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Work around gcc bug with group kernel tables
2018-03-05
Berk Hess
Work ar
o
u
nd gcc
b
u
g
with group ke
r
nel ta
b
les
commit
|
commitdiff
|
tree
2018-03-02
Berk
H
ess
Fix
AWH
b
ias-shari
n
g with para
l
lel simulation
commit
|
commitdiff
|
tree
2018-03-01
B
erk Hess
D
etect AMD SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix
m
drun multisim with separate PME
ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix md inte
g
rator with Nose-Hoover couplin
g
commit
|
commitdiff
|
tree
2018-02-16
Berk He
s
s
C
orre
c
t mu
l
ti
s
im MPI barri
e
r
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix range bu
g
in add_selection_groups in t
n
gio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk H
e
ss
F
i
x g
r
ompp net charge check
commit
|
commitdiff
|
tree
2018-02-14
Berk He
s
s
Fix gro
m
pp
n
et c
h
a
r
ge check
commit
|
commitdiff
|
tree
2018-02-08
B
e
rk Hess
Use SIMD bondeds wit
h
out perturbed interac
t
ions
commit
|
commitdiff
|
tree
2018-02-08
B
e
rk Hess
Al
l
ow bonds wi
t
h
distan
c
e
=0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Set cutoff modifier
s
in
forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
F
ix asse
r
tion failure in TPI
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Fix COMM removal o
n
part
o
f the system
commit
|
commitdiff
|
tree
2018-01-18
Berk Hes
s
Add
c
h
eck in grompp to avoi
d
asse
r
tion
f
ailure
commit
|
commitdiff
|
tree
2018-01-17
Ber
k
Hess
Re
-
enable
G
PU with walls an
d
1
energy group
commit
|
commitdiff
|
tree
2018-01-16
B
e
r
k Hess
Remove tumb
l
ing ice-cube
warning with SD
commit
|
commitdiff
|
tree
2018-01-16
B
e
rk H
e
ss
Avoid mdrun echoing
"
N
o optio
n
-
multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Reword
C
PU/GPU
i
mbalance note
s
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Do not
t
urn
o
n DLB at replica ex
c
h
a
nge
commit
|
commitdiff
|
tree
2018-01-08
B
e
r
k H
e
ss
Fix
triclinic dom
a
in decom
p
osition bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
M
ake a
c
celerati
o
n corr
e
ction VCM mo
d
e
work
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make oversu
b
scription warning consis
t
en
t
commit
|
commitdiff
|
tree
2017-12-14
Be
r
k Hess
Req
u
ire -ntmpi
w
ith s
e
tting -ntomp with
G
PUs
commit
|
commitdiff
|
tree
2017-12-12
Be
r
k Hess
Check
for
lar
g
e
e
n
e
r
gy at first
ste
p
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Avoid yelling about thread pinning twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add gr
o
mpp
n
ote for
PR
p
couple
+ position
restraints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove SI
M
D w
a
rning for AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk He
s
s
Ton
e
d
o
wn note about not pinning
thread
s
commit
|
commitdiff
|
tree
2017-12-08
B
erk H
e
s
s
Cor
r
ect Shake test tolerances
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add
V
iv
e
ca L
i
ndahl as contribut
o
r
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Choose faste
r
nbnxn SIM
D
kernels on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
B
erk Hess
Fix DD exact con
t
in
u
atio
n
b
u
g
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk
Hess
Fi
x
pme gat
h
e
r
in double with A
V
X(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
Hess
Merge "Merge branch release-2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
F
ixed in
i
tial
t
emperature repor
t
i
n
g
commit
|
commitdiff
|
tree
2017-12-04
Berk He
s
s
U
p
date mdr
u
n signa
l
help tex
t
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
O
nly stop at nstl
i
st steps with -repro
d
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
C
l
e
ar vsite velociti
e
s
for
s
imple integrators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hes
s
Tighten B-spline moduli single
precision test
toler
a
nce
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoid assertion
failure
i
n
AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
Change the GPU S
M
T
cut
-
off to qua
d
rati
c
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Updat
e
documention of Nose-Hoov
e
r
output
commit
|
commitdiff
|
tree
2017-11-28
Berk
Hess
R
e
factor nbnxn ex
c
lusion setting
commit
|
commitdiff
|
tree
2017-11-28
Be
r
k Hess
E
x
t
e
n
d
gr
o
mpp m
i
ss
i
ng energy te
r
m message
commit
|
commitdiff
|
tree
2017-11-27
B
erk Hess
Enable auto threa
d
pinning w
i
th t
h
read l
i
m
i
t
i
ng
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Fix PM
E
G
PU with walls
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
Fix compiler warni
n
g wit
h
out MP
I
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
D
i
sabl
e
d CUDA timings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Spee
d
up nb
n
xn buffer
clearing
commit
|
commitdiff
|
tree
2017-11-24
Berk Hes
s
Lim
i
t SMT w
i
th
P
ME o
n
GP
U
commit
|
commitdiff
|
tree
2017-11-23
Berk H
e
ss
U
p
d
at
e
note
i
n man
u
a
l on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Correct PM
E
GPU
timing na
m
ing
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
Prevent PME
tuning excessive grid sc
a
l
i
n
g
commit
|
commitdiff
|
tree
2017-11-19
B
e
r
k Hess
Add SIM
D
f
o
r
AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hes
s
Also print
1
x1 pair-lis
t
setup to log
commit
|
commitdiff
|
tree
2017-11-10
B
erk H
e
ss
Fix ge
n
ion charge summat
i
on accuracy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix
E
kin a
t
s
tep 0 wit
h
COM
removal
commit
|
commitdiff
|
tree
2017-11-02
Ber
k
Hess
Ad
d
missi
n
g
E
wa
l
d correction for pme-user
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove u
n
used sign param
e
t
e
r from
d
i
h_a
n
gle()
commit
|
commitdiff
|
tree
2017-10-29
B
e
rk
H
ess
R
e
move incorrect com
m
en
t
for C
H
ARMM
tips
3
p
commit
|
commitdiff
|
tree
2017-10-24
Ber
k
Hes
s
Fix
gmx check for
t
prs with different #ato
m
s
commit
|
commitdiff
|
tree
2017-10-23
Berk Hess
Fix incorrect dV/dlam
b
da for walls
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
M
e
rge "M
e
rge
b
ranch rel
e
ase-2016"
commit
|
commitdiff
|
tree
2017-10-20
Berk Hes
s
Fix warning f
o
r confout wit
h
per
i
odic molecule
s
commit
|
commitdiff
|
tree
2017-10-18
Berk Hes
s
Made
C
UDA
P
M
E
textur
e
reference c
o
nditi
o
na
l
commit
|
commitdiff
|
tree
2017-10-15
Berk
Hess
Improve vsite parall
e
l checking
commit
|
commitdiff
|
tree
2017-10-12
Berk Hess
Simplify virial handling
commit
|
commitdiff
|
tree
2017-10-11
B
erk Hess
D
i
sable ARM Neon
native rsqrt iteration
commit
|
commitdiff
|
tree
2017-10-06
Berk H
e
ss
Ad
d
accele
r
ation correction VCM mode
commit
|
commitdiff
|
tree
2017-10-06
B
e
rk Hess
F
i
x m
a
x_size() i
n
al
l
ocato
r
.
