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Fix LINCS bug from recent commit 211039fc
2019-01-25
Be
r
k
Hess
Fix L
I
NCS bug from recent commit 211039
f
c
commit
|
commitdiff
|
tree
2019-01-23
Berk Hess
Fix error with 2D/3D DLB
commit
|
commitdiff
|
tree
2019-01-22
Berk
H
ess
Add u
t
ility
m
ethod to Nb
n
xnPa
i
rlistG
p
u
commit
|
commitdiff
|
tree
2019-01-22
Berk
Hess
Rem
o
v
e
now u
s
u
s
ed GPU alloc/free functi
o
ns
commit
|
commitdiff
|
tree
2019-01-22
Berk He
s
s
C
o
nvert
NbnxnP
a
irli
s
tGpu to C
+
+
commit
|
commitdiff
|
tree
2019-01-21
Be
r
k Hess
Convert n
b
n
xn_atom
d
ata_t to C++
commit
|
commitdiff
|
tree
2019-01-16
Berk
He
s
s
Ren
a
me HostVe
c
tor to Padded
H
ostVec
t
o
r
commit
|
commitdiff
|
tree
2019-01-10
B
e
rk Hess
S
p
li
t
nbnx
n
_atomdat
a
_i
n
i
t
()
commit
|
commitdiff
|
tree
2019-01-10
B
erk Hess
Chan
g
e grid pointers in nbnxn searc
h
t
o ref
e
ren
c
es
commit
|
commitdiff
|
tree
2019-01-10
B
e
r
k
Hess
Spl
i
t
nbnxn_list
_
work_t and
change to C+
+
commit
|
commitdiff
|
tree
2019-01-10
Be
r
k
H
e
ss
U
s
e
std::ve
c
tor in NbnxnPairlistC
p
u
commit
|
commitdiff
|
tree
2019-01-09
B
e
r
k
H
ess
Fix gcc-8
r
elease warnings
in
t
ng_i
o
commit
|
commitdiff
|
tree
2019-01-09
Ber
k
Hess
Ad
d
ed Defau
l
tI
n
itializat
i
o
nAllocato
r
commit
|
commitdiff
|
tree
2019-01-04
Berk
H
ess
S
plit nbnxn pa
i
rlist type
s
for CPU and G
P
U
commit
|
commitdiff
|
tree
2019-01-04
Berk H
e
ss
Replace NBNX
N
_
CPU_
C
LUSTE
R
_I
_
SIZE
by c
_
n
b
nxnC
p
uIClusterSize
commit
|
commitdiff
|
tree
2019-01-03
Berk Hess
Fix segm
e
ntat
i
on fau
l
t
i
n
DD code
commit
|
commitdiff
|
tree
2018-12-27
Berk Hes
s
Use AtomPair for L
I
NC
S
i
ndexing
commit
|
commitdiff
|
tree
2018-12-27
Berk Hess
Use a
r
rayref in LI
N
CS
commit
|
commitdiff
|
tree
2018-12-21
Be
r
k
Hes
s
Improve nb
n
x
n cjFrom
C
i(
)
f
u
nction
commit
|
commitdiff
|
tree
2018-12-18
Berk Hess
Use
std:
:
vect
o
r
in LINCS
commit
|
commitdiff
|
tree
2018-12-14
Berk Hess
Fix LINCS tr
i
angle constraining with Op
e
n
MP
commit
|
commitdiff
|
tree
2018-12-14
B
er
k
He
s
s
Fi
x
ed nullptr deref
e
nce
i
n
LI
N
CS error
commit
|
commitdiff
|
tree
2018-12-14
Berk Hess
Fix LINCS
t
riangle constraining with Open
M
P
commit
|
commitdiff
|
tree
2018-12-12
Berk
H
ess
Temporary
f
ix
f
or
OpenCL
P
ME gather
commit
|
commitdiff
|
tree
2018-12-11
B
e
r
k H
e
ss
Fix update g
r
oups with
2D/3D DLB
commit
|
commitdiff
|
tree
2018-12-11
Berk Hess
Make large
P
ME grid
s
work on GPU
commit
|
commitdiff
|
tree
2018-12-11
B
e
r
k H
e
ss
Doc
u
ment
m
drun mdp
o
p
tion
m
odificatio
n
commit
|
commitdiff
|
tree
2018-12-05
B
e
rk
Hess
Add update
groups to par
a
lleli
z
a
t
ion do
c
s
commit
|
commitdiff
|
tree
2018-12-05
Be
r
k Hess
Mak
e
large PME grids
work on GPU
commit
|
commitdiff
|
tree
2018-11-26
Berk Hes
s
Fix FP excep
t
io
n
in pull code
commit
|
commitdiff
|
tree
2018-11-16
Berk Hess
g
rom
p
p no
w
chec
k
s tau-
p
>=2*
t
a
u
-t with NH+PR
