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Remove commrec from set_ddbox()
2018-05-17
B
e
rk Hess
Remove
co
m
mrec from set_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Clean up
PME do
m
ain
count passing
commit
|
commitdiff
|
tree
2018-05-03
B
erk Hess
Ena
b
le
S
IM
D
ve
r
sion of update
commit
|
commitdiff
|
tree
2018-04-27
Be
r
k Hess
Remove pull
MPI
c
ode duplic
a
t
ion
commit
|
commitdiff
|
tree
2018-04-24
Berk Hess
F
ix i
n
dex
i
ng i
s
sue in
the pul
l
c
ode
commit
|
commitdiff
|
tree
2018-04-16
Be
r
k He
s
s
Move natoms_
m
ol out of
gm
x
_m
o
l
b
lock_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert gmx_molblock_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hes
s
Co
n
vert gmx_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
C
h
a
n
ge
w
arninp f
i
lenm t
o
std::stri
n
g
commit
|
commitdiff
|
tree
2018-04-03
Berk He
s
s
Do not ca
l
c
u
l
ate COM for pull
g
roup 0
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move
f
i
le opening out of in
i
t_pu
l
l()
commit
|
commitdiff
|
tree
2018-03-29
Ber
k
Hess
Mo
d
ularize
pull_coord
_
work_
t
commit
|
commitdiff
|
tree
2018-03-28
Berk
H
es
s
Re
m
ove
mols from
gmx_
m
top
_
t
commit
|
commitdiff
|
tree
2018-03-20
B
e
rk
H
ess
Fix gmx dum
p
AWH fo
r
matti
n
g i
s
sue
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow
s
i
ngle simulat
i
on w
i
th multis
i
m
commit
|
commitdiff
|
tree
2018-03-16
Berk H
e
s
s
Corr
e
ct PMF sign error i
n
AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk
H
ess
Fix r
e
cent
m
d
r
un s
i
gnalin
g
bug
commit
|
commitdiff
|
tree
2018-03-15
Berk
H
e
s
s
Fix virial with external p
u
ll
potential and
M
PI
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
ess
Improve
i
nter
-
simulation signalin
g
commit
|
commitdiff
|
tree
2018-03-14
B
er
k
Hess
Fix
m
drun
signalli
n
g with
AWH bias s
h
a
ring
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
e
ss
F
ix COM pullin
g
with externa
l
p
ote
n
tial w
i
th #ranks>32
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix pull
b
ug with geomet
r
y=direction-periodic
commit
|
commitdiff
|
tree
2018-03-13
B
e
rk H
e
ss
A
d
d
AWH fixes to re
l
eas
e
notes
commit
|
commitdiff
|
tree
2018-03-13
Be
r
k Hess
F
i
x
AWH ensembl
e
checkpoin
t
ing
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
F
ix AWH deco
n
vol
u
t
i
o
n when shar
i
ng a b
i
as
commit
|
commitdiff
|
tree
2018-03-09
B
e
rk Hess
C
o
rr
e
ct pdb2gmx -missing op
t
ion
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix memory le
a
k in P
M
E
commit
|
commitdiff
|
tree
2018-03-06
B
erk
Hes
s
C
o
nvert t_filenm to
C++
commit
|
commitdiff
|
tree
2018-03-06
Be
r
k
Hess
Make mul
t
i-ato
m
TPI reproducib
l
e
commit
|
commitdiff
|
tree
2018-03-05
Berk H
e
s
s
Work around gc
c
bug with group kernel t
a
ble
s
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Leave n
u
l
lp
t
r opt in
t
_
filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
F
ix
cpp
c
h
e
ck warning
commit
|
commitdiff
|
tree
2018-03-02
B
e
rk
H
ess
Fix AWH bias-sh
a
r
i
n
g with
parallel simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk H
e
ss
Detect AMD SMT to
p
ol
o
g
y
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
F
ix mdrun
multisim with sep
a
r
a
te PM
E
ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix md integrator wi
t
h Nose-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simplify mdr
u
n t
M
P
I
t
h
read spawning
commit
|
commitdiff
|
tree
2018-02-16
B
e
r
k Hess
C
o
rrect mul
t
isim
MPI ba
r
rier
commit
|
commitdiff
|
tree
2018-02-14
Berk
H
ess
Remove suppor
t
f
o
r
tpx version before 5
8
/gm
x
4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk
Hess
F
i
x
ran
g
e bug
i
n
a
dd_selection_grou
p
s in tngio
.
c
p
p
commit
|
commitdiff
|
tree
2018-02-14
Berk H
e
s
s
F
i
x
grompp net charge ch
e
c
k
commit
|
commitdiff
|
tree
2018-02-14
B
e
r
k
H
ess
Fix gr
o
mpp net charg
e
check
commit
|
commitdiff
|
tree
2018-02-08
Berk Hes
s
Use SIMD
bondeds without perturbe
d
interactions
commit
|
commitdiff
|
tree
2018-02-08
B
erk Hess
Allow
bon
d
s with
di
s
tance=0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Set cutoff modifiers
i
n fo
r
cerec
commit
|
commitdiff
|
tree
2018-02-05
B
er
k
Hess
Fix ass
e
rtion fa
i
lu
r
e
in
T
P
I
commit
|
commitdiff
|
tree
2018-01-30
B
e
rk Hess
Removed
unus
e
d
f
lag
P
CA_
C
A
N_READ_NODE
commit
|
commitdiff
|
tree
2018-01-18
B
e
rk Hess
Fix CO
M
M
removal on part of the system
commit
|
commitdiff
|
tree
2018-01-18
Berk H
e
ss
Add chec
k
i
n g
r
ompp to avoid assertion
failure
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
R
e
place stderr p
r
ints
in
f
il
e
nm
.
