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Move natoms_mol out of gmx_molblock_t
2018-04-16
Berk H
e
ss
Mo
v
e
n
a
toms_mol out of gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-09
Ber
k
Hess
Co
n
vert gmx_
m
olblock_t to C
+
+
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
C
onvert gmx_mtop_t to
C
++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Change w
a
rninp fil
e
nm to
s
td::st
r
ing
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do n
o
t
c
alcula
t
e
COM for
p
u
l
l
grou
p
0
commit
|
commitdiff
|
tree
2018-03-29
B
erk Hess
M
o
ve file opening
out of
in
i
t_pull()
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
ess
M
o
dularize pull_coord_
w
ork_t
commit
|
commitdiff
|
tree
2018-03-28
Berk He
s
s
Remove mols
f
r
om gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-20
B
e
rk Hess
Fix
gmx
d
ump AWH format
t
ing
i
ssue
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallo
w
single sim
u
lation
w
i
th multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct PMF s
i
gn
er
r
o
r
in
AWH bia
s
s
h
aring
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Fix recen
t
md
r
un signaling bug
commit
|
commitdiff
|
tree
2018-03-15
Be
r
k
He
s
s
Fix viria
l
with
external
pull potential and
M
PI
commit
|
commitdiff
|
tree
2018-03-14
Berk H
e
ss
Imp
r
ov
e
inte
r
-
s
imul
a
tion
s
ignaling
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
H
es
s
F
i
x mdrun
s
ignalling with
A
WH bias
sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix
COM pulling with external potential
w
i
th #r
a
nks>32
commit
|
commitdiff
|
tree
2018-03-14
Berk He
s
s
F
i
x
pu
l
l bug wi
t
h
geometry=
d
i
r
ection-p
e
riodic
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
Add AWH fixes to release notes
commit
|
commitdiff
|
tree
2018-03-13
B
e
rk Hess
Fix AWH ens
e
mb
l
e checkpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk
Hes
s
Fix
AWH deconvolu
t
ion when
s
har
i
ng a b
i
as
commit
|
commitdiff
|
tree
2018-03-09
Ber
k
Hess
C
o
rr
e
c
t
pd
b
2gmx -missing option
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix
m
emory
l
e
a
k in PME
commit
|
commitdiff
|
tree
2018-03-06
Be
r
k Hess
C
o
nvert t_fil
e
nm to C++
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Ma
k
e
mult
i
-atom TPI
r
eproducible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hes
s
W
ork
around gcc
bug with group
ker
n
el tables
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Leave nullptr opt in
t_filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk H
e
ss
Fi
x
cp
p
che
c
k warning
commit
|
commitdiff
|
tree
2018-03-02
Berk H
e
s
s
Fix
A
WH bias-sh
a
r
i
n
g
with parallel simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Detect
A
M
D SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix mdrun
m
u
l
t
isim with s
e
parate PM
E
r
anks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix
md integrat
o
r with Nose-Hoover
co
u
p
ling
commit
|
commitdiff
|
tree
2018-02-22
Ber
k
Hess
S
implify
mdrun tMPI threa
d
spawning
commit
|
commitdiff
|
tree
2018-02-16
B
erk H
e
ss
Correct multisim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk
H
es
s
Remov
e
s
uppo
r
t for tpx version before 58/g
m
x4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
i
x
range bu
g
in ad
d
_selection_g
r
o
ups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk H
e
s
s
Fix gr
o
mpp net ch
a
rg
e
check
commit
|
commitdiff
|
tree
2018-02-14
Berk
H
e
ss
Fix grompp
net
c
harge check
commit
|
commitdiff
|
tree
2018-02-08
Berk H
e
ss
Use SIMD bondeds without perturbed interaction
s
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
Allow
bonds with distance=
0
commit
|
commitdiff
|
tree
2018-02-05
Ber
k
Hess
Set cutoff mod
i
fiers in
f
o
r
c
erec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix
assertion failure in TP
I
commit
|
commitdiff
|
tree
2018-01-30
Berk
H
e
ss
Removed unused flag PCA_
C
AN_READ_NODE
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix COMM rem
o
v
al o
n
par
t
o
f
t
he system
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add check
i
n gr
o
mpp to av
o
id assertion failure
commit
|
commitdiff
|
tree
2018-01-17
Berk
Hess
Re
p
lace s
t
de
r
r prints in filenm
.