commit
|
commitdiff
|
tree
2018-11-08
Be
r
k Hess
Fix bug with DD for dims without PBC
commit
|
commitdiff
|
tree
2018-11-01
Berk Hess
Fix broken updat
e
groups
commit
|
commitdiff
|
tree
2018-10-31
B
erk
Hess
L
i
mit auto a
s
signment
of bonded
s
to GPUs
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Pi
n
important buf
f
ers in CUDA bondeds
commit
|
commitdiff
|
tree
2018-10-31
Berk Hes
s
Wo
r
k around
e
xpande
d
ensemble iss
u
es
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Fix FP exce
p
tion in energy
reduc
t
ion
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Correct VV integrator nstcalcene
r
gy use
commit
|
commitdiff
|
tree
2018-10-31
Ber
k
H
e
ss
Corr
e
ct gro
m
pp nstexpanded/nstcalcenergy check
commit
|
commitdiff
|
tree
2018-10-26
Berk
H
ess
Add missing mass term to
d
eltaH
commit
|
commitdiff
|
tree
2018-10-23
Berk He
s
s
Add mi
s
s
ing constraint term to deltaH
commit
|
commitdiff
|
tree
2018-10-21
Berk Hess
Fi
x
md
r
un
start/end time print
commit
|
commitdiff
|
tree
2018-10-18
Berk
Hess
Add en
v
.
var
.
to disable up
d
ate grou
p
s
commit
|
commitdiff
|
tree
2018-10-12
Be
r
k Hes
s
Implement assigning bond
e
ds to the GPU
commit
|
commitdiff
|
tree
2018-10-10
Ber
k
H
es
s
Mov
e
pull outpu
t
function
s
to
outpu
t
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
Berk Hes
s
Minor
refactoring in bonded
threading
commit
|
commitdiff
|
tree
2018-10-09
Berk
H
ess
Fix comp
i
l
er warning
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
Enable update
grou
p
s
commit
|
commitdiff
|
tree
2018-10-05
Berk Hess
Add upda
t
e g
r
oups
t
o DD at
o
m
d
i
spla
c
em
e
n
t
commit
|
commitdiff
|
tree
2018-10-04
Berk
H
ess
Make AVX2 p
a
ss T
S
AN
commit
|
commitdiff
|
tree
2018-10-04
B
erk Hess
A
d
d note to avoid
constra
i
nts=all-bonds
commit
|
commitdiff
|
tree
2018-10-03
Be
r
k Hess
R
e
m
o
v
e unnecessary clearing in
g
mxcpp
commit
|
commitdiff
|
tree
2018-10-03
Berk Hess
Con
v
ert gmx_cpp
to C++
commit
|
commitdiff
|
tree
2018-10-02
Be
r
k Hess
Update DD cutoffs for u
p
date gr
o
ups
commit
|
commitdiff
|
tree
2018-09-30
Berk Hess
Corre
c
t update gr
o
up
angle
param
t
y
p
e
commit
|
commitdiff
|
tree
2018-09-29
B
e
rk Hess
Refact
o
ring i
n
calc_verletbuf
.
c
pp
commit
|
commitdiff
|
tree
2018-09-29
Berk Hes
s
Add
Up
d
ateGroup
s
Cog t
o
DD
commit
|
commitdiff
|
tree
2018-09-27
Ber
k
Hess
Move maxR
e
ferenceTemp
e
rature(
)
to
i
nputre
c
commit
|
commitdiff
|
tree
2018-09-27
Ber
k
H
e
ss
I
m
prov
e
up
d
a
t
e
group radi
i
commit
|
commitdiff
|
tree
2018-09-27
Berk
Hess
R
e
o
r
ganize RVec scaling
functio
n
s
commit
|
commitdiff
|
tree
2018-09-26
Berk Hess
Ex
t
ract settl
e
test water c
o
o
r
d
i
nates
commit
|
commitdiff
|
tree
2018-09-26
Be
r
k Hess
Support atom gr
o
ups in nbnxn_sea
r
ch
commit
|
commitdiff
|
tree
2018-09-25
Berk
H
ess
Add
U
p
d
a
teG
r
o
upsCog clas
s
commit
|
commitdiff
|
tree
2018-09-24
Berk Hess
Fi
x
performance report when init_step
!