h
commit
|
commitdiff
|
tree
2017-10-06
Be
r
k H
e
s
s
Add SIMD in
t
r
i
nsics version of
simple updat
e
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
I
mprove
PaddedRVecVector resizin
g
commit
|
commitdiff
|
tree
2017-10-05
Berk Hess
Make S
I
MD ambig
u
ous te
s
t work with float
/
double
o
nly
commit
|
commitdiff
|
tree
2017-10-04
Berk Hess
R
emo
v
e a force bu
f
fer argument fro
m
IForcePro
v
ider
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
Mov
e
ca
l
ling of special force
functi
o
ns
commit
|
commitdiff
|
tree
2017-10-02
Berk Hes
s
R
e
move hybri
d
gpu+cpu nonbonde
d
mode
commit
|
commitdiff
|
tree
2017-09-25
Ber
k
He
s
s
Put rerun state prepar
a
tion in a fun
c
t
i
on
commit
|
commitdiff
|
tree
2017-09-25
Berk H
e
ss
Set g
l
obal s
t
a
t
e on master
r
ank only
commit
|
commitdiff
|
tree
2017-09-23
Berk Hess
Fix gro
m
pp with
A
ndersen m
a
ssive
and n
o
COM removal
commit
|
commitdiff
|
tree
2017-09-20
B
erk Hess
C
hange
nbn
x
n indexin
g
to templates
commit
|
commitdiff
|
tree
2017-09-15
Berk
H
ess
Remove nb-
p
aram
e
ters from
t_forcerec
commit
|
commitdiff
|
tree
2017-09-14
Berk Hess
Fix nbnxn
SIMD 2xNN PME
tabulated kern
e
l
commit
|
commitdiff
|
tree
2017-09-12
Be
r
k He
s
s
Fix except
i
o
n in SI
M
D LJ PM
E
solve
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Do n
o
t
pass s
t
ate to in
i
t
_replica_ex
c
h
a
n
ge
commit
|
commitdiff
|
tree
2017-09-11
Be
r
k Hess
Fix PBC bugs
in the s
w
ap code
commit
|
commitdiff
|
tree
2017-09-09
Berk
Hes
s
A
v
oid inf in SIMD
do
u
b
l
e sqrt(
)
commit
|
commitdiff
|
tree
2017-09-07
Berk Hess
F
i
x FEP
s
tate with r
e
ru
n
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Fix tw
o
nbnxn
search
indexi
n
g bugs
commit
|
commitdiff
|
tree
2017-09-04
Berk
Hess
Consol
i
d
ate architectur
e
booleans
commit
|
commitdiff
|
tree
2017-09-03
Berk Hess
Put mdrun options in structs
commit
|
commitdiff
|
tree
2017-09-02
Berk Hess
P
u
t all
d
o
m
dec o
p
t
ions in a struct
commit
|
commitdiff
|
tree
2017-09-02
Berk Hess
Fi
x
md
r
un
-
n
b option
p
ointer
commit
|
commitdiff
|
tree
2017-09-01
Berk Hess
Fix mdru
n
-
n
b
op
t
ion p
o
int
e
r
commit
|
commitdiff
|
tree
2017-08-29
Berk Hess
Ma
k
e pull
p
otential r
e
gistration
thread-
s
afe
commit
|
commitdiff
|
tree
2017-08-29
Berk Hess
S
et d
e
fau
l
t
GMX_OPENMP_MAX_THRE
A
DS
t
o 64
commit
|
commitdiff
|
tree
2017-08-28
Berk Hes
s
A
v
oid b
o
nd
e
d fo
r
ces loops/ti
m
e
r
s on
inputs with no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Berk He
s
s
Ena
b
le dyna
m
i
c
pair list pr
u
ni
n
g
commit
|
commitdiff
|
tree
2017-08-18
Berk Hess
A
d
d CPU refe
r
ence and
SI
M
D pruning ker
n
els
commit
|
commitdiff
|
tree
2017-08-16
Ber
k
Hess
Add dynam
i
c pair
-
list pruning framework
commit
|
commitdiff
|
tree
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