repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Fix COM pulling with external potential with #ranks>32
2018-03-14
Berk Hess
Fix COM pulli
n
g with externa
l
p
o
tential with #ranks>32
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
Hes
s
Fix pu
l
l bug w
i
th geometry=directio
n
-
peri
o
d
i
c
commit
|
commitdiff
|
tree
2018-03-13
B
erk
He
s
s
Add
A
W
H fixes to release notes
commit
|
commitdiff
|
tree
2018-03-13
Berk
H
ess
Fix
A
W
H
ensemble checkpointi
n
g
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH dec
o
nvolut
i
on
when shar
i
ng a b
i
as
commit
|
commitdiff
|
tree
2018-03-09
Berk He
s
s
Corre
c
t pdb2gmx -
m
issin
g
option
commit
|
commitdiff
|
tree
2018-03-06
B
e
r
k Hess
Make multi-atom TPI r
e
producible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Wor
k
around gcc bug with gr
o
up kernel
t
a
b
les
commit
|
commitdiff
|
tree
2018-03-02
Berk H
e
ss
F
ix AWH
bias-shari
n
g with pa
r
allel simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
D
e
tect AMD SMT to
p
olog
y
commit
|
commitdiff
|
tree
2018-03-01
Be
r
k Hess
Fix
m
drun multisim w
i
th separate PME ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix md in
t
egrato
r
w
ith Nose-Hoove
r
c
o
upling
commit
|
commitdiff
|
tree
2018-02-16
Ber
k
Hess
Correct m
u
ltisim MPI barr
i
er
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
i
x
range bug i
n
add_select
i
on_groups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net
charge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net ch
a
rg
e
check
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
ess
Use S
I
MD bondeds without pertur
b
ed
interactions
commit
|
commitdiff
|
tree
2018-02-08
Be
r
k H
e
ss
Allow bo
n
ds with
distanc
e
=
0
commit
|
commitdiff
|
tree
2018-02-05
Berk
H
e
s
s
S
et cutoff modifiers in forcere
c
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
F
ix asser
t
i
on fail
u
re in
TPI
commit
|
commitdiff
|
tree
2018-01-18
Berk
H
ess
Fix
C
OMM removal on pa
r
t of the system
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add check in gro
m
pp to avoid a
s
s
ertion failure
commit
|
commitdiff
|
tree
2018-01-17
B
erk
Hess
Re-enable GPU wit
h
walls and 1 energy grou
p
commit
|
commitdiff
|
tree
2018-01-16
B
e
rk Hess
Remove t
u
mbling ice-cube wa
r
nin
g
w
it
h
SD
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Avoid mdrun echoing "
N
o option -multi
"
commit
|
commitdiff
|
tree
2018-01-09
B
e
rk Hess
Re
w
ord C
P
U
/GPU imbalance notes
commit
|
commitdiff
|
tree
2018-01-09
Be
r
k Hess
D
o
not turn on DLB at replica exchan
g
e
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
Fix triclinic do
m
ai
n
deco
m
posi
t
ion bug
commit
|
commitdiff
|
tree
2017-12-19
Ber
k
Hes
s
Make acceleration co
r
rection VCM
m
o
de wo
r
k
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
M
a
k
e oversubscript
i
on w
a
rni
n
g consis
t
e
nt
commit
|
commitdiff
|
tree
2017-12-14
Berk H
e
ss
Require -ntmpi with s
e
tting -ntomp
with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
C
h
e
c
k
for large e
n
er
g
y at first step
commit
|
commitdiff
|
tree
2017-12-12
Berk
H
ess
Avoid
y
elling
a
bout thread p
i
nning twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hes
s
A
d
d
grompp note for PR pcouple + position restraint
s
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove SIMD w
a
rning for AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Be
r
k H
e
ss
Tone
down
n
o
te about not pinning th
r
eads
commit
|
commitdiff
|
tree
2017-12-08
B
e
rk
H
ess
C
orrect Shake
t
e
s
t
t
oler
a
n
ces
commit
|
commitdiff
|
tree
2017-12-08
B
e
r
k Hess
Add Viveca Li
n
dahl as contr
i
butor
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Ch
o
o
se faster nbnxn SIMD
ke
r
n
e
ls on
AMD Z
e
n
commit
|
commitdiff
|
tree
2017-12-05
B
e
rk Hess
Fix DD exact c
o
n
t
inuat
i
on bug
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Fix
p
me gat
h
er
in
double wit
h
A
VX(2)_
1
28
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk Hess
Me
r
g
e
"M
e
rge b
r
a
nc
h
releas
e
-
2
016
into release-2
0
18
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Fixed initia
l
te
m
pera
t
ure
re
p
orting
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
e
ss
Update mdrun si
g
nal help text
commit
|
commitdiff
|
tree
2017-12-04
B
erk
H
es
s
Only stop at nstl
i
st
steps
with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Berk H
e
ss
Cle
a
r vsite
v
elocit
i
es
f
o
r
si
m
ple integrato
r
s
commit
|
commitdiff
|
tree
2017-12-03
Berk H
e
ss
Tighten B-splin
e
m
o
duli s
i
ngl
e
prec
i
sion tes
t
to
l
e
rance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoid
a
sse
r
tion failure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Ber
k
Hess
Change the GPU SM
