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Added the bundled clFFT into OpenCL builds
2018-05-24
Berk
H
ess
Fix
grompp bu
g
w
ith
blo
c
ks of same molecules
commit
|
commitdiff
|
tree
2018-05-24
Be
r
k H
e
ss
Simplify idef_
f
e in
calc
_
listed_lambda
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
C
h
ange nbs i
n
nbv
to std::u
n
ique
commit
|
commitdiff
|
tree
2018-05-24
Be
r
k
H
ess
C
o
nver
t
g
m
x_
d
omdec_m
a
ste
r
_t to C++
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Sp
l
it off
c
oll
e
ct
.
cpp from do
m
d
ec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
B
e
rk Hess
Convert nbnxn_search to C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Cha
n
ge nbnxn
gri
d
reallo
c
atio
n
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use std::vect
o
r in nbnxn_se
a
r
ch_
t
commit
|
commitdiff
|
tree
2018-05-22
B
e
rk Hes
s
Use std::vector
in nbnxn_g
r
id_t
commit
|
commitdiff
|
tree
2018-05-18
Berk Hess
Clean up in nbnx
n
_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
B
erk Hess
Split off d
o
mdec
d
istri
b
ution and cellsizes
commit
|
commitdiff
|
tree
2018-05-17
B
erk Hess
Split atom redistribution o
f
f
f
rom domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk H
e
ss
Remove c
o
mmrec from set_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
B
e
r
k Hess
Cl
e
an up PME domai
n
count passin
g
commit
|
commitdiff
|
tree
2018-05-03
Berk H
e
ss
Enable SIMD
v
ersion
of update
commit
|
commitdiff
|
tree
2018-04-27
Berk Hess
Remo
v
e pull MP
I
co
d
e du
p
lication
commit
|
commitdiff
|
tree
2018-04-24
Ber
k
Hess
Fix indexing issue in the pull code
commit
|
commitdiff
|
tree
2018-04-16
B
erk
H
es
s
Mo
v
e natoms_mol out of gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-09
B
erk He
s
s
Convert gmx_molblock_t t
o
C++
commit
|
commitdiff
|
tree
2018-04-03
B
e
rk Hess
Convert gmx_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Ber
k
Hess
Change warninp filen
m
t
o
std::string
commit
|
commitdiff
|
tree
2018-04-03
Berk
H
e
s
s
D
o
n
ot calc
u
la
t
e
C
OM for
p
u
ll group 0
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
H
e
ss
Move file openi
n
g
out
o
f
init_pull
(
)
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
Hes
s
M
o
dular
i
ze pull_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Berk
H
ess
Re
m
ove mo
l
s from g
m
x_m
t
op_t
commit
|
commitdiff
|
tree
2018-03-20
B
erk
H
e
ss
Fix gmx dump AW
H
f
ormatting
i
ssu
e
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Di
s
allow single simulation with m
u
ltisim
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct PMF sign error in AWH bias shari
n
g
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
F
i
x
re
c
ent mdrun signali
n
g bug
commit
|
commitdiff
|
tree
2018-03-15
B
e
r
k
H
e
ss
Fix vi
r
ial
w
ith ex
t
ernal pull potent
i
al
and
MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
ess
I
mprove inter-simulation s
i
gnalin
g
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fi
x
m
drun signalling with AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
B
erk Hess
Fix COM pulling with external
p
otential
with #
r
anks>32
commit
|
commitdiff
|
tree
2018-03-14
B
erk Hess
Fix pull bug with geometry=d
i
rec
t
ion-
p
eriodic
commit
|
commitdiff
|
tree
2018-03-13
B
er
k
Hess
Ad
d
AWH fixes to re
l
eas
e
notes
commit
|
commitdiff
|
tree
2018-03-13
Be
r
k H
e
ss
Fix AWH e
n
semble
checkpoint
i
ng
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH deconvolution when shar
i
ng a
b
ias
commit
|
commitdiff
|
tree
2018-03-09
B
e
rk
Hess
C
o
r
r
ec
t
pd
b
2g
m
x -
m
issin
g
op
t
ion
commit
|
commitdiff
|
tree
2018-03-07
Berk Hes
s
Fix mem
o
ry
l
eak 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 multi-at
o
m TPI reproducible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hes
s
Wo
r
k around gcc
bug wit
h
g
r
oup kerne
l
tab
l
es
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Leave nullptr opt in t
_
filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix
c
ppcheck
warni
n
g
commit
|
commitdiff
|
tree
2018-03-02
Berk He
s
s
F
i
x AWH bi
a
s-sharing
wi
t
h paral
l
el simu
l
ation
commit
|
commitdiff
|
tree
2018-03-01
Berk
Hess
D
e
tect
A
MD SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Be
r
k Hess
Fix mdrun multisim wi
t
h
separate
P
ME ra
n
ks
commit
|
commitdiff
|
tree
2018-02-23
Berk
Hess
Fix md integrat
o
r
with N
o
se-Hoover couplin
g
commit
|
commitdiff
|
tree
2018-02-22
B
e
rk Hess
S
implify
mdrun t
M
PI
thread s
p
awning
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Correct multisim
MP
I
barrier
commit
|
commitdiff
|
tree
2018-02-14
B
e
rk He
s
s
R
e
move
s
u
ppo
r
t for tpx version before 5
8
/g
m
x4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
Fix range
bug i
n
add_sel
e
ction_grou
p
s in
tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix gromp
p
ne
t
cha
r
ge check
commit
|
commitdiff
|
tree
2018-02-14
Ber
k
Hess
Fix
g
rompp net char
g
e
c
heck
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
Use SIMD bondeds without per
t
urbed
i
nt
e
r
actions
commit
|
commitdiff
|
tree
2018-02-08
Berk Hes
s
Allow
b
onds w
i
th distance=0
commit
|
commitdiff
|
tree
2018-02-05
B
e
r
k
H
e
ss
Se
t
cut
o
f
f modif
i
ers in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix
a
ssertion fai
l
ure in TPI
commit
|
commitdiff
|
tree
2018-01-30
Berk Hess
Removed unu
s
ed flag PCA_C
A
N_R
E
AD_NO
D
E
commit
|
commitdiff
|
tree
2018-01-18
B
erk
H
ess
Fix COMM r
e
moval on part of the sys
t
e
m
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
A
d
d
c
he
c
k
in gro
m
pp to avoid asserti
o
n failure
commit
|
commitdiff
|
tree
2018-01-17
Berk H
e
ss
Repl
a
ce stderr pri
n
ts in filenm
.
