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Reduce rounding errors in SETTLE
2016-08-27
B
e
r
k
H
e
s
s
Reduce rounding
err
o
rs in S
E
TTLE
commit
|
commitdiff
|
tree
2016-08-15
Berk Hes
s
Re
d
uce
F
E pair-
l
ist memory usage
commit
|
commitdiff
|
tree
2016-08-10
Berk H
e
s
s
F
ix deadlock with thread-MPI
commit
|
commitdiff
|
tree
2016-07-07
Ber
k
Hess
Relax pull PBC
c
h
eck
commit
|
commitdiff
|
tree
2016-07-05
Berk Hess
A
d
d checks for too m
u
c
h
memory in g_nmeig
commit
|
commitdiff
|
tree
2016-07-03
Ber
k
Hess
Add grompp
c
he
c
k for pull group
commit
|
commitdiff
|
tree
2016-06-28
B
e
rk
He
s
s
Properly reset CUDA app
l
ication cl
o
cks
commit
|
commitdiff
|
tree
2016-06-27
Be
r
k H
e
ss
U
se sysconf
(
_SC_NPROCE
S
SORS_ONLN)
commit
|
commitdiff
|
tree
2016-06-26
Berk
Hess
Fix vsit
e
bug
w
ith MPI+O
p
e
n
M
P
commit
|
commitdiff
|
tree
2016-06-24
B
erk
Hess
F
i
x
Verle
t
buffer calculation
w
ith
nstlist=1
commit
|
commitdiff
|
tree
2016-06-23
Berk Hess
More accurate GPU list splitting
commit
|
commitdiff
|
tree
2016-06-22
B
e
rk
H
ess
Updated OpenC
L
TODOList
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
A
d
d nbnxn pair-lis
t
re
b
alancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Remove Op
e
nM
P
overhead at h
i
gh parallel
i
zati
o
n
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Co
r
rect GPU pair estimate for
list
s
plit
t
ing
commit
|
commitdiff
|
tree
2016-06-21
Berk Hes
s
Fix b
u
g
wi
t
h fbposres+
M
PI+O
p
enMP
commit
|
commitdiff
|
tree
2016-06-20
Berk
Hess
I
n
creased tpx_incompati
b
le_v
e
rsi
o
n to 30
commit
|
commitdiff
|
tree
2016-06-19
Ber
k
H
e
ss
Remove wa
r
nings on checkpoi
n
t misma
t
ch
commit
|
commitdiff
|
tree
2016-06-17
B
e
r
k Hess
Remove
std:
:
t
hread::hardwar
e
_conc
u
r
r
e
n
cy(
)
commit
|
commitdiff
|
tree
2016-06-14
Berk
Hess
Fix
Ope
n
CL error with empt
y
domai
n
s
commit
|
commitdiff
|
tree
2016-06-13
Berk He
s
s
Handle co
n
stra
i
nt errors with EM
commit
|
commitdiff
|
tree
2016-06-07
Berk Hess
Fix
d
ata ra
c
e in
h
winfo with thread-MPI
commit
|
commitdiff
|
tree
2016-06-03
B
erk
Hess
Handle
p
a
rtial
l
y frozen and constr
a
ined atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk He
s
s
Reposition
nbnxn fil
l
er p
a
rt
i
c
les
commit
|
commitdiff
|
tree
2016-05-31
Berk
H
ess
Avoid num
e
rical overflow with overlapping atoms
commit
|
commitdiff
|
tree
2016-05-31
B
er
k
H
e
ss
Add
c
heck for fin
i
te energies
commit
|
commitdiff
|
tree
2016-05-30
Berk Hess
Ad
d
g
r
ompp check for unbound ato
m
s
commit
|
commitdiff
|
tree
2016-05-23
Berk
H
ess
Fix bug in v-r
e
scale thermostat & replica exchange
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Optimized the v
s
i
te threa
d
ing
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
F
i
x CUDA shmem bug
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Support cm
a
p with QMMM
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Update mdrun
t
er
m
ination
i
nfo
commit
|
commitdiff
|
tree
2016-05-06
Ber
k
Hess
OpenMP pa
r
allelizati
o
n for pul
l
commit
|
commitdiff
|
tree
2016-04-20
Ber
k
H
e
ss
F
i
x
p
ull le
g
end with exte
r
n
a
