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Basic support for transforming KeyValueTrees
2016-08-27
Be
r
k Hess
Reduc
e
roundin
g
e
rror
s
i
n SETTL
E
commit
|
commitdiff
|
tree
2016-08-15
Berk He
s
s
Reduce FE pair-l
i
st memor
y
u
sage
commit
|
commitdiff
|
tree
2016-08-10
B
e
rk
H
ess
Fix deadlock with t
h
re
a
d-MPI
commit
|
commitdiff
|
tree
2016-07-07
B
e
rk
H
es
s
Relax pull
P
B
C
check
commit
|
commitdiff
|
tree
2016-07-05
Berk Hes
s
Add
c
hecks for too much memo
r
y in g
_
nmeig
commit
|
commitdiff
|
tree
2016-07-03
B
e
rk H
e
ss
Add grompp chec
k
f
or
pull
group
commit
|
commitdiff
|
tree
2016-06-28
Berk Hess
Properl
y
reset C
U
DA applic
a
tio
n
clo
c
ks
commit
|
commitdiff
|
tree
2016-06-27
Berk Hess
Use s
y
sconf(_
S
C
_NP
R
OCESSO
R
S_ONLN)
commit
|
commitdiff
|
tree
2016-06-26
Be
r
k
Hes
s
Fix
v
site bug
w
ith MPI+OpenM
P
commit
|
commitdiff
|
tree
2016-06-24
Berk Hess
Fix
Verlet buffer
c
alcula
t
ion with nstlist=
1
commit
|
commitdiff
|
tree
2016-06-23
Berk He
s
s
Mo
r
e a
c
curate GPU lis
t
split
t
ing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Updated OpenC
L
TO
D
OList
.
txt
commit
|
commitdiff
|
tree
2016-06-22
B
e
r
k Hess
Ad
d
n
bn
x
n p
a
ir-list
r
ebalanci
n
g
commit
|
commitdiff
|
tree
2016-06-22
Berk Hes
s
Remove OpenMP ov
e
rhe
a
d at
hig
h
parallelization
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
C
o
rrect GPU
p
air estimate for list split
t
ing
commit
|
commitdiff
|
tree
2016-06-21
Berk Hess
Fix bug with fbposres+MPI+Open
M
P
commit
|
commitdiff
|
tree
2016-06-20
Berk Hes
s
Incr
e
ased tpx_incompatib
l
e_
v
e
r
s
i
on to 30
commit
|
commitdiff
|
tree
2016-06-19
B
e
rk
Hess
Remove warnings on checkpoint mismatch
commit
|
commitdiff
|
tree
2016-06-17
B
e
rk He
s
s
Remove s
t
d::th
r
ea
d
::hardware_concurrency()
commit
|
commitdiff
|
tree
2016-06-14
Berk
H
ess
Fix OpenCL
error w
i
th e
m
pty dom
a
ins
commit
|
commitdiff
|
tree
2016-06-13
Be
r
k
Hess
H
a
ndle c
o
ns
t
rai
n
t errors with E
M
commit
|
commitdiff
|
tree
2016-06-07
Berk Hess
F
i
x d
a
ta race in hwinfo with thread-MP
I
commit
|
commitdiff
|
tree
2016-06-03
B
erk Hess
H
a
ndle partially frozen and constrained
a
toms
commit
|
commitdiff
|
tree
2016-05-31
B
e
r
k
Hess
Rep
o
sition nbn
x
n filler
p
a
r
ticles
commit
|
commitdiff
|
tree
2016-05-31
Be
r
k He
s
s
A
v
oid numerical ov
e
rflow wit
h
o
v
e
rlappin
g
atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Add check for finite
e
nergies
commit
|
commitdiff
|
tree
2016-05-30
Berk Hess
Add
g
rompp ch
e
ck for
u
nbound
a
tom
s
commit
|
commitdiff
|
tree
2016-05-23
Be
r
k Hes
s
Fix
bug in v-r
e
sca
l
e thermostat & re
p
lica exchange
commit
|
commitdiff
|
tree
2016-05-10
Berk He
s
s
Opt
i
miz
e
d the vsite threading
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
F
ix
C
U
DA shmem
b
ug
commit
|
commitdiff
|
tree
2016-05-10
B
erk He
s
s
Su
p
port cmap
w
ith QMMM
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Updat
e
md
r
un
termination info
commit
|
commitdiff
|
tree
2016-05-06
Ber
k
Hess
Op
e
nMP parallelization for pull
commit
|
commitdiff
|
tree
2016-04-20
Berk