cpp by asserts
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Re-enable GPU with wal
l
s
a
nd 1 energy gr
o
up
commit
|
commitdiff
|
tree
2018-01-16
Berk H
e
ss
R
e
mo
v
e tumbli
n
g ice-c
u
be warning with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk He
s
s
Avoid
mdrun echoi
n
g "N
o
option -multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Reword CPU/GPU imbalanc
e
n
otes
commit
|
commitdiff
|
tree
2018-01-09
Ber
k
H
ess
Do
not turn on DL
B
at
replica exchange
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
Fix tr
i
clinic doma
i
n decom
p
osition bug
commit
|
commitdiff
|
tree
2017-12-19
Berk
Hes
s
M
ake
a
cceleration c
o
rrection VCM mode work
commit
|
commitdiff
|
tree
2017-12-19
B
e
rk Hess
M
ak
e
o
v
ersubscripti
o
n
w
arning consistent
commit
|
commitdiff
|
tree
2017-12-14
Be
r
k He
s
s
Re
q
uire
-ntmpi with
s
e
tting
-
ntomp with GPU
s
commit
|
commitdiff
|
tree
2017-12-12
Berk He
s
s
Ch
e
ck for large energy at firs
t
step
commit
|
commitdiff
|
tree
2017-12-12
B
e
rk Hess
Avoid yell
i
ng about thre
a
d pinni
n
g t
w
i
c
e
commit
|
commitdiff
|
tree
2017-12-11
B
e
rk Hess
A
dd grompp note for
P
R
pcoup
l
e
+ positio
n
restraints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove
SIMD
warning
f
or
A
MD Zen
commit
|
commitdiff
|
tree
2017-12-10
B
e
rk
H
e
ss
Tone
d
own n
o
te about
n
ot p
i
nning threads
commit
|
commitdiff
|
tree
2017-12-08
Ber
k
Hess
Co
r
r
ect
S
hak
e
test tole
r
ances
commit
|
commitdiff
|
tree
2017-12-08
Be
r
k Hess
Add Viv
e
c
a
Lindah
l
a
s
cont
r
i
but
o
r
commit
|
commitdiff
|
tree
2017-12-07
Be
r
k Hess
Choose faster n
b
n
x
n SI
M
D kernels o
n
AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fix
DD exact con
t
inuation bug
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k Hess
Fix pme gath
e
r
i
n
d
ouble with AVX
(
2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
M
e
rge "Me
r
ge branch re
l
ease-2016 into releas
e
-
2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
B
erk H
e
ss
F
ixed ini
t
i
al tempera
t
ure
r
eporti
n
g
commit
|
commitdiff
|
tree
2017-12-04
B
erk He
s
s
Update mdrun sign
a
l help
t
e
xt
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Only
s
top
a
t nstlist step
s
with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Clear
vsite velo
c
i
ti
e
s for simple i
n
t
e
grato
r
s
commit
|
commitdiff
|
tree
2017-12-03
Berk He
s
s
Ti
g
hten B-spline modu
l
i sing
l
e precision test tole
r
ance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Ber
k
Hess
Avoi
d
as
s
e
r
tio
n
failure
i
n AWH
commit
|
commitdiff
|
tree
2017-11-29
B
erk Hess
Change the
G
PU SMT cut
-
o
ff to quadrat
i
c
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Update documention
o
f Nose-Hoov
e
r output
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Ref
a
ctor
nbnx
n
e
x
c
lusion s
e
tting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend grom
p
p mi
s
sing energy term mes
s
age
commit
|
commitdiff
|
tree
2017-11-27
Berk Hes
s
Enable
auto t
h
rea
d
p
inning w
i
t
h
thread limiting
commit
|
commitdiff
|
tree
2017-11-27
B
e
rk Hess
Fix PME GPU with
walls
commit
|
commitdiff
|
tree
2017-11-25
B
erk Hess
Fix com
p
i
ler warning
w
ithout MPI
commit
|
commitdiff
|
tree
2017-11-24
Ber
k
Hess
D
isabled CUDA timings
commit
|
commitdiff
|
tree
2017-11-24
B
erk Hes
s
Spe
e
d
u
p nbnxn buffer
c
learing
commit
|
commitdiff
|
tree
2017-11-24
Berk He
s
s
L
imit SMT
w
it
h
PME on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk He
s
s
Up
d
ate note in m
a
nu
a
l on SD
commit
|
commitdiff
|
tree
2017-11-23
Be
r
k He
s
s
Cor
r
ec
t
PME GPU tim
i
n
g na
m
i
n
g
commit
|
commitdiff
|
tree
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