-22
B
e
r
k Hess
U
s
e s
t
d::vector in
n
b
nxn_search_t
commit
|
commitdiff
|
tree
2018-05-22
Berk H
e
ss
Us
e
std::vector i
n
nbnxn_gri
d
_t
commit
|
commitdiff
|
tree
2018-05-18
Ber
k
H
e
ss
Clean up
i
n
n
b
nxn_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split of
f
domde
c
d
is
t
ribution and cellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split
a
t
o
m
redistributi
o
n off fro
m
domd
e
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Ber
k
Hess
Remove co
m
m
r
ec from set_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Clean
up PM
E
d
omain c
o
unt passing
commit
|
commitdiff
|
tree
2018-05-03
Berk Hess
En
a
ble SIMD version of up
d
ate
commit
|
commitdiff
|
tree
2018-04-27
B
e
rk
Hess
R
e
move pul
l
MP
I
cod
e
d
u
plica
t
ion
commit
|
commitdiff
|
tree
2018-04-24
B
erk
Hess
Fix indexing iss
u
e
in th
e
pull code
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Move natoms_mol
out
o
f
gmx
_
molblock_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
C
o
nvert g
m
x_molblock_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Convert g
m
x_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Cha
n
g
e warninp f
i
lenm to s
t
d::string
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do not calculate
COM for pull
group 0
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
M
ove
file opening out
o
f init
_
p
u
l
l(
)
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modula
r
ize
pull_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remove mols from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fix gmx dump AWH fo
r
matting is
s
ue
commit
|
commitdiff
|
tree
2018-03-20
Be
r
k Hess
D
i
s
allow sing
l
e simulation with
m
u
l
t
isi
m
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct PMF sign
e
r
r
o
r
in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk
Hess
Fix recen
t
m
drun signaling bu
g
commit
|
commitdiff
|
tree
2018-03-15
Berk Hess
Fix virial wit
h
exter
n
a
l
pull potential and M
P
I
commit
|
commitdiff
|
tree
2018-03-14
B
e
r
k
H
e
ss
Improve inter-simu
l
a
t
i
on s
i
gna
l
i
n
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix mdru
n
signalling with AWH
b
ias shar
i
n
g
commit
|
commitdiff
|
tree
2018-03-14
Berk H
e
ss
Fix COM pulling with external
potential with
#ranks>32
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix pull bug with ge
o
metry=direction-period
i
c
commit
|
commitdiff
|
tree
2018-03-13
B
erk Hess
Add AWH fixes to rele
a
se notes
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensembl
e
checkpoint
i
n
g
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
F
i
x
A
WH decon
v
oluti
o
n when sharing a bias
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
C
o
rrect pdb2g
m
x
-
miss
i
ng option
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix
me
m
ory leak
in P
M
E
commit
|
commitdiff
|
tree
2018-03-06
Ber
k
H
ess
Convert t
_
fil
e
nm to C
+
+
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Make
m
ulti-atom
TPI repr
o
duci
b
le
commit
|
commitdiff
|
tree
2018-03-05
B
erk Hess
Work aro
u
nd gcc bug with g
r
oup k
e
rnel tables
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
L
eav
e
nullptr opt
in
t
_
fil
e
nm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix cppcheck
war
n
ing
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
F
i
x AWH
b
ias-s
h
aring with par
a
l
l
el s
i
mul
a
t
i
on
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect AMD S
M
T topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix mdr
u
n multisim with separate
P
ME ranks
commit
|
commitdiff
|
tree
2018-02-23
B
erk
H
ess
Fix md integrat
o
r with
Nose-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-22
Ber
k
H
ess
Sim
p
l
ify mdr
u
n
tMPI threa
d
spawning
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Correct m
u
l
t
isim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Rem
o
ve support for tpx versi
o
n
b
efore 58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Be
r
k Hess
Fi
x
ran
g
e
bug
in add_se
l
ection_groups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk He
s
s
Fix grompp net charge
chec
k
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk
Hess
Fi
x
grompp
net charge check
commit
|
commitdiff
|
tree
2018-02-08
Berk Hes
s
Use SIMD bon
d
eds wi
t
h
out pertur
b
ed interactions
commit
|
commitdiff
|
tree
2018-02-08
B
erk Hess
Allow bonds wi
t
h di
s
tance=0
commit
|
commitdiff
|
tree
2018-02-05
B
e
rk Hess
Set cutoff mo
d
ifiers i
n
forcerec
commit
|
commitdiff
|
tree
2018-02-05
Ber
k
Hess
Fix assertion fail
u
re in TPI
commit
|
commitdiff
|
tree
2018-01-30
Berk Hess
Remo
v
ed unus
e
d f
l
ag PCA_CAN
_
READ_NODE
commit
|
commitdiff
|
tree
2018-01-18
Berk H
e
ss
Fix COMM
r
emoval on part of the system
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add check i
n
grompp to avoid assertion failure
commit
|
commitdiff
|
tree
2018-01-17
B
erk H
e
s
s
Replace stde
r
r pri
n
ts in f
i
lenm
.