H
ess
F
i
x pu
l
l legend with exte
r
nal potential
commit
|
commitdiff
|
tree
2016-04-19
Berk H
e
ss
A
l
low rc
o
ulomb>rvdw with
PME
commit
|
commitdiff
|
tree
2016-04-19
Berk
H
ess
Br
o
adcast pull external pot
e
n
t
ial provider string
commit
|
commitdiff
|
tree
2016-04-19
B
e
rk Hess
Fix gmx
h
bon
d
group ov
e
rlap
c
heck
commit
|
commitdiff
|
tree
2016-04-14
Berk
H
e
s
s
Add QMMM ch
e
cks
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
Correct nrdf for
1
D/2D syst
e
m
s
commit
|
commitdiff
|
tree
2016-03-31
Be
r
k He
s
s
F
ix i
n
c
l
udes
i
n
read
p
ull
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk H
e
ss
Add option for
e
xternal pull
p
o
t
e
ntial
commit
|
commitdiff
|
tree
2016-03-30
Be
r
k
H
e
ss
Cor
r
ect mdrun tMPI (non-)paralle
l
er
r
or message
commit
|
commitdiff
|
tree
2016-03-26
Berk Hess
Add
r
eal/SIMD
t
empl
a
t
e
for LJ-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Avoid assertion failure in pme_loadbal_do
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
M
a
ke gmx van
h
ove
work w
i
thout PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hes
s
L
J co
m
binatio
n
rule kernels for CUDA
commit
|
commitdiff
|
tree
2016-03-21
Berk Hess
M
o
ved pull initialization ba
c
k
t
o
m
drun
n
er
commit
|
commitdiff
|
tree
2016-03-18
Berk H
e
s
s
Fix n
o
n-n
o
rm
a
lization of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
Berk Hess
Remove
r
estriction on dihdraltypes order
commit
|
commitdiff
|
tree
2016-03-12
Berk Hess
Split off Fermi kernel
f
r
om CUDA
kern
e
l
commit
|
commitdiff
|
tree
2016-03-09
Berk He
s
s
Fix Ew
a
ld 3DC dipole with
Ver
l
e
t scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk He
s
s
Con
v
e
r
t
ed csettle() to
use real/Simd
R
eal te
m
plate
commit
|
commitdiff
|
tree
2016-03-03
Berk H
e
ss
Use SIMD trans
p
ose sc
a
t
t
er in bonde
d
s
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use rvec4 for listed force buffer
commit
|
commitdiff
|
tree
2016-02-27
Berk He
s
s
Remove e
p
sfac from GPU kernel inner-
l
oops
commit
|
commitdiff
|
tree
2016-02-27
Berk He
s
s
Mi
n
o
r code reo
r
d
e
r
in
g
in GPU kernels
commit
|
commitdiff
|
tree
2016-02-26
B
erk H
e
s
s
Fi
x
compilati
o
n with Simd4Float, without Simd4
D
ouble
commit
|
commitdiff
|
tree
2016-02-19
Berk
Hess
Fix ex
c
essive list splittin
g
commit
|
commitdiff
|
tree
2016-02-17
Berk Hess
Renam
e
d nbnxn stat
i
c c
o
nst ints
commit
|
commitdiff
|
tree
2016-02-11
Berk Hess
A
dd SIMD
version of
pbc
_
d
x_aiuc
commit
|
commitdiff
|
tree
2016-02-09
Be
r
k
Hes
s
Rep
l
ac
e
d
n
b
n
x
n
search+grid simd macro
s
commit
|
commitdiff
|
tree
2016-02-07
Berk Hess
F
ix i
n
correct cmap parsing
commit
|
commitdiff
|
tree
2016-02-05
Berk
Hess
F
ix
incorr
e
c
t
cma
p
pars
i
ng
commit
|
commitdiff
|
tree
2016-02-03
Ber
k
Hess
Replaced literals
in n
b
nxn li
s
ts b
y
ints
commit
|
commitdiff
|
tree
2016-02-03
Berk
Hess
Fix mdrun removing Verlet buffer with EM
commit
|
commitdiff
|
tree
2016-02-03
Berk He
s
s
Fix SETTLE err
o
r handli
n
g
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Added documentat
i
on for pme
grid
in
d
exing
