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Partial conversion of gmx_domdec_t to C++
2018-06-13
Berk Hess
Partial c
o
nversio
n
of gmx_domd
e
c_t
t
o C++
commit
|
commitdiff
|
tree
2018-06-06
Berk Hes
s
Clean up
m
a
ke_at2con
commit
|
commitdiff
|
tree
2018-06-05
B
e
r
k
H
ess
Make nbnxn_
g
rid_t counts and size
s
arrays
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
F
ix grompp bug
w
ith blocks of same molecules
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Simp
l
ify idef_fe in
c
alc_l
i
sted_lambda
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Change nbs in nb
v
to std::unique
commit
|
commitdiff
|
tree
2018-05-24
Berk H
e
ss
Co
n
vert
g
mx_d
o
mdec_
m
aster_
t
to C++
commit
|
commitdiff
|
tree
2018-05-23
Ber
k
H
ess
Spl
i
t
off c
o
llect
.
cpp
f
rom dom
d
ec
.
cp
p
commit
|
commitdiff
|
tree
2018-05-23
Be
r
k Hess
Convert nbnxn_search to C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Change n
b
nxn grid realloc
a
tion
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
Hess
Use std::ve
c
tor in n
b
nxn_searc
h
_
t
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
Hess
Use std::v
e
ctor in
n
bnx
n
_grid_
t
commit
|
commitdiff
|
tree
2018-05-18
Berk He
s
s
Cle
a
n up i
n
nbnxn_gri
d
.
cp
p
commit
|
commitdiff
|
tree
2018-05-17
Be
r
k Hess
Split off domd
e
c distrib
u
tio
n
and cellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
S
p
lit ato
m
redistrib
u
tion
o
ff from domdec
.
c
pp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
R
e
mo
v
e
c
ommr
e
c
fro
m
s
e
t_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
B
e
rk Hess
C
lean up PME
d
omain count pass
i
ng
commit
|
commitdiff
|
tree
2018-05-03
Be
r
k H
e
ss
E
n
able SIMD version
o
f
update
commit
|
commitdiff
|
tree
2018-04-27
Berk
Hess
Remove p
u
ll MPI co
d
e
dupli
c
ation
commit
|
commitdiff
|
tree
2018-04-24
Berk Hess
F
ix
i
ndexi
n
g i
s
su
e
in the pull code
commit
|
commitdiff
|
tree
2018-04-16
Berk H
e
ss
Move natom
s
_mol out o
f
gmx_mo
l
blo
c
k
_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert gmx_molblock_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Conver
t
g
mx_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Be
r
k He
s
s
C
h
ange warnin
p
fi
l
enm to st
d
::string
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do not calc
u
late COM
for pull
group 0
commit
|
commitdiff
|
tree
2018-03-29
Berk He
s
s
Move file opening out of init_p
u
ll()
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Mo
d
ularize pull_coord_w
o
rk_t
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remov
e
mol
s
from gmx_
m
top_t
commit
|
commitdiff
|
tree
2018-03-20
B
erk H
e
ss
Fi
x
gmx dump AWH form
a
tting issu
e
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow singl
e
simula
t
i
on with
m
ulti
s
im
commit
|
commitdiff
|
tree
2018-03-16
Berk
H
ess
Co
r
rect PMF sign error in AWH
b
ias sharin
g
commit
|
commitdiff
|
tree
2018-03-16
Berk He
s
s
Fix recent
m
drun signal
i
ng
bu
g
commit
|
commitdiff
|
tree
2018-03-15
Berk Hess
Fix viri
a
l wi
t
h
externa
l
pu
l
l potent
i
a
l
a
nd MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve inter-si
m
ulation si
g
na
l
ing
commit
|
commitdiff
|
tree
2018-03-14
Be
r
k
He
s
s
Fix mdrun signalling wi
t
h AWH bias
s
haring
commit
|
commitdiff
|
tree
2018-03-14
Be
r
k Hess
Fix
COM
pu
l
l
i
ng with exter
n
al
p
oten
t
ial with #ra
n
ks>32
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk Hess
Fix pull bug
w
ith geometry=direction-pe
r
iodic
commit
|
commitdiff
|
tree
2018-03-13
Berk
H
ess
Add AWH fixes t
o
releas
e
notes
commit
|
commitdiff
|
tree
2018-03-13
Be
r
k
H
e
s
s
Fix AWH ensemble c
h
eckpointi
n
g
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH deconvolut
i
o
n when sharing a bias
commit
|
commitdiff
|
tree
2018-03-09
B
e
rk Hess
Correct pdb2gmx
-
m
i
ssing option
commit
|
commitdiff
|
tree
2018-03-07
Berk
H
e
ss
Fix memory leak in
PME
commit
|
commitdiff
|
tree
2018-03-06
Berk
H
es
s
Convert t_filenm to C++
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
M
ake multi-a
t
om T
P
I reproducible
commit
|
commitdiff
|
tree
2018-03-05
Berk
He
s
s
Wor
k
a
ro
u
nd gcc bug w
i
th group k
e
r
nel
tables
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Le
a
ve
null
p
tr opt i
n
t_file
n
m
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
F
ix
cppcheck warning
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AWH bias-sharing with parallel simu
l
a
t
ion
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Det
e
ct A
M
D SMT topol
o
gy
commit
|
commitdiff
|
tree
2018-03-01
Berk
H
ess
Fix mdrun multisim with
s
eparate P
M
E ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk
Hess
F
i
x
m
d
i
nteg
r
ator with
N
ose-Hoove
r
coupling
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simpl
i
f
y
mdrun tMPI thr
e
ad s
p
aw
n
ing
commit
|
commitdiff
|
tree
2018-02-16
B
e
rk
H
e
s
s
Correct multisim MPI barrie
r
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk Hess
Remove su
p
port for tpx version b
e
fore 58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix
r
ange bug in add_selec
t
ion_groups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
B
e
r
k Hess
Fix grompp n
e
t charge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix gromp
p
net charge check
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
e
s
s
Use SIMD bondeds w
i
t
hout p
e
r
turbed
intera
c
tion
s
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
e
s
s
Allow bonds with distance=0
commit
|
commitdiff
|
tree
2018-02-05
Ber
k
Hess
Set
cutoff modifiers in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
F
i
x asser
t
i
o
n failure
in T
P
I
commit
|
commitdiff
|
tree
2018-01-30
Berk Hess
Remo
v
ed unused f
l
a
g PC
A
_
C
AN_READ_N
O
DE
commit
|
commitdiff
|
tree
2018-01-18
Berk
He
s
s
Fix COMM removal on
part of the
syst
e
m
commit
|
commitdiff
|
tree
2018-01-18
Berk Hes
s
Add check
i
n gromp
p
to avoid assertion failure
commit
|
commitdiff
|
tree
2018-01-17
Berk
H
ess
Replace stderr
p
rints i
n
filenm
.
