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Reduce nbnxm CPU kernel arguments
2019-04-17
Berk Hess
Reduce nbnxm CP
U
kernel
a
rguments
commit
|
commitdiff
|
tree
2019-04-17
Berk
H
ess
Simplify
n
b
nxm shift for
c
e h
a
ndling
commit
|
commitdiff
|
tree
2019-04-16
Berk He
s
s
Simplify nbnxm buffer clearin
g
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Rem
o
v
e
RF_e
x
cl_cor
r
e
ct
i
on
(
)
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
S
i
m
plify
nbnxm final
forc
e
reduction
commit
|
commitdiff
|
tree
2019-03-28
Berk
H
ess
Move early
retu
r
n for nbnxm force reduct
i
on
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Move P
a
irlistSet
d
eclar
a
t
ion
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Move nbn
x
m domai
n
S
etup
t
o GridS
e
t
commit
|
commitdiff
|
tree
2019-03-28
B
e
rk Hess
Extract nbnxm Pairlis
t
Sets
commit
|
commitdiff
|
tree
2019-03-27
Berk Hess
F
i
x
nbnx
m
Op
e
nCL wi
t
h cl
u
ster size
4
commit
|
commitdiff
|
tree
2019-03-25
Berk Hess
Co
n
vert nbnxn_pairlist_set_t to c
l
a
s
s
Pairlist
S
et
commit
|
commitdiff
|
tree
2019-03-20
B
erk Hes
s
Mov
e
around PairSearch
c
ode
commit
|
commitdiff
|
tree
2019-03-19
Berk Hess
Reduce
d
e
pende
n
cies of nbnxn_atomdata_t
commit
|
commitdiff
|
tree
2019-03-15
B
e
rk Hess
Change nbnxn
_
search to class PairSearch
commit
|
commitdiff
|
tree
2019-03-15
Berk Hess
E
xtract Domain
S
etup from nb
n
x
n
_search
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
Cha
n
ge nbnxm macros to
c
o
nstexpr
commit
|
commitdiff
|
tree
2019-03-14
Ber
k
Hess
Move func
t
ions
to gridset
.
cpp
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
A
d
d
nbn
x
m
G
r
idSet clas
s
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
Fix compilation issue
commit
|
commitdiff
|
tree
2019-03-12
Be
r
k Hess
Move nbnxm atom mac
r
os to
a
tomd
a
t
a
.
h
commit
|
commitdiff
|
tree
2019-03-08
Berk Hess
Cl
e
a
n
up calc_verlet_
b
uffer_size()
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Clean up nbnx
m
b
o
unding box
funct
i
ons
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Clean up nbnxm bounding boxes
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Conv
e
rt nbnxm
b
o
u
nding box
to
a str
u
c
t
commit
|
commitdiff
|
tree
2019-03-05
Berk
Hess
Fix po
s
t-s
u
bmit
w
arnings
commit
|
commitdiff
|
tree
2019-03-05
Berk H
e
ss
Move nbnxm at
o
mdata types t
o
atomdata
.
h
commit
|
commitdiff
|
tree
2019-03-05
Berk H
e
ss
T
u
r
n nbnxn
_
g
rid_t into a
c
lass
commit
|
commitdiff
|
tree
2019-02-28
Berk Hess
Use unique_ptr in nonb
o
nded_verle
t
_
t
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
Use new/delete for t_forcerec
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
Cle
a
n
up
d
ispersioncorrecti
o
n
.
cpp
commit
|
commitdiff
|
tree
2019-02-27
Be
r
k Hess
Fix 4
c
o
mp
i
lers
warnings
commit
|
commitdiff
|
tree
2019-02-27
Berk He
s
s
Col
l
ect dispersio
n
correcti
o
n co
d
e
commit
|
commitdiff
|
tree
2019-02-26
Berk Hes
s
Correct
grompp index fil
e
e
rror message
commit
|
commitdiff
|
tree
2019-02-26
Berk Hess
Clean up
m
top p
b
c functions
commit
|
commitdiff
|
tree
2019-02-23
B
e
rk Hess
Move all nbn
x
m pruning
d
etails into m
o
dule
commit
|
commitdiff
|
tree
2019-02-23
Berk Hess
Hide internals of nbnxm
p
arlist
commit
|
commitdiff
|
tree
2019-02-22
Be
r
k
H
ess
Formali
z
e dyna
m
ic pruning with GPU emulation
commit
|
commitdiff
|
tree
2019-02-21
Berk H
e
s
s
Mo
v
e free-energy ker
n
el
d
ispatc
h
int
o
n
b
nxm module
commit
|
commitdiff
|
tree
2019-02-21
Berk Hess
Minor nbnxm cleanu
p
commit
|
commitdiff
|
tree
2019-02-21
Berk Hess
Cl
e
an up nbnxm enums
commit
|
commitdiff
|
tree
2019-02-21
Berk Hess
S
implify
make_pai
r
list()
c
all signatu
r
e
commit
|
commitdiff
|
tree
2019-02-20
B
erk
Hess
Add havePPDomainDecomposi
t
ion()
commit
|
commitdiff
|
tree
2019-02-20
B
e
rk
Hess
Refactor
DLB region handling
commit
|
commitdiff
|
tree
2019-02-17
Ber
k
Hess
U
se e
n
um cla
s
s
for
n
bnxm locality
commit
|
commitdiff
|
tree
2019-02-17
Berk Hes
s
Extract nbn
x
m
grid
.
