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Change image conversion to only be build once
2018-04-16
Berk
He
s
s
Mo
v
e natoms_mol out of gm
x
_molb
l
o
c
k
_
t
commit
|
commitdiff
|
tree
2018-04-09
B
erk Hess
C
on
v
ert gmx_mol
b
lock_t t
o
C++
commit
|
commitdiff
|
tree
2018-04-03
Ber
k
Hess
C
onver
t
gmx
_
mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Change warninp f
i
lenm to std::string
commit
|
commitdiff
|
tree
2018-04-03
Berk Hes
s
Do n
o
t calculate COM for pull gro
u
p 0
commit
|
commitdiff
|
tree
2018-03-29
Berk
Hess
Move
f
ile opening
out o
f
init_
p
u
ll()
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
M
o
dularize
pu
l
l
_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Ber
k
Hess
Re
m
ove
m
o
l
s fro
m
gm
x
_mtop_t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fix gmx d
u
mp AWH formatting
is
s
ue
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow single simulation with multis
i
m
commit
|
commitdiff
|
tree
2018-03-16
Be
r
k H
e
ss
C
orr
e
ct
P
M
F
sign error
in AW
H
bias
sharing
commit
|
commitdiff
|
tree
2018-03-16
B
er
k
Hess
Fix recent
mdrun signa
l
ing bug
commit
|
commitdiff
|
tree
2018-03-15
Berk Hess
Fix viria
l
with external
p
u
ll potential and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk
He
s
s
Improve i
n
ter-sim
u
l
ation signaling
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix md
r
un si
g
nalling with AWH bi
a
s sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
F
ix COM pulling with external potent
i
al with #ra
n
ks>32
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix
p
ull bug with geometry=d
i
r
ec
t
io
n
-periodic
commit
|
commitdiff
|
tree
2018-03-13
Berk
Hess
Add AWH fixes to release note
s
commit
|
commitdiff
|
tree
2018-03-13
Berk
Hess
Fix A
W
H ensemble checkpointing
commit
|
commitdiff
|
tree
2018-03-13
B
e
rk Hess
Fix AWH deco
n
vo
l
uti
o
n
w
hen s
h
arin
g
a bias
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Cor
r
ect pdb
2
gmx -missing opt
i
on
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix
m
e
mory leak in PME
commit
|
commitdiff
|
tree
2018-03-06
Berk Hes
s
Conve
r
t t_filenm to C++
commit
|
commitdiff
|
tree
2018-03-06
Berk H
e
ss
Make mul
t
i
-
a
t
om TPI reproducib
l
e
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Wor
k
aro
u
n
d
g
c
c
bug with gr
o
up
k
e
r
n
e
l
tables
commit
|
commitdiff
|
tree
2018-03-05
Berk Hes
s
Le
a
ve nullptr opt in t_filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix cppcheck warning
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AWH bias-sharing w
i
th parallel
si
m
ul
a
tion
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
D
e
t
ect A
M
D
SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
F
ix
m
drun multisim
with sepa
r
ate PME rank
s
commit
|
commitdiff
|
tree
2018-02-23
Berk
H
ess
Fix md
i
n
t
egrator with
Nos
e
-Hoov
e
r coupling
commit
|
commitdiff
|
tree
2018-02-22
B
e
r
k
H
ess
Si
m
p
lify mdrun tMPI
t
hread spawnin
g
commit
|
commitdiff
|
tree
2018-02-16
B
erk
H
e
s
s
Cor
r
ect mul
t
isim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Rem
o
ve support f
o
r tpx ver
s
ion before
5
8/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Be
r
k He
s
s
Fix range bu
g
in add_select
i
on_groups in tngio
.
c
p
p
commit
|
commitdiff
|
tree
2018-02-14
Berk H
e
ss
Fix grompp net cha
r
ge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix gromp
p
net
c
harge check
commit
|
commitdiff
|
tree
2018-02-08
Ber
k
Hess
Use SIMD b
o
ndeds
w
ith
o
ut p
e
rturbed interactio
n
s
commit
|
commitdiff
|
tree
2018-02-08
Berk H
e
ss
Allow bonds with distanc
e
=0
commit
|
commitdiff
|
tree
2018-02-05
Be
r
k Hess
S
e
t cutof
f
modifiers i
n
forc
e
rec
commit
|
commitdiff
|
tree
2018-02-05
Berk He
s
s
Fix a
s
s
ertion failu
r
e in TPI
commit
|
commitdiff
|
tree
2018-01-30
Berk He
s
s
Remo
v
ed
u
nused flag PC
A
_CAN_READ_NODE
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix COMM re
m
o
v
a
l
o
n
part of
t
he system
commit
|
commitdiff
|
tree
2018-01-18
Ber
k
Hes
s
Add che
c
k in grom
p
p to
avoid assert
i
on failure
commit
|
commitdiff
|
tree
2018-01-17
B
e
r
k
Hes
s
Replace st
d
err prints i
n
f
ilenm
.