cpp by
as
s
erts
commit
|
commitdiff
|
tree
2018-01-17
Berk He
s
s
Re
-
ena
b
le GPU with walls a
n
d 1 energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Remove tumblin
g
i
ce-cube warning with
S
D
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Avoid mdrun echoing "No option -
m
ulti"
commit
|
commitdiff
|
tree
2018-01-09
Berk
H
ess
Reword CPU/GP
U
imba
l
ance notes
commit
|
commitdiff
|
tree
2018-01-09
Ber
k
Hess
Do not tur
n
on DLB
at r
e
plica exchan
g
e
commit
|
commitdiff
|
tree
2018-01-08
B
erk Hess
F
ix triclini
c
domain decompos
i
tion bug
commit
|
commitdiff
|
tree
2017-12-19
B
erk Hess
Make acceleration correction VCM mode work
commit
|
commitdiff
|
tree
2017-12-19
Berk
Hess
Make oversubs
c
r
iption wa
r
ning consistent
commit
|
commitdiff
|
tree
2017-12-14
B
erk Hess
Require -ntmpi
with s
e
tting -ntomp
w
i
t
h
GPUs
commit
|
commitdiff
|
tree
2017-12-12
Be
r
k
Hess
Chec
k
for large energy at fi
r
st
step
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Avoid
y
elling about t
h
read
p
i
nn
i
ng
twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add grompp note for P
R
pcouple + posit
i
on restraints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove SIMD warning f
o
r
A
M
D Z
e
n
commit
|
commitdiff
|
tree
2017-12-10
Berk
H
e
ss
To
n
e
down
n
ote about n
o
t pinning threads
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Corr
e
ct Shake test tolera
n
ces
commit
|
commitdiff
|
tree
2017-12-08
Berk
H
ess
Add Viveca Lin
d
ahl as c
o
ntributor
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Choose fa
s
ter nb
n
xn SIMD kernels on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fix DD exact continuati
o
n bug
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
e
s
s
Fix pme
g
a
ther in dou
b
le wi
t
h AVX(2)_
1
28
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
ess
Merge
"
Merge
b
ranc
h
releas
e
-
2
01
6
i
nt
o
release-2
0
1
8
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
Fixed initial tempe
r
atu
r
e report
i
ng
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
He
s
s
Upd
a
te mdrun signal help text
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
O
n
ly st
o
p
at
nstlist steps with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Be
r
k H
e
ss
Clear
vsit
e
vel
o
citie
s
for
s
imple integrators
commit
|
commitdiff
|
tree
2017-12-03
Berk
Hes
s
T
ight
e
n B-spline moduli s
i
n
g
l
e prec
i
si
o
n
test
t
ole
r
a
nce
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avo
i
d
a
s
sertion failure
in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk
Hess
Change the
G
PU
S
MT cut-off to q
u
adratic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
U
p
date documention of
N
ose-Hoover outp
u
t
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Refa
c
to
r
nbnx
n
exclusion settin
g
commit
|
commitdiff
|
tree
2017-11-28
Berk
H
ess
Exten
d
gro
m
pp mi
s
sing e
n
ergy ter
m
mes
s
age
commit
|
commitdiff
|
tree
2017-11-27
Berk He
s
s
Enable auto
thre
a
d
pinning with thread limiting
commit
|
commitdiff
|
tree
2017-11-27
Berk
H
ess
Fix PME
GPU with w
a
lls
commit
|
commitdiff
|
tree
2017-11-25
Be
r
k Hess
Fix comp
i
ler warnin
g
withou
t
M
P
I
commit
|
commitdiff
|
tree
2017-11-24
Berk
Hess
Di
s
abled C
U
DA timings
commit
|
commitdiff
|
tree
2017-11-24
B
erk Hess
Speed
u
p
nbnxn buffer clearing
commit
|
commitdiff
|
tree
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