cpp by asserts
commit
|
commitdiff
|
tree
2018-01-17
Berk Hes
s
Re-enab
l
e GPU with walls and 1
e
nergy g
r
oup
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Rem
o
v
e tumbling ice-cube w
a
r
n
i
ng w
i
th SD
commit
|
commitdiff
|
tree
2018-01-16
B
erk
H
ess
Avoid mdrun ech
o
ing
"N
o
optio
n
-multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Reword CPU/G
P
U imbal
a
n
ce notes
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do not t
u
rn on DLB at replica exchange
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
Fix
t
riclinic domain
d
ecompos
i
tion bug
commit
|
commitdiff
|
tree
2017-12-19
Berk He
s
s
Make a
c
celerati
o
n correct
i
on VCM mode work
commit
|
commitdiff
|
tree
2017-12-19
B
er
k
Hess
Mak
e
over
s
ubscr
i
ption warnin
g
c
onsistent
commit
|
commitdiff
|
tree
2017-12-14
Ber
k
Hess
R
e
qu
i
re -ntmpi
with setting -ntomp with GP
U
s
commit
|
commitdiff
|
tree
2017-12-12
Berk
H
e
s
s
Check for large energy at first step
commit
|
commitdiff
|
tree
2017-12-12
Berk He
s
s
A
void yellin
g
about threa
d
pinning twi
c
e
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add grom
p
p note for
P
R pcouple + position res
t
ra
i
nts
commit
|
commitdiff
|
tree
2017-12-10
Berk He
s
s
Remo
v
e SIMD w
a
rning
for AMD
Zen
commit
|
commitdiff
|
tree
2017-12-10
Be
r
k He
s
s
Tone down note about not p
i
nning t
h
reads
commit
|
commitdiff
|
tree
2017-12-08
B
e
rk H
e
ss
Corr
e
ct Shake
t
est
t
olerances
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Ad
d
Vi
v
eca L
i
nd
a
hl as contribu
t
or
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Choose
fast
e
r nbnx
n
SIM
D
ker
n
el
s
o
n
AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fix D
D
e
x
act continuation bu
g
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Fix pme gather in doubl
e
with AVX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Me
r
g
e
"Me
r
g
e
branch
relea
s
e-2016 in
t
o release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
Fi
x
ed
i
n
itial t
e
mperature
r
e
po
r
ting
commit
|
commitdiff
|
tree
2017-12-04
Berk He
s
s
Update mdru
n
sig
n
al
h
e
l
p te
x
t
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
ess
O
n
ly stop at nstli
s
t steps with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Ber
k
Hess
C
l
e
a
r
vs
i
te velocities for simp
l
e i
n
te
g
rators
commit
|
commitdiff
|
tree
2017-12-03
B
e
rk
H
ess
Tight
e
n B-splin
e
moduli
s
ingle precisio
n
t
est tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
B
e
rk Hess
Avoid assertion failure in A
W
H
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
Change the GP
U
SMT
c
ut-off to qu
a
dratic
commit
|
commitdiff
|
tree
2017-11-28
B
e
rk Hess
Up
d
ate documention
o
f
Nose-Hoover ou
t
pu
t
commit
|
commitdiff
|
tree
2017-11-28
B
erk Hess
Refactor nbnxn
exc
l
u
sion set
t
ing
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Ex
t
end g
r
o
mpp
missi
n
g energy term mes
s
ag
e
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Enabl
e
auto
t
hread pinning with threa
d
l
imiting
commit
|
commitdiff
|
tree
2017-11-27
Berk Hes
s
Fix PME GPU with w
a
l
ls
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
Fix comp
i
ler warning without MP
I
commit
|
commitdiff
|
tree
2017-11-24
Ber
k
H
ess
Disabled CUDA timi
n
g
s
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
S
p
eed up nbnxn buf
f
er
clearing
commit
|
commitdiff
|
tree
2017-11-24
B
erk Hess
Limi
t
SMT
with PME
on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Updat
e
n
o
t
e in
m
anual o
n
SD
commit
|
commitdiff
|
tree
2017-11-23
B
e
r
k Hess
C
orrect P
M
E GPU tim
i
ng naming
commit
|
commitdiff
|
tree
2017-11-20
Berk H
e
ss
Prevent PME tuning exces
s
ive grid
scaling
commit
|
commitdiff
|
tree
2017-11-19
Berk
H
ess
A
d
d
SIMD for AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Also pr
i
nt 1x1 pa
i
r-lis
t
setup to log
commit
|
commitdiff
|
tree
2017-11-10
B
erk Hess
Fix genion charge summation ac
c
uracy
commit
|
commitdiff
|
tree
2017-11-02
B
e
rk Hes
s
Fix Ekin at
step 0 with
COM removal
commit
|
commitdiff
|
tree
2017-11-02
Ber
k
Hess
Ad
d
missing Ewa
l
d correction f
o
r
pme-user
commit
|
commitdiff
|
tree
2017-10-30
Be
r
k
H
ess
Remove un
u
s
e
d sign
p
aramete
r
from dih_angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk
Hess
Remov
e
incorrect comm
e
nt for
C
HARMM tips3p
commit
|
commitdiff
|
tree
2017-10-24
Berk
H
ess
F
i
x gmx
c
heck for t
p
rs with di
f
ferent #ato
m
s
commit
|
commitdiff
|
tree
2017-10-23
Berk Hess
Fix incor
r
ect
d
V/dlambda for walls
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
Merge "Merge br
a
nch release-2016"
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix warning for confo
u
t with pe
r
iodic mol
e
cules
commit
|
commitdiff
|
tree
2017-10-18
Berk H
e
ss
M
ade CUD
A
PME texture reference c
o
ndi
t
i
onal
commit
|
commitdiff
|
tree
2017-10-15
Berk He
s
s
Improve
vsite
p
arallel checking
commit
|
commitdiff
|
tree
2017-10-12
Be
r
k Hess
Simp
l
ify virial
h
andling
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disa
b
le AR
M
Neon native rsqrt ite
r
ation
commit
|
commitdiff
|
tree
2017-10-06
Be
r
k
Hess
Add acceleration corr
e
ction VCM mode
commit
|
commitdiff
|
tree
next