cpp by asserts
commit
|
commitdiff
|
tree
2018-01-17
B
erk
Hess
Re-e
n
able GPU with walls and 1
e
n
ergy group
commit
|
commitdiff
|
tree
2018-01-16
B
e
rk Hess
R
e
move
t
umb
l
ing ice
-
cube warning with
S
D
commit
|
commitdiff
|
tree
2018-01-16
Berk
H
e
s
s
Avoid mdrun echoing "No
option -mul
t
i"
commit
|
commitdiff
|
tree
2018-01-09
B
e
rk H
e
ss
Rewor
d
CPU
/
GPU imbalance
notes
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do not turn on DLB at
r
ep
l
ica e
x
change
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
Fix triclinic
d
o
mai
n
de
c
ompos
i
tion bug
commit
|
commitdiff
|
tree
2017-12-19
B
erk Hes
s
Make ac
c
eleration corr
e
ction
V
C
M mode work
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
M
ake over
s
ubs
c
ript
i
on
w
ar
n
ing consist
e
nt
commit
|
commitdiff
|
tree
2017-12-14
B
e
rk Hes
s
Require -ntmpi with se
t
tin
g
-ntomp with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Berk H
e
s
s
C
heck for large energy a
t
first s
t
e
p
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Avoid yellin
g
about thre
a
d pinning
twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add grom
p
p no
t
e
f
or
P
R pcouple + positio
n
restraints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove SIMD warning
for AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Tone d
o
w
n
no
t
e
about n
o
t pinning
t
h
r
eads
commit
|
commitdiff
|
tree
2017-12-08
B
e
rk
H
ess
Correct Shake test tolerances
commit
|
commitdiff
|
tree
2017-12-08
Berk He
s
s
Add Vi
v
eca L
i
ndahl
a
s
co
n
t
r
ibutor
commit
|
commitdiff
|
tree
2017-12-07
B
e
rk Hess
Choose faster n
b
n
x
n SIMD kernels on AMD
Zen
commit
|
commitdiff
|
tree
2017-12-05
B
erk Hess
Fix DD exact
c
ontin
u
ation bug
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fix pme gather in double with AVX(2)_12
8
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk Hess
Merge
"Me
r
ge b
r
anc
h
r
elease
-
2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k Hess
F
i
xed initia
l
tem
p
eratur
e
rep
o
r
t
ing
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Update
m
drun signal help text
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
O
n
ly stop at nstlist steps
wi
t
h
-
re
p
rod
commit
|
commitdiff
|
tree
2017-12-03
Berk
H
ess
Clear vsite velocities
for simple in
t
egra
t
o
rs
commit
|
commitdiff
|
tree
2017-12-03
B
erk Hess
Tighten
B-spl
i
ne moduli
s
ingle pre
c
ision
test tole
r
ance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoid assertion failure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hes
s
Chang
e
t
he
G
PU SMT
c
ut-off
to quadrat
i
c
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
U
p
d
ate documentio
n
of Nos
e
-Hoover
o
utput
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Refactor
nbnxn exclusion
s
etting
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Extend gromp
p
missin
g
energy term
message
commit
|
commitdiff
|
tree
2017-11-27
Berk He
s
s
Enable
auto thread p
i
nni
n
g w
i
th thread li
m
iting
commit
|
commitdiff
|
tree
2017-11-27
Berk H
e
ss
F
i
x
PME
GP
U
with
w
alls
commit
|
commitdiff
|
tree
2017-11-25
B
erk Hess
F
i
x
c
omp
i
ler warning w
i
thout MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk H
e
ss
Disabled
CUDA timings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hes
s
Spee
d
up nbn
x
n buffer clearing
commit
|
commitdiff
|
tree
2017-11-24
B
e
rk Hess
Limit
S
MT with PME on
G
PU
commit
|
commitdiff
|
tree
2017-11-23
Berk
Hess
U
p
d
ate note in manual on SD
commit
|
commitdiff
|
tree
2017-11-23
B
e
r
k H
e
ss
Co
r
re
c
t PME GPU t
i
ming nam
i
ng
commit
|
commitdiff
|
tree
2017-11-20
Berk Hes
s
Pre
v
ent PME tuning exc
e
ssive grid scal
i
ng
commit
|
commitdiff
|
tree
2017-11-19
Berk Hess
A
d
d SI
M
D
fo
r
AWH
commit
|
commitdiff
|
tree
2017-11-16
Ber
k
Hess
Also pr
i
nt 1
x
1 pair-
l
i
st setup t
o
log
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
Fix genion charge s
u
mm
a
tio
n
acc
u
racy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix E
k
in at s
t
e
p 0 wi
t
h CO
M
removal
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Add missing Ewald co
r
r
e
ction for pme-user
commit
|
commitdiff
|
tree
2017-10-30
B
e
rk Hess
R
emove unused sign parame
t
er from dih_a
n
g
le()
commit
|
commitdiff
|
tree
2017-10-29
Berk
H
ess
Rem
o
ve incorrect comme
n
t
for CHARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Ber
k
Hess
Fix gmx ch
e
ck
f
or tprs with
d
ifferent
#atoms
commit
|
commitdiff
|
tree
2017-10-23
B
erk Hess
Fix
i
nco
r
rect dV/
d
lambda fo
r
walls
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
Mer
g
e "Merge branch release-2016
"
commit
|
commitdiff
|
tree
2017-10-20
Berk H
e
ss
Fix wa
r
n
i
ng f
o
r confout
w
ith
pe
r
i
odic molecules
commit
|
commitdiff
|
tree
2017-10-18
Berk Hes
s
Made
CUD
A
PME t
e
xture re
f
erence
c
onditional
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Improv
e
vsite pa
r
allel chec
k
i
ng
commit
|
commitdiff
|
tree
2017-10-12
Berk H
e
ss
Si
m
plify virial handlin
g
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disable AR
M
Neon nativ
e
r
s
qrt ite
r
ation
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Add accelerati
o
n correct
i
on VCM mo
d
e
commit
|
commitdiff
|
tree
next