=0
commit
|
commitdiff
|
tree
2018-09-22
B
erk Hess
Add upda
t
e g
r
oups
boolean to DD
commit
|
commitdiff
|
tree
2018-09-22
Berk Hess
Rename
DD constraint booleans
commit
|
commitdiff
|
tree
2018-09-22
Berk
H
e
ss
Add update gro
u
ps
commit
|
commitdiff
|
tree
2018-09-20
B
erk Hess
Change pull buff
e
r
s
to std::vector
commit
|
commitdiff
|
tree
2018-09-20
Berk Hess
Fi
x
type
bug in trilinic DD code
commit
|
commitdiff
|
tree
2018-09-19
B
e
rk H
e
s
s
Con
v
ert gmx_cm
a
p_t to
C
++
commit
|
commitdiff
|
tree
2018-09-19
B
erk
H
ess
C
o
nvert gmx_ffp
a
ra
m
s_t to C++
commit
|
commitdiff
|
tree
2018-09-18
Berk He
s
s
Introduce extractILists helper
f
unction
commit
|
commitdiff
|
tree
2018-09-18
Berk H
e
ss
R
efactor ddbox handling
commit
|
commitdiff
|
tree
2018-09-17
Berk Hes
s
Move ifunc
stuff
f
rom id
e
f
.
h to ifunc
.
h
commit
|
commitdiff
|
tree
2018-09-17
Berk Hess
Cha
n
ge pointers t
o
InteractionList to reference
s
commit
|
commitdiff
|
tree
2018-09-16
B
erk H
e
ss
Ref
a
c
t
orin
g
in DD
r
edist
r
ibute
commit
|
commitdiff
|
tree
2018-09-14
Berk Hes
s
Refact
o
r getAtomGrou
p
Dist
r
i
but
i
on()
commit
|
commitdiff
|
tree
2018-09-14
B
er
k
Hess
Change g
m
x
_moltype_t
.
i
list to In
t
eractionL
i
sts
commit
|
commitdiff
|
tree
2018-09-13
B
e
rk Hes
s
Add C++ ver
s
ion of t_ilist
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Convert v
s
it
e
st
r
ucts to C
+
+
commit
|
commitdiff
|
tree
2018-09-12
Berk Hess
Conver
t
DD gmx_reverse_top_t t
o
C++
commit
|
commitdiff
|
tree
2018-09-10
B
erk He
s
s
Fix PME
forces with FE wit
h
out
pertu
r
bed q
/
LJ
commit
|
commitdiff
|
tree
2018-08-29
Berk Hess
Refactor wall potential calculation
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk
H
e
s
s
Repl
a
ce g
m
x_ha
s
h
_t by HashedMap
commit
|
commitdiff
|
tree
2018-08-24
Be
r
k
Hes
s
M
e
rge "Merg
e
br
a
nch
r
el
e
ase-201
8
"
commit
|
commitdiff
|
tree
2018-08-24
B
e
rk
H
e
s
s
Add
s
ize
o
ptimization to
H
ashedMap
commit
|
commitdiff
|
tree
2018-08-24
Ber
k
Hes
s
Ad
d
t
ests for HashedMap
commit
|
commitdiff
|
tree
2018-08-22
Berk Hess
F
ix
m
issin
g
interactions
with GPU
a
nd DD
commit
|
commitdiff
|
tree
2018-08-21
Ber
k
Hess
Ensure d
o
mains are lar
g
e enough fo
r
ato
m
m
o
tion
commit
|
commitdiff
|
tree
2018-08-21
B
e
rk Hess
Fixed mdrun segv with QM/MM ONIOM sch
e
me
commit
|
commitdiff
|
tree
2018-08-20
B
e
rk
He
s
s
Refactor
c
a
l
c
_verlet_buffer_
s
ize()
commit
|
commitdiff
|
tree
2018-08-20
B
er
k
Hess
Remove co
m
pacting fr
o
m DD redi
s
tribute
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
F
ix
V
erl
e
t buffer estimate
with B
D
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
F
i
x clang names
p
ace comment warning
commit
|
commitdiff
|
tree
2018-08-20
Berk
Hess
Fix
assertion failure in
C
G
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Reall
y
f
i
x
CG with
multip
l
e d
o
mains
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Make gmx_ga2la_t a proper cl
a
ss
commit
|
commitdiff
|
tree
2018-08-18
Berk He
s
s
A
d
d check
for p
u
ll gr
o
u
p
PBC to gr
o
m
p
p
commit
|
commitdiff
|
tree
2018-08-17
Berk Hess
M
a
ke pull pbc atom use LocalAtomSet
commit
|
commitdiff
|
tree
2018-07-18
Berk
He
s
s
Apply lo
c
a
l
atom set
s
in
pull code
commit
|
commitdiff
|
tree
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