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Enable TPI with the Verlet cut-off scheme
2019-09-12
Ber
k
Hess
En
a
b
l
e
TPI wit
h
the V
e
rlet cut-of
f
sch
e
me
commit
|
commitdiff
|
tree
2019-09-09
B
e
r
k
Hess
Remove inco
r
rect check
with rf-zero
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Extra
c
t Cartesian
data from
DDRan
k
Setu
p
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Rename DDSetup to DD
G
r
idSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Clean
u
p PM
E
rank
v
a
riables
commit
|
commitdiff
|
tree
2019-09-09
B
e
r
k
Hess
Refactor ini
t
_
domain_
d
ecomposition()
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Extract getting of DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
Ber
k
Hess
Add PP grid info
to DDRa
n
kS
e
tup
commit
|
commitdiff
|
tree
2019-09-05
Berk
H
ess
E
xtract
DDRankS
e
tup f
r
om gmx
_
domdec_comm
_
t
commit
|
commitdiff
|
tree
2019-09-05
Berk H
e
ss
Split off ge
t
t
i
n
g of
t
h
e DD setup
commit
|
commitdiff
|
tree
2019-09-04
B
e
rk Hess
C
o
llect settings for DD in DDSet
t
ings
commit
|
commitdiff
|
tree
2019-09-04
Berk Hes
s
Extract ge
t
t
ing of
DDSy
s
temI
n
fo
commit
|
commitdiff
|
tree
2019-09-04
Berk
Hess
Simplify handling of DD b
o
nded di
s
tances
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Mo
v
e co
n
straint and
b
on
d
ed filtering in
f
o i
n
to
DDSyste
m
Info
commit
|
commitdiff
|
tree
2019-09-04
B
e
rk H
e
s
s
M
ove update grouping to DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Change DD pme for
c
e buffer to std::v
e
ctor
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Initializ
e
all me
m
bers of g
m
x_dom
d
ec
_
t
commit
|
commitdiff
|
tree
2019-09-03
Be
r
k Hess
Extract DDSystemInf
o
from gmx_dom
d
ec_comm_
t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Unify manual
a
nd auto D
D
grid choices
commit
|
commitdiff
|
tree
2019-09-03
Berk He
s
s
Remove gmx_domdec_t from
d
d_choose_g
r
i
d
()
commit
|
commitdiff
|
tree
2019-09-03
Ber
k
Hess
Extac
t
UnitC
e
llInfo from g
m
x_domdec_
t
commit
|
commitdiff
|
tree
2019-09-02
B
erk
Hess
Only us
e
fs
h
i
ft when needed
commit
|
commitdiff
|
tree
2019-08-22
Berk
H
e
s
s
Fix perturbed b
o
n
d
ed
bug
commit
|
commitdiff
|
tree
2019-08-20
B
erk He
s
s
M
e
rge tw
o
dih
e
dral funct
i
ons
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
U
s
e shiftForces i
n
F
o
rceOuputs
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make bo
n
ded
v
irial
c
omputation
conditional
commit
|
commitdiff
|
tree
2019-08-20
B
e
rk Hess
F
i
x
mis
s
i
n
g bonde
d
for
c
es with
CU
D
A GPUs an
d
D
D
commit
|
commitdiff
|
tree
2019-08-15
Berk Hess
T
e
mp
l
ate bonded interaction
s
on kernel flavor
commit
|
commitdiff
|
tree
2019-08-09
B
erk Hess
Move b
o
nd
e
d
fu
n
c
t
ion table in
t
o bonded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
SIMD acceler
a
tion for
F_FOURDIHS an
d
F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-06
Berk Hes
s
Add For
c
eWit
h
Shift
F
orces class
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
Fi
x
latex formu
l
a in refe
r
ence manual
commit
|
commitdiff
|
tree
2019-08-05
Ber
k
Hess
Mak
e
box const in
do
_
force(
