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Quotes from Gottingen workshop
2017-05-26
Berk
H
ess
Improve V
e
rlet buffer constraint estimate
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2017-05-23
Be
r
k Hess
Add conserved q
u
a
ntity for
Berendsen P-c
o
uple
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2017-05-23
Berk
H
e
ss
Add
c
o
n
s
erved q
.
for P
R
and Berendsen T-c
o
uple
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2017-05-23
B
e
rk He
s
s
Make DD
setup obey PME restrictions
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2017-05-22
Berk Hess
Introduce Observables
H
is
t
or
y
container
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tree
2017-05-16
B
e
r
k Hess
F
ix c
o
nfout
.
gro wi
t
h e
n
er
g
y
minim
i
z
ation
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tree
2017-04-21
B
erk Hess
F
i
x bugs
in double AV
X
(2)_256 Simd4
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2017-04-19
Berk Hes
s
F
ix unused
SIM
D
P
M
E
table kernel
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tree
2017-04-18
Berk H
e
s
s
Suppress two com
p
iler warnings
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2017-03-16
Berk Hess
Replace i
n
stance
o
f group b
y
c
oord in pull mdp docs
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2017-03-14
Berk
H
es
s
Make
g
ro
m
p
p
-r obligatory with posres
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2017-02-28
Berk Hess
Add loa
d
b
a
lanc
e
fraction to DLB print
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tree
2017-02-07
Berk Hess
Add mdp optio
n
check with
d
e
c
o
upled modes
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2017-02-02
Berk Hess
Really fix array of c
o
mplex
in cross_corr
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2017-02-02
Berk Hess
Fix arra
y
of
c
ompl
e
x in cross_corr
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tree
2017-01-20
B
e
rk Hess
D
i
sa
l
l
ow
o
verwri
t
ing of dihedral
typ
e
9
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2017-01-20
Berk Hess
O
n
ly
predict shells with velocit
i
es
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tree
2017-01-19
Berk Hess
Fix PME order
a
nd gri
d
si
z
e check
s
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tree
2017-01-17
B
e
rk He
s
s
Correct assert
on
pme-order
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tree
2017-01-05
Berk Hess
Fix flat-bot
t
om position
restrai
n
t
s
+ D
D
+ OpenM
P
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2016-12-14
Ber
k
Hess
Add bonded #thread
run
t
ime check
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2016-12-08
B
e
rk Hess
M
ade mdrun -pforce te
r
minat
e
wit
h
non-finite forces
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2016-11-24
Berk Hess
Chan
g
e s
p
line moduli cal
c
ulation to double
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tree
2016-11-23
Berk Hess
Convert
energyhist
o
ry_t to use std::vec
t
o
r
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2016-11-23
B
e
rk Hess
Use te
m
plating in che
c
kpoint
.
c
p
p
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2016-11-01
B
e
rk Hess
Fix time
label print in
g
mx v
a
nh
o
ve
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tree
2016-10-29
Berk Hess
Add gmx dump option
for
printing parameters
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2016-10-28
Ber
k
Hess
DLB can now turn
o
ff, when
s
lower
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2016-10-28
Berk Hess
Fix DL
B
timing with
C
UDA and OpenCL
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2016-10-15
Berk Hess
Move energyhist
o
ry_t ou
t
of t_state
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2016-10-14
Berk
Hess
Ap
p
ly
B
erendsen P-couple
a
t nstpcouple
s
teps
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2016-10-13
B
e
rk
Hess
Extend mtop_looku
p
.
h
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2016-10-12
Berk Hess
F
i
xed
e
xception in usused res
u
lt
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2016-10-12
Berk Hess
Fixed print bug in gmx wham
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2016-10-12
Berk Hes
s
Refactor NPT energy calculation
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2016-10-12
Be
r
k Hess
Restr
u
ct
u
re
leap-frog integra
t
ors
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2016-10-11
Berk Hess
Speed up mtop_ut
i
l atom look
u
p
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2016-10-08
Berk
Hess
Add readConfA
n
dTopolo
g
y
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2016-10-07
Be
r
k Hess
Changed
fr->f_novirsum
to Padde
d
RVecVect
o
r
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|
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2016-10-01
Berk
Hess
Fix in
p
utrec
i
n
i
tialization in 4 tools
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|
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2016-09-29
Berk Hess
U
s
e
std::vector in
t_state
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|
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2016-09-29
Berk Hess
Add fla
g
s
f
o
r
o
ptional t_atoms ent
r
ies
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2016-09-22
Berk Hes
s
F
i
x gcc war
n
ing i
n
A
l
ignedAllocat
o
r
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2016-09-20
Berk Hess
Remove state dupl
i
c
a
t
i
on in serial r
u
ns
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2016-09-16
Be
r
k Hess
Fixed unuse
d
va
r
ia
b
le
s
in domdec
.