commit
|
commitdiff
|
tree
2016-01-29
Be
r
k
Hess
Fi
x
TP
I
ignori
n
g P
M
E mesh con
t
ribution
s
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Update -ntomp_pme -npme ch
e
ck
commit
|
commitdiff
|
tree
2016-01-29
Ber
k
Hess
Add c
h
eck for double perturbation
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix LINCS tr
i
angle constr
a
int thread iss
u
e
commit
|
commitdiff
|
tree
2016-01-28
Ber
k
Hess
Update pair-li
s
t buffe
r
m
anual
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix
exact continuation from non-e
n
ergy st
e
ps
commit
|
commitdiff
|
tree
2016-01-24
Berk He
s
s
Fix energy file
co
n
tinuation with md-vv
commit
|
commitdiff
|
tree
2016-01-24
B
erk Hess
Fix energy a
v
erage
with c
o
ntinuation
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
F
i
x PME load
balancing skippi
n
g a
s
etup
commit
|
commitdiff
|
tree
2015-12-29
B
e
rk
Hess
C
o
r
rect v
e
cto
r
ch
e
ck of
gmx
check
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Reor
g
ani
z
ed domdec
i
nitialization
commit
|
commitdiff
|
tree
2015-12-20
Berk Hess
Merge release-5-1 into maste
r
commit
|
commitdiff
|
tree
2015-12-19
Berk Hess
Bring perf
o
r
m
ance estimatio
n
up to date
commit
|
commitdiff
|
tree
2015-12-17
B
erk Hes
s
Removed
t
opology poi
n
ters from D
D
stru
c
t
commit
|
commitdiff
|
tree
2015-12-16
Berk
H
e
s
s
A
dd
o
ne element t
o
state rvec arrays
commit
|
commitdiff
|
tree
2015-12-12
Berk Hess
Removed unus
e
d mdr
u
n
o
p
tion -dn
commit
|
commitdiff
|
tree
2015-12-11
B
e
rk
Hess
F
i
x bug with pull group w
e
ights
commit
|
commitdiff
|
tree
2015-12-07
Berk Hess
M
ov
e
d pul
l
param
s
to md
t
ypes/pull-params
.
h
commit
|
commitdiff
|
tree
2015-12-02
Ber
k
Hes
s
Inc
r
ease pdb chain ids to 62 i
n
ou
t
put
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Refa
c
tored s
e
t
_pbc_dd
commit
|
commitdiff
|
tree
2015-12-02
B
e
rk Hess
Made t_inputrec const i
n
PME
l
o
ad balancing
commit
|
commitdiff
|
tree
2015-12-01
Berk H
e
s
s
Pull group count f
o
r coord
s
stored in t
p
r
commit
|
commitdiff
|
tree
2015-11-19
Berk Hess
R
emoved mdrun fatal_error with P3M-
A
D
commit
|
commitdiff
|
tree
2015-11-18
Berk H
e
ss
Re
m
oved Rea
c
tion-Field-nec
commit
|
commitdiff
|
tree
2015-11-14
Berk H
e
s
s
Optimized the bo
n
d
e
d thread f
o
rce
reduction
commit
|
commitdiff
|
tree
2015-11-11
Be
r
k Hess
Fixed (harm
l
ess) fp exception in wallcycle_
s
um
commit
|
commitdiff
|
tree
2015-11-09
Berk Hes
s
Corre
c
t LINCS dHdl contribution
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Fix no wallcycle
support
commit
|
commitdiff
|
tree
2015-11-03
Ber
k
Hess
Removed nbnxn kerne
l
blendv optimization
commit
|
commitdiff
|
tree
2015-11-02
Berk
Hess
F
ix intermole
c
ular interact
i
on
s
with small mols
commit
|
commitdiff
|
tree
2015-10-15
B
e
r
k H
e
s
s
Fixed nbnx
n
_4xN
perfo
r
man
c
e regression
commit
|
commitdiff
|
tree
2015-10-07
Berk
Hess
Fi
x
bugs with inte
r
m
o
l inte
r
actions and DD
commit
|
commitdiff
|
tree
2015-10-01
Berk He
s
s
R
e
moved CUDA pollin
g
wait
commit
|
commitdiff
|
tree
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