)
commit
|
commitdiff
|
tree
2019-08-05
Ber
k
H
e
ss
Change ForceOutputs
t
o a class
commit
|
commitdiff
|
tree
2019-08-03
Berk Hess
Re
m
o
v
e
sem
i
colo
n
from GPU TERM macr
o
s
commit
|
commitdiff
|
tree
2019-08-02
B
erk H
e
ss
Made g
m
x disre
w
ork with non-consecutive
l
y labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk
H
ess
R
e
mov
e
a
p
ointer in
t_forcer
e
c
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Fix nbnxm GPU m
e
mory
r
e
se
r
v
a
tio
n
issu
e
commit
|
commitdiff
|
tree
2019-07-31
Berk H
e
ss
Remov
e
u
n
u
s
e
d
CG
L
O_IN
I
T
IALIZ
A
TION
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Rem
o
v
e vcm removal from compute
_
globals()
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
A
dd g
r
o
m
p
p w
a
rni
n
g wi
t
h
u
s
e
of GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Ber
k
H
ess
Remove need
f
o
r GROMOS F
F
in t
e
st
commit
|
commitdiff
|
tree
2019-07-30
Berk Hess
U
s
e invsqrt and cbrt in
free energy kernel
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
R
e
move LJ Ewald c
o
rre
c
t
i
on tables
commit
|
commitdiff
|
tree
2019-07-29
Berk H
e
ss
Add initialization to t_n
r
nb
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Fix segmentation fault with c
o
sine pulling
commit
|
commitdiff
|
tree
2019-07-28
Berk
Hess
Removed gen
e
ralized reaction-fiel
d
commit
|
commitdiff
|
tree
2019-07-28
Berk Hess
C
onv
e
rt Ewald correction t
a
b
les to C++
commit
|
commitdiff
|
tree
2019-07-26
B
e
rk Hess
Add default ini
t
ialization to i
n
terac
t
ion_
c
o
nst_t
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
Remove
s
h_invrc
6
fro
m
i
n
t
eraction_const_t
commit
|
commitdiff
|
tree
2019-07-25
Berk
H
ess
Split ca
n
DetectGpus
(
)
commit
|
commitdiff
|
tree
2019-07-08
Ber
k
Hes
s
Store nbnxm grid
S
e
t
data in Gri
d
S
e
tData
commit
|
commitdiff
|
tree
2019-07-05
Berk H
e
s
s
Change affinit
y
enum to
enum cla
s
s
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Refac
t
o
r
thr
e
ad affi
n
i
ty c
h
ecking
commit
|
commitdiff
|
tree
2019-07-02
Be
r
k
H
ess
R
e-enable affini
t
y diagonost
i
cs
w
i
th MPI
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Fix MPI deadlo
c
k in affini
t
y setting
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Template
f
r
ee-energy
k
ernel on differin
g
cou
l
/v
d
w so
f
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Berk Hess
Remove tabulation from free-energy kernel
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Remove u
n
necessary #if GMX_MPI
i
n
p
me
c
o
d
e
commit
|
commitdiff
|
tree
2019-06-20
Berk He
s
s
Te
m
p
l
ate
f
re
e
-energy kernel on soft-core
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
R
e
fac
t
or PME a
t
o
m
h
andling
commit
|
commitdiff
|
tree
2019-06-19
Ber
k
H
e
ss
Rem
o
ved unused code
paths in
the N
B
FE kern
e
l
commit
|
commitdiff
|
tree
2019-06-18
B
erk
Hess
M
ak
e
f
or
c
erec c
o
nst i
n
dispatchNonbondedKernel(
)
commit
|
commitdiff
|
tree
2019-06-17
Berk He
s
s
Si
m
plify GPU nbnxm x conversion
commit
|
commitdiff
|
tree
2019-06-17
Berk Hes
s
Remove un
u
sed nbnx
m
include files
commit
|
commitdiff
|
tree
2019-06-11
Ber
k
Hess
Allow AWH geometry 'dire