l potential
commit
|
commitdiff
|
tree
2016-04-19
B
e
rk Hess
Allow
r
coulo
m
b>rvdw with PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Broadc
a
st pull
e
xternal
p
otential pr
o
vi
d
er str
i
ng
commit
|
commitdiff
|
tree
2016-04-19
Berk
H
ess
Fi
x
gmx hbond g
r
oup overlap check
commit
|
commitdiff
|
tree
2016-04-14
B
erk Hess
Ad
d
QMMM checks
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
Correct nrd
f
f
o
r
1D/2D systems
commit
|
commitdiff
|
tree
2016-03-31
Be
r
k
H
e
ss
Fix includ
e
s in readpull
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Ad
d
option for extern
a
l
pull potential
commit
|
commitdiff
|
tree
2016-03-30
Be
r
k
Hess
C
o
r
r
e
c
t md
r
un tMPI (non-)
p
aral
l
el error mess
a
g
e
commit
|
commitdiff
|
tree
2016-03-26
Berk Hess
Add re
a
l/SIMD
templa
t
e for LJ-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk
H
e
ss
Avoid
a
ssertion failure in
p
me
_
loadbal_do
commit
|
commitdiff
|
tree
2016-03-22
Berk
Hess
Mak
e
g
mx vanh
o
ve work wit
h
out
P
BC
commit
|
commitdiff
|
tree
2016-03-22
Berk H
e
ss
LJ combina
t
io
n
rule kernels for CUDA
commit
|
commitdiff
|
tree
2016-03-21
Berk Hess
M
o
ved pull initi
a
l
i
z
ation bac
k
to mdrunner
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fix non-normalization
of FFT aut
o
c
o
rr
commit
|
commitdiff
|
tree
2016-03-14
Ber
k
H
ess
Rem
o
ve restriction on dihdraltypes order
commit
|
commitdiff
|
tree
2016-03-12
Berk Hess
S
plit off Ferm
i
ke
r
nel from CUDA kernel
commit
|
commitdiff
|
tree
2016-03-09
Berk Hess
Fix Ewal
d
3DC dipole with Verle
t
scheme
commit
|
commitdiff
|
tree
2016-03-04
B
e
rk
H
e
ss
Converte
d
csettle()
t
o
use real/SimdReal template
commit
|
commitdiff
|
tree
2016-03-03
Berk
Hess
Use SIMD tr
a
nspose s
c
a
tter in bondeds
commit
|
commitdiff
|
tree
2016-03-03
Berk
H
ess
Use rvec4 for listed for
c
e b
u
ffer
commit
|
commitdiff
|
tree
2016-02-27
Be
r
k Hess
R
e
m
ove epsfac fr
o
m GPU ke
r
nel
inner-lo
o
p
s
commit
|
commitdiff
|
tree
2016-02-27
Berk
Hess
Mi
n
or c
o
d
e reordering in GP
U
kernels
commit
|
commitdiff
|
tree
2016-02-26
Berk Hess
F
i
x compilation
with Simd4Floa
t
, w
i
tho
u
t Simd4D
o
uble
commit
|
commitdiff
|
tree
2016-02-19
Ber
k
Hess
Fix excessive list splittin
g
commit
|
commitdiff
|
tree
2016-02-17
Berk Hes
s
Ren
a
m
ed nbnxn
s
tatic const ints
commit
|
commitdiff
|
tree
2016-02-11
Ber
k
Hess
Add SIMD ver
s
ion of pbc_
d
x
_aiuc
commit
|
commitdiff
|
tree
2016-02-09
Berk
Hess
Repla
c
ed nbnxn
sea
r
ch+grid simd ma
c
ros
commit
|
commitdiff
|
tree
2016-02-07
Berk Hess
Fix
incor
r
ect
c
map parsi
n
g
commit
|
commitdiff
|
tree
2016-02-05
Ber
k
Hess
Fix incorrect
c
ma
p
parsing
commit
|
commitdiff
|
tree
2016-02-03
B
e
rk Hess
Replaced lite
r
a
ls in nb
n
xn lists by
i
nts
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix
m
drun rem
o
ving Verl
e
t
buffer with EM
commit
|
commitdiff
|
tree
2016-02-03
Ber
k
Hess
F
ix
S
ETTLE error ha
n
dli
n
g
commit
|
commitdiff
|
tree
2016-01-29
B
e
r
k
Hess
Ad
d
ed documentati
o
n for pm
e
grid ind
e
xing
commit
|
commitdiff
|
tree
2016-01-29
B
e
rk Hess
Fix TP
I
i
g
noring PME mesh contributions
.
