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Improve handling of task-assignment exceptions
2019-11-20
Be
r
k Hess
Quiet pdb2g
m
x and use gm
x
_fatal
commit
|
commitdiff
|
tree
2019-11-19
Berk Hess
Fix bo
n
ded
a
tom
communication p
e
rformance
commit
|
commitdiff
|
tree
2019-11-18
Berk He
s
s
Fix intermolecular interactio
n
s
w
ith
D
D
commit
|
commitdiff
|
tree
2019-11-07
B
e
rk Hess
Fix
.
g
r
o
l
a
rge
box writing
commit
|
commitdiff
|
tree
2019-11-06
Berk He
s
s
D
eprec
a
t
ed
s
c-r-pow
e
r=48
commit
|
commitdiff
|
tree
2019-11-01
B
erk Hess
Add ha
v
e
E
w
a
ldSurfaceCo
n
tribution to Simulation
W
o
r
kl
o
ad
commit
|
commitdiff
|
tree
2019-10-31
Be
r
k
Hess
Update
GPU up
d
at
e
res
t
riction
s
commit
|
commitdiff
|
tree
2019-10-30
Berk He
s
s
Fix walls
w
ith G
P
U upda
t
e
commit
|
commitdiff
|
tree
2019-10-29
Berk
Hes
s
A
dd
mdrun GPU update do
c
umentation
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Fix Ewald dipole correcti
o
n
wit
h
G
PU update
commit
|
commitdiff
|
tree
2019-10-29
B
er
k
Hess
Disable p
r
essure coupling with GPU update
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
A
dd bool u
s
eDo
m
ainDe
c
omposition
i
n mdrunner
commit
|
commitdiff
|
tree
2019-10-24
B
e
rk He
s
s
Add gmx_
m
top_interaction
_
co
u
n
t()
commit
|
commitdiff
|
tree
2019-10-24
B
e
r
k
H
e
ss
Fix initializers in loc
a
lit
y
.
h
commit
|
commitdiff
|
tree
2019-10-23
B
erk Hess
Move l
o
c
ality
.
h from
n
bnxm to mdtypes
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Use gmx:
:
Range in
N
bnx
m
g
ridding function
s
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Fix illegal memory ac
c
e
ss in FE
c
alculations
commit
|
commitdiff
|
tree
2019-10-23
Berk
H
ess
Expand
d
ocumentation for nb
n
xn
_
put_o
n
_grid()
commit
|
commitdiff
|
tree
2019-10-22
Berk
Hess
Re
q
uire
-
ei for es
s
e
ntial dynamics
commit
|
commitdiff
|
tree
2019-10-18
Berk Hess
Upd
a
te grompp cut
o
ff-schem
e
warni
n
gs
commit
|
commitdiff
|
tree
2019-10-15
Berk Hess
Const correctne
s
s for genhy
d
ro
commit
|
commitdiff
|
tree
2019-10-12
Ber
k
Hess
A
dd
c
lass
FixedCapacityVect
o
r
commit
|
commitdiff
|
tree
2019-10-09
Berk He
s
s
Increase spc minimization test tol
e
rance
commit
|
commitdiff
|
tree
2019-10-09
B
e
rk Hess
Fix harmless OpenMP write race
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Fix GPU atom dat
a
init timer
i
ssue
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Fix ra
n
dom energy and virial wi
t
h PME
on GPU o
n
a
PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
B
erk Hess
Make nbnxm
a
proper modu
l
e
commit
|
commitdiff
|
tree
2019-10-08
B
erk H
e
ss
Simpl
i
fy ewald_LRcorrection
(
) cal
l
signatur
e
commit
|
commitdiff
|
tree
2019-10-04
B
e
rk
Hess
F
ix
r
ando
m
e
nergy and
virial with PME on GPU on a
PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Fix GPU
a
tom dat
a
init timer issue
commit
|
commitdiff
|
tree
2019-10-03
Berk He
s
s
Use gmx::Range for i
Z
ones in pair search
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
F
i
x se
t
t
in
g
maxNumCo
l
u
m
ns in Nbn
x
m::GridSet
commit
|
commitdiff
|
tree
2019-10-02
B
e
rk Hes
s
Fix harmless