c
tion' to
b
e periodic
commit
|
commitdiff
|
tree
2019-06-10
B
erk Hess
Fix gmx wham with angle geometries
commit
|
commitdiff
|
tree
2019-06-05
Berk Hess
Fix
r
e
ference SIMD
m
emory alig
n
ment
commit
|
commitdiff
|
tree
2019-05-29
B
e
rk Hess
Fix missing int
e
rmolecu
l
ar intera
c
t
ions wi
t
h
D
D
commit
|
commitdiff
|
tree
2019-05-27
Berk H
e
ss
Work aroun
d
gcc 7 avx51
2
bug
commit
|
commitdiff
|
tree
2019-05-23
Berk Hes
s
Fix SHAKE dH/dlambda co
n
tribu
t
ions
commit
|
commitdiff
|
tree
2019-05-14
Berk
He
s
s
Make all do_f
o
rce_lowlevel()
input const
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
Correct use
r
guide postion re
s
train
t
virial
commit
|
commitdiff
|
tree
2019-05-04
Berk Hess
Remove PME exclusion corre
c
t
i
on
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Removed non-exist
e
nt
AWH mdp option
commit
|
commitdiff
|
tree
2019-05-03
Berk
Hess
Co
n
v
e
rt manage_threading_t a
n
d gmx_en
e
rdata_t to
C++
commit
|
commitdiff
|
tree
2019-05-02
Berk Hess
Change nbnxm FEP po
i
nter to
unique_ptr
commit
|
commitdiff
|
tree
2019-04-30
Berk Hess
Ad
d
con/des
t
ru
c
to
r
for t_forcetab
l
e
commit
|
commitdiff
|
tree
2019-04-30
Be
r
k
Hess
Con
v
ert DispersionCorrectio
n
to a class
commit
|
commitdiff
|
tree
2019-04-18
B
erk Hess
Remove nbnxm kern
e
l
type from pairlist
g
e
neration
commit
|
commitdiff
|
tree
2019-04-18
B
e
rk
Hess
R
emove ch
a
rge groups from domdec and lo
c
altop
commit
|
commitdiff
|
tree
2019-04-18
Berk
Hess
Fix pdb-r
e
lated
issues
commit
|
commitdiff
|
tree
2019-04-17
Berk He
s
s
Re
m
ov
e
group scheme search cod
e
commit
|
commitdiff
|
tree
2019-04-17
B
erk
H
ess
Sim
p
lify vs
i
te PBC
handling
commit
|
commitdiff
|
tree
2019-04-17
B
e
r
k He
s
s
Reduce nbnxm
CPU kernel
ar
g
ume
n
ts
commit
|
commitdiff
|
tree
2019-04-17
Ber
k
Hess
S
implify nb
n
xm shift f
o
rce han
d
l
i
ng
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Simplify nbnxm
buffe
r
cle
a
ri
n
g
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Remove RF_excl_
c
o
r
r
e
ction()
commit
|
commitdiff
|
tree
2019-04-16
B
erk Hess
Make mdrun
-
ns
t
eps wor
k
again
.
commit
|
commitdiff
|
tree
2019-04-15
B
erk Hess
U
p
d
ate
2
019 r
e
l
ease notes
f
or issue 2845
commit
|
commitdiff
|
tree
2019-04-15
Berk He
s
s
Fix pdb-
r
ela
t
ed issues
commit
|
commitdiff
|
tree
2019-04-15
Ber
k
H
ess
Dis
a
llo
w
pull ge
o
m
et
r
y directio
n
-periodic with
A
WH
commit
|
commitdiff
|
tree
2019-03-28
Berk
Hess
S
implify n
b
n
xm
final force reduction
commit
|
commitdiff
|
tree
2019-03-28
Berk Hes
s
Move ear
l
y retu
r
n for nbnxm
f
orce re
d
uction
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Mo
v
e P
a
ir
l
i
stSet de
c
laration
commit
|
commitdiff
|
tree
2019-03-28
Berk
Hess
Mo
v
e nbnxm domainS
e
tup to
G
ridSet
commit
|
commitdiff
|
tree
2019-03-28
Be
r
k Hess
Extr
a
c
t nbnxm
P
airlistSets
commit
|
commitdiff
|
tree
2019-03-27
B
e
rk Hess
Fix nbnxm OpenCL with clu
s
ter size 4
commit
|
commitdiff
|
tree
2019-03-25
Berk Hess
C
o
nvert nbnxn_pairlist_set_t to clas
s
Pair
l
istSet
commit
|
commitdiff
|
tree
2019-03-20
Berk H
e
ss
Move around Pa
i
rSearch code
commit
|
commitdiff
|
tree
next