commit
|
commitdiff
|
tree
2016-01-29
Ber
k
Hess
U
p
d
a
t
e -ntomp_pme
-
n
pme
c
heck
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Add check fo
r
double perturbation
commit
|
commitdiff
|
tree
2016-01-29
Berk He
s
s
Fix
LINCS
t
r
iangle
c
ons
t
raint threa
d
iss
u
e
commit
|
commitdiff
|
tree
2016-01-28
Berk Hess
Update pair-list buff
e
r ma
n
ual
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
F
i
x
exact cont
i
nuation
f
r
om non-en
e
rgy steps
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix energ
y
file continuat
i
on with
m
d-v
v
commit
|
commitdiff
|
tree
2016-01-24
Berk
Hess
F
i
x energy
average with continuation
commit
|
commitdiff
|
tree
2016-01-08
Berk H
e
ss
Fix PME
load bala
n
ci
n
g skipping a setup
commit
|
commitdiff
|
tree
2015-12-29
Be
r
k Hess
C
orrect vec
t
or
c
he
c
k
of gmx check
commit
|
commitdiff
|
tree
2015-12-27
Be
r
k Hess
Reorganized
dom
d
ec initi
a
li
z
atio
n
commit
|
commitdiff
|
tree
2015-12-20
B
e
rk
H
ess
Merg
e
r
elease-5-1 into master
commit
|
commitdiff
|
tree
2015-12-19
Ber
k
He
s
s
Bring
p
erformance estimation up to dat
e
commit
|
commitdiff
|
tree
2015-12-17
B
e
rk Hess
Removed t
o
pology
po
i
n
t
e
r
s
from DD struct
commit
|
commitdiff
|
tree
2015-12-16
Berk Hess
Add one e
l
eme
n
t
to
s
tate rvec arrays
commit
|
commitdiff
|
tree
2015-12-12
Berk Hess
Re
m
oved unused m
d
run opt
i
on -
d
n
commit
|
commitdiff
|
tree
2015-12-11
Berk Hess
Fix bug
w
ith
pull group w
e
ights
commit
|
commitdiff
|
tree
2015-12-07
Berk He
s
s
Mo
v
e
d pull params to
m
d
t
y
pes/p
u
l
l
-
params
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk He
s
s
Incr
e
ase pdb chain ids to 62 in output
commit
|
commitdiff
|
tree
2015-12-02
Ber
k
Hess
R
efactored set_pbc_d
d
commit
|
commitdiff
|
tree
2015-12-02
Ber
k
Hess
M
a
de
t
_inp
u
trec con
s
t in PME l
o
a
d b
a
lancing
commit
|
commitdiff
|
tree
2015-12-01
Berk He
s
s
Pull gr
o
up count for
c
oor
d
s st
o
red in tpr
commit
|
commitdiff
|
tree
2015-11-19
Berk
Hess
Removed
m
drun
fat
a
l_error with P3M-
A
D
commit
|
commitdiff
|
tree
2015-11-18
Berk Hess
R
emoved R
e
action-Fi
e
ld-nec
commit
|
commitdiff
|
tree
2015-11-14
B
erk Hess
Optimized th
e
bo
n
ded thread fo
r
ce reduction
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
Fix
e
d (harml
e
ss) fp except
i
on in wallcyc
l
e_sum
commit
|
commitdiff
|
tree
2015-11-09
Berk Hess
Cor
r
ect
L
IN
C
S
d
H
dl contribution
commit
|
commitdiff
|
tree
2015-11-03
B
e
rk He
s
s
F
i
x
no wallcycle support
commit
|
commitdiff
|
tree
2015-11-03
Berk
Hes
s
R
em
o
ved
nbnxn kernel ble
n
dv optimization
commit
|
commitdiff
|
tree
2015-11-02
Berk
Hess
Fix intermolecul
a
r
inter
a
ctions with smal
l
mols
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
Fixed
n
bnxn_4xN performance
r
egr
e
ssion
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
Fi
x
bugs wi
t
h intermol int
e
ractions a
n
d DD
commit
|
commitdiff
|
tree
2015-10-01
B
e
rk Hess
Removed CUD
A
p
o
llin
g
w
a
it
commit
|
commitdiff
|
tree
next