h and pairlistwork
.
h
commit
|
commitdiff
|
tree
2019-02-17
Berk He
s
s
Fix compiler
warnings
commit
|
commitdiff
|
tree
2019-02-17
B
e
rk He
s
s
Move
nbn
x
m
det
a
ils from sim_util
.
cpp
to module
commit
|
commitdiff
|
tree
2019-02-16
B
erk Hess
Move nb
n
x
n
files
t
o nbnxm
d
i
rectory
commit
|
commitdiff
|
tree
2019-02-15
B
e
rk
Hess
Fix mas
s
Delt
a
H
double counting
commit
|
commitdiff
|
tree
2019-02-09
Berk Hess
Disallow
rerun with perturbed masses or constraints
commit
|
commitdiff
|
tree
2019-02-06
Berk Hess
Fix segfa
u
lt with
EM, D
D
and group scheme
commit
|
commitdiff
|
tree
2019-02-01
Berk Hess
Fix incorrect
LJ
r
e
p
ulsion forc
e
s
witching o
n
GPU
s
commit
|
commitdiff
|
tree
2019-01-25
Berk H
e
ss
Fix
LI
N
CS
b
ug fro
m
re
c
ent commi
t
211039
f
c
commit
|
commitdiff
|
tree
2019-01-23
Berk Hess
Fix error
w
ith 2D/3D
DLB
commit
|
commitdiff
|
tree
2019-01-22
Ber
k
Hess
Add utility
m
e
t
hod to
N
bn
x
nPairlistGpu
commit
|
commitdiff
|
tree
2019-01-22
Berk
Hess
Remove now ususe
d
G
P
U
alloc
/
free function
s
commit
|
commitdiff
|
tree
2019-01-22
Berk Hess
Convert NbnxnPai
r
lis
t
G
pu to C+
+
commit
|
commitdiff
|
tree
2019-01-21
Ber
k
He
s
s
Convert nbnxn_ato
m
d
ata_
t
to C
+
+
commit
|
commitdiff
|
tree
2019-01-16
Berk Hess
Rename
H
o
s
tV
e
ctor
t
o
PaddedHostVector
commit
|
commitdiff
|
tree
2019-01-10
Berk Hess
Split nbn
x
n_atomdat
a
_init
(
)
commit
|
commitdiff
|
tree
2019-01-10
Berk Hess
C
hang
e
grid p
o
in
t
er
s
in nbnxn search to
r
eferences
commit
|
commitdiff
|
tree
2019-01-10
Berk
H
ess
Split nbnxn_li
s
t_work
_
t and change to C++
commit
|
commitdiff
|
tree
2019-01-10
B
erk Hess
Use
s
t
d::
v
ecto
r
in NbnxnPairlistCp
u
commit
|
commitdiff
|
tree
2019-01-09
Berk Hess
Fix gcc-8
r
elease war
n
ings in t
n
g_io
commit
|
commitdiff
|
tree
2019-01-09
Berk Hess
Added DefaultI
n
itializationAllo
c
ator
commit
|
commitdiff
|
tree
2019-01-04
B
erk Hess
Sp
l
it
nbnxn pairl
i
st ty
p
es for CPU and GPU
commit
|
commitdiff
|
tree
2019-01-04
B
erk Hess
Replace NBNX
N
_
CPU_C
L
USTER_I_SIZE by c_nbn
x
nCpu
I
C
l
usterSize
commit
|
commitdiff
|
tree
2019-01-03
B
e
rk Hess
Fix segmentation fau
l
t
i
n DD code
commit
|
commitdiff
|
tree
2018-12-27
Be
r
k Hess
Use
A
tomPair for
L
INCS index
i
n
g
commit
|
commitdiff
|
tree
2018-12-27
B
e
rk Hess
Use arrayref in LINCS
commit
|
commitdiff
|
tree
2018-12-21
Berk
He
s
s
I
mprove nbnxn cjFro
m
C
i() f
u
nction
commit
|
commitdiff
|
tree
2018-12-18
Berk Hess
Us
e
std
:
:vec
t
or in LINCS
commit
|
commitdiff
|
tree
2018-12-14
Berk Hess
Fix
L
INCS triangle c
o
ns
t
