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Add CPU reference and SIMD pruning kernels
2017-08-18
B
e
rk Hess
A
d
d CPU reference and SI
M
D
p
runi
n
g
k
e
rne
l
s
commit
|
commitdiff
|
tree
2017-08-16
Berk
Hess
Add
dynamic pair-l
i
st
pruning frame
w
ork
commit
|
commitdiff
|
tree
2017-08-16
Berk Hess
Cl
e
a
n
up nbnxn clust
e
r pair addi
t
ion code
commit
|
commitdiff
|
tree
2017-08-15
B
erk
H
ess
Add Ope
n
MP for
o
r
i
entati
o
n restraints
commit
|
commitdiff
|
tree
2017-08-15
Be
r
k
H
e
s
s
Use
g
raph with
orientati
o
n rest
r
aints
commit
|
commitdiff
|
tree
2017-08-12
Ber
k
Hess
Remov
e
l
oop ov
e
r all a
t
o
m
s in
i
nit_mda
t
o
m
s
commit
|
commitdiff
|
tree
2017-08-02
Berk
Hess
Cle
a
n
up matrix inversion
commit
|
commitdiff
|
tree
2017-08-02
B
erk Hess
Fix orientation restr
a
i
nt
r
efe
r
ence
commit
|
commitdiff
|
tree
2017-08-02
B
erk Hess
Make loop variables in o
r
ires
.
cpp lo
c
al
commit
|
commitdiff
|
tree
2017-08-02
Berk
H
ess
Ad
d
check for nr of ori
e
nt
a
tion restraints
commit
|
commitdiff
|
tree
2017-07-25
Berk Hess
Fix b
u
gs wit
h
ori
e
nt
a
tion restraints
commit
|
commitdiff
|
tree
2017-07-09
Berk
H
ess
Restructure the load balancing timing
commit
|
commitdiff
|
tree
2017-07-04
Berk Hess
Unify nbnxn k
e
rnel dispatchers
commit
|
commitdiff
|
tree
2017-07-03
Berk H
e
ss
Remove
g
mx_constexpr
commit
|
commitdiff
|
tree
2017-06-17
Berk Hess
Add
t
olerance
t
o calc_ve
r
letbuf test
commit
|
commitdiff
|
tree
2017-06-12
B
e
rk Hess
Fix n
u
ll
poin
t
e
r
pri
n
t in DD
commit
|
commitdiff
|
tree
2017-06-10
B
erk Hess
Put repli
c
a e
x
change paramet
e
rs in a st
r
uct
commit
|
commitdiff
|
tree
2017-06-09
Berk Hess
Repla
c
e
iso
by i
n
stead
of
commit
|
commitdiff
|
tree
2017-06-08
Berk Hess
Fix C
O
M pull
force with SD
commit
|
commitdiff
|
tree
2017-06-07
Berk Hess
Avo
i
d grom
p
p c
h
arge
w
a
rning wit
h
r
oundi
n
g
commit
|
commitdiff
|
tree
2017-06-04
Be
r
k Hess
F
i
x checkpoint reading
wi
t
hout energy hist
o
ry
commit
|
commitdiff
|
tree
2017-06-02
Berk Hess
Fix
ini
t
ial temp
e
ratur
e
report
i
ng
commit
|
commitdiff
|
tree
2017-05-27
Berk
Hes
s
Made duplic
a
t
e
atom
s
in bonde
d
s an er
r
or
commit
|
commitdiff
|
tree
2017-05-26
Berk Hess
Improve Verl
e
t
b
uffer constra
i
nt estimate
commit
|
commitdiff
|
tree
2017-05-23
Berk He
s
s
Add conser
v
e
d quan
t
ity for Beren
d
sen P-c
o
uple
commit
|
commitdiff
|
tree
2017-05-23
Berk Hess
Add co
n
served q
.
for
P
R and Berends
e
n T-c
o
uple
commit
|
commitdiff
|
tree
2017-05-23
Berk Hess
Make DD setup obey
P
ME
r
e
stricti
o
ns
commit
|
commitdiff
|
tree
2017-05-22
B
er
k
H
e
ss
Introdu
c
e
Obse
r
vabl
e
sHistory cont
a
iner
commit
|
commitdiff
|
tree
2017-05-16
Ber
k
Hess
Fix confout
.