T
cut-off to qua
d
ratic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
U
p
da
t
e documention of Nose-Hoo
v
er output
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Refactor
n
bnxn exc
l
usion setting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Exte
n
d grompp missing
en
e
rgy
t
erm
m
essag
e
commit
|
commitdiff
|
tree
2017-11-27
Berk Hes
s
Enable a
u
to thread pinning with thread limi
t
ing
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Fix PME GPU with walls
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
Fix co
m
p
iler
w
arning without M
P
I
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Disabled CUDA timings
commit
|
commitdiff
|
tree
2017-11-24
Berk
H
ess
Speed up nbnxn buffer clea
r
i
n
g
commit
|
commitdiff
|
tree
2017-11-24
B
erk Hess
Limit SM
T
with PME on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Updat
e
note in manual on SD
commit
|
commitdiff
|
tree
2017-11-23
B
erk Hes
s
Correct PME GP
U
tim
i
ng na
m
ing
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
Prevent PME tuning
ex
c
essi
v
e grid scal
i
ng
commit
|
commitdiff
|
tree
2017-11-19
Berk H
e
ss
Add SIMD for AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk He
s
s
Also print 1x1
p
air-lis
t
s
etup
to log
commit
|
commitdiff
|
tree
2017-11-10
B
e
rk Hess
Fix g
e
n
ion char
g
e
s
ummation accuracy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
F
i
x Ekin
at step 0 with COM removal
commit
|
commitdiff
|
tree
2017-11-02
Berk He
s
s
Add missing Ewald corr
e
ction for
p
m
e
-user
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove
unused sig
n
parameter fr
o
m dih
_
angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
Re
m
ove inco
r
rect comment
for CHARMM tips
3
p
commit
|
commitdiff
|
tree
2017-10-24
Berk Hess
Fix gmx chec
k
for tprs
w
ith different #atoms
commit
|
commitdiff
|
tree
2017-10-23
Berk
Hess
F
i
x
inco
r
r
ect dV/dlamb
d
a for wall
s
commit
|
commitdiff
|
tree
2017-10-21
B
e
r
k
H
e
ss
Merge "Merge br
a
nch releas
e
-
2
016"
commit
|
commitdiff
|
tree
2017-10-20
Berk
H
ess
Fix
warn
i
ng f
o
r confout w
i
th periodic
molecules
commit
|
commitdiff
|
tree
2017-10-18
B
erk Hess
M
ade CUD
A
PME textu
r
e reference
co
n
ditional
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Impr
o
ve vsite parallel checking
commit
|
commitdiff
|
tree
2017-10-12
Berk Hess
Simplify virial handling
commit
|
commitdiff
|
tree
2017-10-11
Berk Hes
s
D
i
sable ARM Neon native rs
q
rt iteration
commit
|
commitdiff
|
tree
2017-10-06
B
e
rk H
e
ss
Add acceleration c
o
rrection V
C
M mode
commit
|
commitdiff
|
tree
2017-10-06
Be
r
k
Hess
Fi
x
max_size() in allocator
.
h
commit
|
commitdiff
|
tree
2017-10-06
B
e
rk
Hess
A
dd SIMD
intrins
i
cs
v
ersio
n
of
s
imple update
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Impr
o
ve Pad
d
edRVecVector re
s
izing
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
Make SIMD ambiguous test work with float/double only
commit
|
commitdiff
|
tree
2017-10-04
Berk Hes
s
Remove a force buf
f
er
a
rgum
e
nt from
I
ForcePr
o
vi
d
er
commit
|
commitdiff
|
tree
2017-10-03
Berk Hes
s
Move
c
alling
of special forc
e
f
u
nctions
commit
|
commitdiff
|
tree
2017-10-02
Ber
k
Hess
Remove hybr
i
d gpu+cpu non
b
o
nded mode
commit
|
commitdiff
|
tree
2017-09-25
Berk He
s
s
P
u
t
rerun state preparation in a
f
unction
commit
|
commitdiff
|
tree
2017-09-25
Be
r
k He
s
s
S
e
t global
s
tate on master r
a
n
k
only
commit
|
commitdiff
|
tree
2017-09-23
B
e
r
k Hess
Fix grompp wit
h
Andersen massive and
n
o C
O
M r
e
moval
commit
|
commitdiff
|
tree
2017-09-20
B
e
rk Hess
Change n
b
nxn
indexing t
o
templates
commit
|
commitdiff
|
tree
2017-09-15
Be
r
k Hess
Remove n
b
-paramete
r
s from t_forcerec
commit
|
commitdiff
|
tree
2017-09-14
B
e
rk Hess
F
i
x nbnxn SIMD 2
x
NN PM
E
tabulated ke
r
nel
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Fix exception in SIMD LJ PM
E
s
olve
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Do not
pa
s
s
s
t
ate to init_re
p
lica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Berk
H
es
s
F
i
x PBC bugs
i
n
the sw
a
p c
o
de
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
Avoid in
f
i
n SIMD double sqrt()
commit
|
commitdiff
|
tree
2017-09-07
Berk Hess
Fix F
E
P
state with reru
n
commit
|
commitdiff
|
tree
2017-09-04
Be
r
k Hess
Fix two nbnxn s
e
arch inde
x
ing bugs
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Consolidate architecture bo
o
leans
commit
|
commitdiff
|
tree
2017-09-03
Berk Hess
Put m
d
r
un options in
structs
commit
|
commitdiff
|
tree
2017-09-02
Berk Hess
Put all domdec options in a s
t
ruc
t
commit
|
commitdiff
|
tree
2017-09-02
Berk Hess
Fix mdrun -nb
o
ption pointer
commit
|
commitdiff
|
tree
next