rain
i
n
g with Open
M
P
commit
|
commitdiff
|
tree
2018-12-14
Berk
Hess
Fixed nullptr derefence in LINCS
error
commit
|
commitdiff
|
tree
2018-12-14
Berk H
e
ss
Fix LI
N
CS tr
i
angle c
o
nstraining with OpenMP
commit
|
commitdiff
|
tree
2018-12-12
Berk Hess
T
e
mporary fi
x
for Op
e
nCL PME gather
commit
|
commitdiff
|
tree
2018-12-11
B
erk Hes
s
Fix update group
s
wit
h
2D/3D DLB
commit
|
commitdiff
|
tree
2018-12-11
Be
r
k
He
s
s
Ma
k
e large PME gri
d
s work on GPU
commit
|
commitdiff
|
tree
2018-12-11
Berk
H
e
ss
Docum
e
nt
m
drun mdp o
p
tion modi
f
i
cati
o
n
commit
|
commitdiff
|
tree
2018-12-05
Ber
k
Hess
Add u
p
d
a
te group
s
to par
a
l
l
elizat
i
o
n
do
c
s
commit
|
commitdiff
|
tree
2018-12-05
Be
r
k He
s
s
Make large
P
M
E g
r
ids wo
r
k
on
GP
U
commit
|
commitdiff
|
tree
2018-11-26
Berk Hess
Fi
x
FP
exception in
pu
l
l code
commit
|
commitdiff
|
tree
2018-11-16
Berk Hess
grompp
n
ow che
c
ks tau-p>=
2
*tau-t
wi
t
h NH+PR
commit
|
commitdiff
|
tree
2018-11-08
Berk Hess
Fix
bug wi
t
h D
D
for dims
w
ithout
PBC
commit
|
commitdiff
|
tree
2018-11-01
Berk H
e
ss
F
i
x broken
updat
e
grou
p
s
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
L
im
i
t a
u
to a
s
signment of bondeds to GPUs
commit
|
commitdiff
|
tree
2018-10-31
B
e
rk Hess
Pin impor
t
ant
b
uffers in CUD
A
bondeds
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Work arou
n
d e
x
panded ensemb
l
e i
s
sues
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Fix
F
P exception in ener
g
y re
d
uctio
n
commit
|
commitdiff
|
tree
2018-10-31
B
er
k
Hess
Correct VV int
e
g
rator ns
t
c
alce
n
e
r
g
y use
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Correct grompp nstexpanded/nstcalcenergy chec
k
commit
|
commitdiff
|
tree
2018-10-26
Be
r
k
Hess
A
dd
mis
s
ing mass term
t
o deltaH
commit
|
commitdiff
|
tree
2018-10-23
Berk
Hess
Add missing const
r
ai
n
t term
to d
e
l
t
a
H
commit
|
commitdiff
|
tree
2018-10-21
Berk Hess
Fix mdrun start
/
end time print
commit
|
commitdiff
|
tree
2018-10-18
Berk Hess
Add env
.
var
.
t
o
d
i
sable u
p
date groups
commit
|
commitdiff
|
tree
2018-10-12
Berk Hess
Imp
l
e
ment assigning
b
o
n
deds
t
o
t
he GPU
commit
|
commitdiff
|
tree
2018-10-10
Berk Hess
Mo
v
e
pu
l
l
out
p
ut functio
n
s to ou
t
put
.
cpp
commit
|
commitdiff
|
tree
2018-10-10
Berk Hess
Minor re
f
actorin
g
in
b
onded threading
commit
|
commitdiff
|
tree
2018-10-09
Berk Hess
Fi
x
compiler w
a
r
ning
commit
|
commitdiff
|
tree
2018-10-08
Berk Hess
Enable update
group
s
commit
|
commitdiff
|
tree
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