gr
o
with ener
g
y minimiza
t
ion
commit
|
commitdiff
|
tree
2017-05-15
Berk Hess
Fix
LJP
M
E + sw
i
tch gromp
p
e
r
ror
commit
|
commitdiff
|
tree
2017-05-14
Berk Hess
F
ix bugs in
d
oub
l
e Si
m
d
4 implement
a
ti
o
ns
commit
|
commitdiff
|
tree
2017-04-21
Berk Hess
F
i
x bugs in
d
ouble AV
X
(
2
)
_
256 Simd
4
commit
|
commitdiff
|
tree
2017-04-19
Berk
H
ess
Fix
u
nused SIMD P
M
E table kern
e
l
commit
|
commitdiff
|
tree
2017-04-18
B
e
r
k Hess
Suppress t
w
o
c
ompiler warnings
commit
|
commitdiff
|
tree
2017-03-16
Berk Hess
Replace
i
nstanc
e
of group by coord
i
n pull mdp docs
commit
|
commitdiff
|
tree
2017-03-14
Berk Hess
Make gromp
p
-r o
b
l
igatory with posres
commit
|
commitdiff
|
tree
2017-02-28
B
e
rk Hess
Add
l
oad balan
c
e fracti
o
n to D
L
B print
commit
|
commitdiff
|
tree
2017-02-07
Ber
k
Hess
Add m
d
p op
t
ion
c
heck with decoupled modes
commit
|
commitdiff
|
tree
2017-02-02
Berk H
e
s
s
Rea
l
ly fix
a
r
r
ay of complex i
n
c
ro
s
s_corr
commit
|
commitdiff
|
tree
2017-02-02
Berk He
s
s
Fix arr
a
y of c
o
mple
x
in cross_
c
orr
commit
|
commitdiff
|
tree
2017-01-20
Berk
Hes
s
D
i
sallow
o
v
erwrit
i
ng o
f
dihed
r
a
l type 9
commit
|
commitdiff
|
tree
2017-01-20
Berk He
s
s
Onl
y
predict s
h
e
l
ls
w
ith v
e
l
o
cities
commit
|
commitdiff
|
tree
2017-01-19
B
e
rk Hess
Fix P
M
E o
r
d
er
and
g
rid s
i
ze
c
h
ecks
commit
|
commitdiff
|
tree
2017-01-17
Berk Hess
Correct
a
sser
t
on pme-ord
e
r
commit
|
commitdiff
|
tree
2017-01-05
Berk Hess
Fix flat-b
o
ttom po
s
ition restraints + D
D
+
O
penMP
commit
|
commitdiff
|
tree
2016-12-14
Berk Hess
Add
bond
e
d
#
thre
a
d runtime check
commit
|
commitdiff
|
tree
2016-12-08
Ber
k
Hess
Made mdrun -pforce terminat
e
w
i
th non-finite forces
commit
|
commitdiff
|
tree
2016-11-24
Berk Hess
Chang
e
spline moduli calculation to dou
b
l
e
commit
|
commitdiff
|
tree
2016-11-23
Berk H
e
ss
Convert e
n
e
rgyh
i
stor
y
_
t
to use
s
td::vector
commit
|
commitdiff
|
tree
2016-11-23
Berk Hess
Use tem
p
lat
i
ng i
n
check
p
oint
.
cpp
commit
|
commitdiff
|
tree
2016-11-01
Berk Hess
Fi
x
tim
e
label pr
i
n
t
i
n
gmx v
a
nhove
commit
|
commitdiff
|
tree
2016-10-29
Berk Hess
Ad
d
g
mx dump option for pri
n
ting paramete
r
s
commit
|
commitdiff
|
tree
2016-10-28
Berk Hes
s
DLB can now turn
off, whe
n
s
l
ower
commit
|
commitdiff
|
tree
2016-10-28
Berk
H
ess
Fix
D
LB timing with CUDA and OpenC
L
commit
|
commitdiff
|
tree
2016-10-15
Berk Hess
M
o
ve ene
r
gyh
i
story_t
out
of t_state
commit
|
commitdiff
|
tree
2016-10-14
Berk Hess
Apply B
e
rend
s
e
n
P-coupl
e
at
nstpcouple steps
commit
|
commitdiff
|
tree
2016-10-13
B
e
rk Hess
Ext
e
n
d mt
o
p_lookup
.
h
commit
|
commitdiff
|
tree
2016-10-12
Be
r
k H
e
ss
Fi
x
ed ex
c
eption in usused result
commit
|
commitdiff
|
tree
2016-10-12
Ber
k
H
ess
Fixed print bug in gmx wha
m
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
Re
f
a
c
t
o
r NPT energy calculation
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
R
estru
c
ture
leap-fr
o
g integrato
r
s
commit
|
commitdiff
|
tree
2016-10-11
Be
r
k
H
e
ss
Speed up m
t
op_util
atom lookup
commit
|
commitdiff
|
tree
2016-10-08
Ber
k
Hes
s
Add
readC
o
n
f
AndTopology
commit
|
commitdiff
|
tree
2016-10-07
Berk Hess
Ch
a
nged
fr->f_novir
s
um to
Pa
d
dedRVecVector
commit
|
commitdiff
|
tree
2016-10-01
Berk Hess
Fix inputre
c
initialization in 4 tools
commit
|
commitdiff
|
tree
2016-09-29
B
erk Hess
Use
st
d
::v
e
c
t
or in t_state
commit
|
commitdiff
|
tree
2016-09-29
Berk
H
e
ss
Add fla
g
s for optional t_atoms en
t
ries
commit
|
commitdiff
|
tree
2016-09-22
Berk Hess
F
i
x
gcc
wa
r
ning in A
l
ig
n
e
d
A
llocator
commit
|
commitdiff
|
tree
2016-09-20
Berk Hess
Rem
o
v
e
st
a
te dup
l
icati
o
n in serial runs
commit
|
commitdiff
|
tree
2016-09-16
Berk
H
e
s
s
F
ixed unused vari
a
bles
i
n
domdec
.