cpp by
a
sserts
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Re
-
en
a
ble GPU wi
t
h walls and
1 energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk
H
ess
Remove t
u
mbling ice-cube warnin
g
with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
A
v
oid mdrun echoi
n
g "
N
o
o
ption -m
u
lti"
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
R
eword CPU/GPU i
m
balan
c
e notes
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do
not tu
r
n on DL
B
at rep
l
i
c
a
e
x
c
hange
commit
|
commitdiff
|
tree
2018-01-08
Berk H
e
ss
Fix triclin
i
c do
m
ain decomposition bug
commit
|
commitdiff
|
tree
2017-12-19
Berk H
e
ss
M
ake acce
l
eration correction VCM mode work
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make oversubscripti
o
n
w
ar
n
ing consiste
n
t
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Require -nt
m
pi with
s
etti
n
g -ntomp with GPUs
commit
|
commitdiff
|
tree
2017-12-12
B
erk Hess
Check for large
e
nergy at first s
t
e
p
commit
|
commitdiff
|
tree
2017-12-12
Ber
k
Hes
s
Avoid yelling about t
h
read pinning twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add gr
o
mpp
n
ote for PR pcouple +
position restraints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
R
emove SIMD
w
arning
fo
r
AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
B
er
k
Hess
Tone down
n
ote ab
o
ut
n
ot p
i
nning
t
hreads
commit
|
commitdiff
|
tree
2017-12-08
Berk He
s
s
Correct Sha
k
e test tolerances
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add
V
iveca Lindahl a
s
contribu
t
or
commit
|
commitdiff
|
tree
2017-12-07
Berk H
e
ss
Choo
s
e faster nbn
x
n
SIMD kernels on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fix DD exact
co
n
tinua
t
ion bug
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Fix pme
g
a
t
h
er
in
double with
AVX(2)_1
2
8
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Merge "Merge branch relea
s
e-2
0
16 into
release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fixed
initial temperature reporting
commit
|
commitdiff
|
tree
2017-12-04
B
e
r
k Hess
U
p
date mdrun si
g
nal help text
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk Hess
On
l
y stop
at nstlist steps with -
r
eprod
commit
|
commitdiff
|
tree
2017-12-03
B
erk Hess
Clea
r
vsit
e
v
elocit
i
es f
o
r
si
m
p
le integr
a
t
ors
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Tighten B-spline moduli si
n
gle
p
reci
s
ion test tolera
n
ce
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Be
r
k Hess
A
void asse
r
tion failure
i
n
A
WH
commit
|
commitdiff
|
tree
2017-11-29
B
e
rk Hes
s
Change the GPU SMT cut-off to quadratic
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
U
pdat
e
d
o
cumenti
o
n of Nose-Hoover output
commit
|
commitdiff
|
tree
2017-11-28
Berk Hes
s
Refactor nbnxn exclusio
n
s
et
t
in
g
commit
|
commitdiff
|
tree
2017-11-28
Berk He
s
s
Extend grompp
m
i
ssing
e
nergy ter
m
mess
a
g
e
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Enable auto thread
p
i
nning with
thr
e
ad li
m
itin
g
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Fix P
M
E
GPU with wall
s
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
Fi
x
compiler war
n
i
ng without
M
PI
commit
|
commitdiff
|
tree
2017-11-24
Berk
Hes
s
D
i
s
abled CUDA tim
i
n
gs
commit
|
commitdiff
|
tree
2017-11-24
Berk H
e
ss
Sp
e
e
d
up nbnxn buffer
c
learing
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Limit SMT with PME o
n
G
PU
commit
|
commitdiff
|
tree
2017-11-23
Be
r
k Hess
Upda
t
e note i
n
manua
l
o
n
S
D
commit
|
commitdiff
|
tree
2017-11-23
B
erk Hess
Corre
c
t
PME G
P
U ti
m
ing naming
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
Pr
e
vent PME tuning excessi
v
e gri
d
sca
l
ing
commit
|
commitdiff
|
tree
2017-11-19
Berk Hess
Add SIMD for A
W
H
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Al
s
o pr
i
nt 1x
1
pair-li
s
t
setup t
o
log
commit
|
commitdiff
|
tree
2017-11-10
Berk
Hess
Fix
genion charge summation accuracy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix
E
kin
at
step 0 wi
t
h C
O
M remova
l
commit
|
commitdiff
|
tree
2017-11-02
Berk
H
e
s
s
Add missing Ewa
l
d correction for
p
me-user
commit
|
commitdiff
|
tree
2017-10-30
Ber
k
Hess
Rem
o
ve
u
nused sign parameter f
r
om dih_angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk He
s
s
Re
m
o
ve i
n
correct
commen
t
for CHARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Berk
H
ess
Fix gmx check for t
p
r
s with
d
i
ffe
r
e
n
t #atoms
commit
|
commitdiff
|
tree
2017-10-23
Be
r
k
H
ess
Fix incorre
c
t
d
V/
d
l
a
mbda for walls
commit
|
commitdiff
|
tree
2017-10-21
Berk
Hess
Merge "Me
r
ge branch re
l
ease-20
1
6
"
commit
|
commitdiff
|
tree
2017-10-20
Berk H
e
ss
Fix warni
n
g for confout with periodic molecule
s
commit
|
commitdiff
|
tree
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