c
pp by a
s
serts
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Re-en
a
bl
e
GPU with walls a
n
d
1
energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk Hes
s
R
e
m
ove tu
m
bling ice-cu
b
e warning wi
t
h SD
commit
|
commitdiff
|
tree
2018-01-16
Ber
k
Hess
Avoid mdrun e
c
hoing "No op
t
ion -multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Reword CPU/G
P
U imba
l
ance notes
commit
|
commitdiff
|
tree
2018-01-09
Be
r
k Hess
D
o
n
o
t turn o
n
DLB
a
t
replic
a
excha
n
g
e
commit
|
commitdiff
|
tree
2018-01-08
Berk H
e
ss
Fix triclinic domai
n
decompo
s
itio
n
bug
commit
|
commitdiff
|
tree
2017-12-19
Be
r
k H
e
ss
M
a
k
e accele
r
ation
c
o
rre
c
tion VCM mo
d
e
wor
k
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make
o
v
er
s
u
b
scription w
a
rning consiste
n
t
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Requir
e
-n
t
mpi
w
ith setting -ntomp with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
C
h
eck fo
r
lar
g
e ener
g
y at first step
commit
|
commitdiff
|
tree
2017-12-12
Ber
k
He
s
s
Avoid
yelling
a
b
o
u
t
thread
pinni
n
g twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add grompp
n
ote for PR pcouple + positi
o
n restra
i
nt
s
commit
|
commitdiff
|
tree
2017-12-10
B
erk
H
ess
Remove SIM
D
warning f
o
r AM
D
Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Tone down note a
b
out not pinning
t
hreads
commit
|
commitdiff
|
tree
2017-12-08
Berk
Hess
Correct S
h
ake test tolerances
commit
|
commitdiff
|
tree
2017-12-08
B
e
r
k
Hess
A
d
d
V
iveca Linda
h
l as
c
ontributor
commit
|
commitdiff
|
tree
2017-12-07
Be
r
k H
e
ss
Choose faster nbnxn SIMD
k
erne
l
s o
n
AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fi
x
DD exact continuation
b
ug
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk
H
e
s
s
Fix pme gather in do
u
b
l
e with AVX(
2
)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
M
e
rge "Mer
g
e bra
n
ch release-201
6
into relea
s
e-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
F
i
xed in
i
tial temperature reporting
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
ess
U
pdate mdru
n
signal help text
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
O
nl
y
s
top at nstli
s
t
step
s
w
i
th
-reprod
commit
|
commitdiff
|
tree
2017-12-03
B
e
r
k
Hess
Clear vsite velo
c
it
i
es for si
m
ple integrat
o
rs
commit
|
commitdiff
|
tree
2017-12-03
Ber
k
Hess
Ti
g
ht
e
n B-spline
m
oduli single precis
i
o
n
te
s
t tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Ber
k
Hess
Avo
i
d asserti
o
n failure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
Change
t
he GPU SMT cut-off to
quadrati
c
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
U
p
date documentio
n
of Nose-
H
oove
r
output
commit
|
commitdiff
|
tree
2017-11-28
B
erk Hess
Refactor nbnxn exc
l
usion s
e
tting
commit
|
commitdiff
|
tree
2017-11-28
B
e
rk Hess
E
x
tend grompp missing energy term messag
e
commit
|
commitdiff
|
tree
2017-11-27
Berk Hes
s
Enable au
t
o
t
hread
p
i
nning w
i
th thread limiti
n
g
commit
|
commitdiff
|
tree
2017-11-27
B
erk
H
ess
F
ix
PME GPU with walls
commit
|
commitdiff
|
tree
2017-11-25
Berk
H
e
ss
Fi
x
c
ompiler warni
n
g without MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk H
e
ss
D
i
sabled CUDA timi
n
gs
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Speed up
n
bnxn buff
e
r clear
i
n
g
commit
|
commitdiff
|
tree
2017-11-24
B
erk Hess
L
imit SMT
with PME
o
n
GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Update
note in manu
a
l on SD
commit
|
commitdiff
|
tree
2017-11-23
Ber
k
Hess
Correct PME GP
U
timing naming
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
Preven
t
PM
E
tuni
n
g
excessive grid scaling
commit
|
commitdiff
|
tree
2017-11-19
Berk Hess
Add SIMD
f
or AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Also print 1
x
1 p
a
i
r
-list se
t
up to log
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
Fix genio
n
c
har
g
e sum
m
ation ac
c
u
ra
c
y
commit
|
commitdiff
|
tree
2017-11-02
Ber
k
Hess
Fix
Ekin a
t
step 0 with COM
r
emoval
commit
|
commitdiff
|
tree
2017-11-02
B
e
rk Hess
Add missing
E
wald corre
c
tion
for
pme-user
commit
|
commitdiff
|
tree
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