O
p
enMP write r
a
ce
commit
|
commitdiff
|
tree
2019-10-01
B
e
rk Hess
Use gmx::R
a
nge in
d
omdec
commit
|
commitdiff
|
tree
2019-10-01
B
erk Hes
s
Completel
y
remove charge gr
o
up
s
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Simplif
y
D
D
e
x
c
lusion
c
ounting
commit
|
commitdiff
|
tree
2019-10-01
Be
r
k Hess
Always o
u
t
p
ut correct k
i
neti
c
at last s
t
ep
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
R
emove c
h
arge gr
o
up code from forcerec
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Ac
t
ually fix gmx wha
m
with angle
ge
o
m
etries
commit
|
commitdiff
|
tree
2019-09-29
Berk
H
ess
Inc
r
ease ti3p
5
minimi
z
a
t
ion test tolerance
commit
|
commitdiff
|
tree
2019-09-28
Berk H
e
ss
Fix CG min
i
mi
z
ati
o
n with DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hes
s
Extract gmx::Range
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Fix location of angle
in vsite
figure
commit
|
commitdiff
|
tree
2019-09-26
B
e
rk Hess
Made md
r
un appendin
g
work again
commit
|
commitdiff
|
tree
2019-09-24
Berk Hes
s
R
em
o
ve obsolete dd_get_ns_ra
n
ges()
commit
|
commitdiff
|
tree
2019-09-23
Berk Hess
L
imit Z
e
n nb
n
xm kernel choice to Zen 1
commit
|
commitdiff
|
tree
2019-09-22
Berk
H
ess
Remove cgs_gl from gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-21
Berk Hess
Fix inco
r
rect sh
i
f
t
forces for CMA
P
commit
|
commitdiff
|
tree
2019-09-20
B
erk Hess
Fix
DD 1 pu
l
se checks without DLB
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
R
emove bLocalCG from
DD c
o
de
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove obsole
t
e ma
k
e
_
exclusions_zone_c
g
(
)
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove
c
harge
group data from
t_
f
orcer
e
c
commit
|
commitdiff
|
tree
2019-09-19
Berk He
s
s
Add
haveFreeEnergyWork
t
o DomainLif
e
t
i
meWorkloa
d
flags
commit
|
commitdiff
|
tree
2019-09-18
B
er
k
He
s
s
Added fre
e
-
energy kerne
l
perf
o
rman
c
e
n
ot
e
commit
|
commitdiff
|
tree
2019-09-18
B
e
rk Hess
Fix
i
ncor
r
ect DD
n
dim assertion
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
R
emove spurious
n
ewline from log
f
ile
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
F
i
x todos
f
or update groups
commit
|
commitdiff
|
tree
2019-09-16
Be
r
k Hess
Rem
o
ve obsolet
e
mdp option ns-ty
p
e
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
A
d
d
virtu
a
l si
t
e type
2FD
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hess
Remove c
u
t
-
of
f
schem
e
s from manual
commit
|
commitdiff
|
tree
2019-09-16
Berk
Hess
Add option reque
s
t 1
D
DD wi
t
h 1 pulse
commit
|
commitdiff
|
tree
2019-09-13
Berk He
s
s
Fix no
n
bonded-bench co
m
pilat
i
on issue
commit
|
commitdiff
|
tree
2019-09-13
Berk Hess
Add nbnxm k
e
rnel
b
e
nchmark tool
commit
|
commitdiff
|
tree
2019-09-12
Be
r
k
Hess
U
p
da
t
ed mdp documentati
o
n
for gro
u
p
s
cheme re
m
ov
a
l
commit
|
commitdiff
|
tree
2019-09-12
Berk He
s
s
Fix mas
t
er not compilin
g
commit
|
commitdiff
|
tree
2019-09-12
Berk
Hess
Ena
b
l
e
TPI wi
t
h the
V
e
rlet cut-off scheme
commit
|
commitdiff
|
tree
2019-09-09
B
e
rk
H
ess
Remove incorrec
t
check w
i
th rf-zero