c
p
p
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2016-09-16
Berk Hess
M
erge
b
ranch rel
e
ase-2016
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2016-09-16
Ber
k
H
e
ss
Mad
e
distance restr
a
ints w
o
rk with
t
hreads and DD
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|
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2016-09-13
Berk He
s
s
Mov
e
d exp
a
nded ensemble
h
istory t
o
pointer in t_state
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2016-09-13
B
e
rk
Hess
Chan
g
e ED and swa
p
s
tate to point
e
rs in t_state
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|
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2016-09-12
Berk Hess
Add const to thread-MPI functi
o
ns
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2016-09-10
Berk H
e
ss
Rem
o
ve conti
n
uation f
r
o
m
c
o
n
vert_tpr
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2016-09-06
Ber
k
Hess
Fix b
u
g with con
j
ugate-gradient and
OpenMP
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|
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2016-09-06
Berk
Hess
Consolidat
e
MD algori
t
hm at
o
m setu
p
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tree
2016-09-05
Be
r
k Hess
Re-enable
f
lexible c
o
n
stra
i
nts
wit
h
DD
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2016-09-04
Berk He
s
s
M
e
rge branch re
l
ease-2016
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|
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2016-09-03
Berk Hess
Clea
n
u
p
PME flags variable us
e
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2016-09-02
B
er
k
Hes
s
Merge bran
c
h rele
a
se-5-1 into release
-
2
016
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2016-09-02
Berk Hess
F
ix
P
arrine
l
lo-
R
ah
m
a
n with ns
t
pcouple>1
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|
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2016-08-30
Be
r
k Hess
Make virial reprodu
c
ibl
e
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|
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2016-08-27
Berk He
s
s
Reduce rounding erro
r
s in S
E
TTLE
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|
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2016-08-24
Berk Hess
Fix Ewald surface+3DC correct
i
ons
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2016-08-24
Be
r
k H
e
ss
Merg
e
b
ranch release-5-1 into relea
s
e-2016
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2016-08-23
Berk Hess
Remove
v
a
riable p
r
e
ci
s
i
o
n gro writ
i
ng
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|
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2016-08-17
B
e
rk Hess
F
i
xed opening of
w
all table files
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|
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tree
2016-08-15
Berk
Hess
Reduce FE pair-list memory
usage
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|
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tree
2016-08-10
Berk Hes
s
Fix dea
d
lock with thread-MPI
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|
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tree
2016-08-09
Berk Hess
Fi
x
twin-cutoff fo
r
GPU LJ pot-switch
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|
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tree
2016-07-07
Berk H
e
s
s
Relax pull PBC chec
k
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|
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2016-07-05
Berk Hess
Add che
c
k
s
for too much memory in g_nmeig
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|
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2016-07-03
Ber
k
Hess
Add grompp chec
k
fo
r
pu
l
l
group
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|
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2016-06-28
Berk
Hes
s
Pro
p
e
r
ly res
e
t CUDA appli
c
atio
n
clocks
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|
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tree
2016-06-27
Ber
k
He
s
s
Us
e
sysconf(_SC_NPROCESSO
R
S_ONLN)
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|
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2016-06-26
Berk Hess
Fix vs
i
te b
u
g with MPI+OpenMP
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|
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2016-06-24
Berk
H
ess
Fi
x
V
e
rlet buffer c
a
lculation with ns
t
list=1
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|
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2016-06-23
Berk Hess
More accurate GPU li
s
t splitting
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|
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2016-06-22
Be
r
k
Hes
s
Updated OpenCLT
O
DOList
.
t
x
t
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|
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2016-06-22
Berk Hess
Add
nbnxn pa
i
r-lis
t
rebalancing
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|
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tree
2016-06-22
B
e
rk He
s
s
Re
m
o
v
e
OpenMP overhead at high paralle
l
i
z
ation
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|
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2016-06-22
B
e
rk Hess
Corr
e
ct GPU pair es
t
imate for list splitting
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|
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2016-06-21
Berk He
s
s
F
ix bug w
i
t
h
fb
p
osr
e
s
+
M
P
I+OpenMP
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|
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2016-06-20
B
erk Hess
Increase
d
tp
x
_incompatible_v
e
rsion to 30
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|
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2016-06-19
Berk
Hess
R
emove w
a
rnings
o
n checkpoint mismatc
h
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|
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tree
2016-06-17
Be
r
k
H
e
ss
Remo
v
e std::thread::hardw
a
re_c
o
ncurrency()
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|
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2016-06-14
Ber
k
Hess
Fix OpenCL er
r
or with empty domains
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|
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tree
2016-06-13
B
e
rk Hess
Handle
c
on
s
t
r
a
int errors with EM
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|
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tree
2016-06-07
Berk
He
s
s
F
ix data race in hwinfo with thread-M
P
I
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|
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2016-06-03
Berk Hes
s
H
an
d
le
partially frozen
a
nd
c
ons
t
rained a
t
oms
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|
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tree
2016-05-31
Ber
k
H
ess
Rep
o
sition
n
bnxn
f
il
l
er p
a
rticles
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|
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tree
2016-05-31
Berk Hess
Avoid n
u
m
eric
a
l overflow with o
v
erlapping atoms
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|
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2016-05-31
Ber
k
He
s
s
Add
c
heck for
f
init
e
energ
i
es
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|
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tree
2016-05-30
Berk Hess
Add
grompp chec
k
for unbo
u
nd atoms
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|
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tree
2016-05-23
Berk He
s
s
Fix bug in v-rescale
t
hermostat & replica exchange
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|
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tree
2016-05-10
B
erk He
s
s
Optimized the
v
si
t
e thread
i
ng
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tree
2016-05-10
Berk
H
ess
F
ix CUDA shmem bug
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|
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tree
2016-05-10
Berk Hess
Support
c
map with QMMM
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tree
2016-05-08
Berk
Hess
Update mdrun terminat
i
o
n
info
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|
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2016-05-06
Berk Hess
OpenMP parallelizatio
n
for p
u
ll
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|
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2016-04-20
Berk Hess
F
ix pu
l
l l
e
ge
n
d with
ex
t
ernal potential
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|
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2016-04-19
Ber
k
Hes
s
Allow rcoulomb>rvdw with PME
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|
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2016-04-19
Berk Hess
B
roadca
s
t p
u
ll
external potentia
l
prov
i
d
e
r
string
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