c
p
p
commit
|
commitdiff
|
tree
2016-09-16
Berk
H
ess
M
erge b
r
anch release-2016
commit
|
commitdiff
|
tree
2016-09-16
Berk
H
ess
Made
d
istance restraints work with thre
a
ds an
d
DD
commit
|
commitdiff
|
tree
2016-09-13
B
e
rk Hes
s
Moved expanded ensemb
l
e histor
y
to
p
oin
t
er in t_sta
t
e
commit
|
commitdiff
|
tree
2016-09-13
B
erk He
s
s
Ch
a
nge ED and s
w
apstate t
o
poin
t
ers i
n
t
_
s
tate
commit
|
commitdiff
|
tree
2016-09-12
Berk
Hess
Add const to thread-MPI functions
commit
|
commitdiff
|
tree
2016-09-10
Be
r
k Hess
Remove con
t
in
u
ation from convert_
t
pr
commit
|
commitdiff
|
tree
2016-09-06
Berk Hess
Fix bug with conjugate
-
gra
d
ient and O
p
enMP
commit
|
commitdiff
|
tree
2016-09-06
Berk He
s
s
Consolid
a
te MD a
l
gorithm ato
m
s
e
tup
commit
|
commitdiff
|
tree
2016-09-05
Berk
H
ess
Re-
e
nab
l
e flexible constrai
n
t
s
with DD
commit
|
commitdiff
|
tree
2016-09-04
Berk Hes
s
Merge branch releas
e
-2016
commit
|
commitdiff
|
tree
2016-09-03
Berk
H
es
s
Cl
e
a
n
up PME f
l
ags variable
u
s
e
commit
|
commitdiff
|
tree
2016-09-02
Berk Hes
s
Merge branch release-5-1 into re
l
e
ase-2016
commit
|
commitdiff
|
tree
2016-09-02
Berk
Hess
Fi
x
Parrinell
o
-Rahman with nstpcouple>
1
commit
|
commitdiff
|
tree
2016-08-30
Berk Hess
Mak
e
virial r
e
producib
l
e
commit
|
commitdiff
|
tree
2016-08-27
Berk Hess
Reduce rounding errors
in SETTLE
commit
|
commitdiff
|
tree
2016-08-24
Berk Hes
s
Fix Ew
a
ld surface+3DC cor
r
ectio
n
s
commit
|
commitdiff
|
tree
2016-08-24
Ber
k
Hess
Merge bran
c
h
r
elease-5-1 into
release-2016
commit
|
commitdiff
|
tree
2016-08-23
Berk Hess
Remove var
i
a
ble precision gro w
r
iting
commit
|
commitdiff
|
tree
2016-08-17
Be
r
k
H
es
s
F
i
x
e
d opening of wall ta
b
l
e
f
i
le
s
commit
|
commitdiff
|
tree
2016-08-15
Berk
H
ess
Reduce F
E
pair-list me
m
ory usage
commit
|
commitdiff
|
tree
2016-08-10
Ber
k
Hes
s
Fix deadlock
w
it
h
t
h
r
e
a
d-MPI
commit
|
commitdiff
|
tree
2016-08-09
Berk
H
ess
Fix
twin-cuto
f
f for GPU LJ
p
ot-sw
i
tch
commit
|
commitdiff
|
tree
2016-07-07
Berk Hess
Relax pul
l
P
B
C
ch
e
c
k
commit
|
commitdiff
|
tree
2016-07-05
B
erk He
s
s
Add checks for t
o
o
much memory i
n
g_nmeig
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Ad
d
grompp
che
c
k for pull group
commit
|
commitdiff
|
tree
2016-06-28
Berk Hess
Pro
p
erly reset CUDA applica
t
ion clocks
commit
|
commitdiff
|
tree
2016-06-27
Berk Hess
Us
e
sysconf(_SC_NPR
O
CESSOR
S
_ONLN)
commit
|
commitdiff
|
tree
2016-06-26
Berk Hess
F
ix
v
sit
e
bug with MPI+OpenMP
commit
|
commitdiff
|
tree
2016-06-24
Berk
H
es
s
Fix Verlet buffer ca
l
cula
t
io
n
with n
s
tlist=
1
commit
|
commitdiff
|
tree
2016-06-23
Ber
k
Hess
More accurate G
P
U lis
t
splitting
commit
|
commitdiff
|
tree
next