commit
|
commitdiff
|
tree
2019-09-09
B
erk Hess
E
x
tract
C
artesian da
t
a from D
D
RankSetup
commit
|
commitdiff
|
tree
2019-09-09
B
erk H
e
s
s
Rename DDSetup to DDGr
i
dSetup
commit
|
commitdiff
|
tree
2019-09-09
B
e
rk
H
ess
C
l
ean
u
p PME r
a
nk vari
a
bles
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Ref
a
ctor init_domain_decomposition()
commit
|
commitdiff
|
tree
2019-09-06
Berk He
s
s
Extract
g
et
t
ing of DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
Berk He
s
s
Add PP grid info
to DDRan
k
Set
u
p
commit
|
commitdiff
|
tree
2019-09-05
Berk He
s
s
Extract DDRan
k
Setup from gmx_domdec_
c
omm_t
commit
|
commitdiff
|
tree
2019-09-05
Berk H
e
ss
Split off getting
of th
e
DD setup
commit
|
commitdiff
|
tree
2019-09-04
B
e
rk Hess
Colle
c
t se
t
tings for DD in DDSettings
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Extra
c
t getting of DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk He
s
s
Simplify hand
l
ing of D
D
bond
e
d
d
ist
a
nces
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move constraint and bo
n
de
d
f
i
ltering info into DD
S
ystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move
u
pda
t
e
groupin
g
t
o
DDSyste
m
Info
commit
|
commitdiff
|
tree
2019-09-04
B
erk
H
e
s
s
Change DD pme force buf
f
er to std::vector
commit
|
commitdiff
|
tree
2019-09-04
Berk H
e
s
s
Initialize
all member
s
of gmx
_
domdec_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Extract
D
DSystemInfo fro
m
gm
x
_domdec_comm_
t
commit
|
commitdiff
|
tree
2019-09-03
B
e
rk
He
s
s
Unify manual and auto D
D
grid
c
hoices
commit
|
commitdiff
|
tree
2019-09-03
Berk
H
e
s
s
Remov
e
gmx_domd
e
c_t
fro
m
dd_c
h
oose_gri
d
()
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Extact UnitCe
l
lInfo fr
o
m gmx_domd
e
c_t
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
F
i
x incorrect rvdw
on GP
U
w
i
t
h
rvdw<rcoulomb
commit
|
commitdiff
|
tree
2019-09-02
B
er
k
H
ess
Only use fshift when n
e
eded
commit
|
commitdiff
|
tree
2019-08-26
Berk Hess
Fi
x
g
rom
p
p con
s
tr
a
ints=a
l
l-angles with constrain
t
s
commit
|
commitdiff
|
tree
2019-08-22
B
erk Hess
F
ix pertur
b
ed bonded bug
commit
|
commitdiff
|
tree
2019-08-20
Berk
H
es
s
Merge two
dihedral functions
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
U
se shift
F
o
rces in ForceOuputs
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make b
o
nded
v
irial computation conditional
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
F
ix missin
g
bonded forces w
i
th CUDA GP
U
s
and DD
commit
|
commitdiff
|
tree
2019-08-15
B
erk Hess
T
e
m
pla
t
e
bonded interactions
on kernel flavor
commit
|
commitdiff
|
tree
2019-08-09
Berk
H
ess
M
o
v
e
b
onded func
t
ion table
i
n
to bonded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
B
erk Hess
SIMD acc
e
le
r
at
i
on for F_FOURD
I
HS and F_PIDIH
S
commit
|
commitdiff
|
tree
2019-08-06
B
e
rk H
e
ss
Add ForceWithShiftForces class
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
F
ix latex formula
i
n refer
e
nce m
a
n
ual
commit
|
commitdiff
|
tree
2019-08-05
Berk Hess
Mak
e
box cons
t
in
d
o_force(
)
commit
|
commitdiff
|
tree
next