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Move constraint and bonded filtering info into DDSystemInfo
2019-09-04
Berk Hess
M
ove constraint and bonded
filterin
g
i
n
fo
into DDSys
t
emI
n
f
o
commit
|
commitdiff
|
tree
2019-09-04
B
e
rk
Hess
Move
u
p
d
a
t
e
g
r
oup
i
ng to DDSystemI
n
fo
commit
|
commitdiff
|
tree
2019-09-04
B
erk Hess
Change DD pme fo
r
ce buf
f
er
to
s
td::vector
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Ini
t
ialize all m
e
mbers
of gmx_domdec_t
commit
|
commitdiff
|
tree
2019-09-03
Berk
Hess
E
x
tract
DDSystemI
n
fo fro
m
gmx_d
o
md
e
c_comm_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
U
n
ify
m
an
u
al
and auto
D
D
grid choices
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Remove gmx
_
domdec_t fro
m
dd_choo
s
e_gri
d
(
)
commit
|
commitdiff
|
tree
2019-09-03
Be
r
k Hess
Extact U
n
itCellInfo
from gmx
_
domdec_t
commit
|
commitdiff
|
tree
2019-09-02
Berk H
e
ss
Only use fsh
i
ft wh
e
n
n
e
eded
commit
|
commitdiff
|
tree
2019-08-22
Berk Hess
Fix
p
erturbed bonded bug
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
M
erge two
d
ihe
d
r
al
functio
n
s
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Use shiftForces in ForceOuputs
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make bonded v
i
rial computation
c
onditional
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
F
i
x missing bonded forc
e
s wi
t
h
C
U
DA GPUs
and D
D
commit
|
commitdiff
|
tree
2019-08-15
Berk Hess
Templ
a
te bond
e
d intera
c
t
ions on kernel flavor
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
Move bonded function tabl
e
into bon
d
ed
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
SIMD acceleration for
F
_FOURDI
H
S a
n
d
F
_
PIDIHS
commit
|
commitdiff
|
tree
2019-08-06
Berk H
e
s
s
Add ForceWithShiftFor
c
es cla
s
s
commit
|
commitdiff
|
tree
2019-08-06
B
erk H
e
s
s
Fix latex
for
m
ula in reference manual
commit
|
commitdiff
|
tree
2019-08-05
Berk Hess
Make box
const in do_force()
commit
|
commitdiff
|
tree
2019-08-05
Berk Hess
Chan
g
e ForceOutputs to a class
commit
|
commitdiff
|
tree
2019-08-03
Berk Hess
Remove s
e
m
i
colon
fr
o
m GPU TERM m
a
c
r
os
commit
|
commitdiff
|
tree
2019-08-02
Berk Hess
Made gmx disr
e
w
o
rk with non-consecu
t
iv
e
ly labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
R
e
m
ove a
pointer
in t_forcerec
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Fix nbnxm
GPU memor
y
re
s
ervati
o
n i
s
s
u
e
commit
|
commitdiff
|
tree
2019-07-31
Berk He
s
s
Remove u
n
u
s
ed CGLO_
I
NITI
A
L
I
Z
ATION
commit
|
commitdiff
|
tree
2019-07-31
Be
r
k
Hess
Remove v
c
m
r
emoval from
c
o
m
pute_globals()
commit
|
commitdiff
|
tree
2019-07-31
Berk H
e
ss
Add g
r
ompp warning with u
s
e
o
f GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Be
r
k Hes
s
R
e
move ne
e
d for GROM
O
S FF in test
commit
|
commitdiff
|
tree
2019-07-30
Berk Hess
Us
e
invsqrt and cbrt i
n
free
e
nergy kern
e
l
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Remove LJ Ewald
co
r
re
c
t
ion tabl
e
s
commit
|
commitdiff
|
tree
2019-07-29
Berk He
s
s
Ad
d
init
i
ali
z
ation to t_nrnb
commit
|
commitdiff
|
tree
2019-07-29
Ber
k
Hess
Fix segmen
t
atio
n
f
aul
t
with cosine pulling
commit
|
commitdiff
|
tree
2019-07-28
Berk
H
ess
Re
m
ov
e
d generalized reaction-field
commit
|
commitdiff
|
tree
2019-07-28
Berk H
e
s
s
Convert Ewald correction table
s
t
o
C++
commit
|
commitdiff
|
tree
2019-07-26
B
e
rk Hess
Add defaul
t
initialization t
o
in
t
e
r
a
ct
i
on_const_
t
commit
|
commitdiff
|
tree
2019-07-26
B
e
rk H
e
ss
Remove sh
_
invrc6 from in
t
eraction_co
n
st_t
commit
|
commitdiff
|
tree
2019-07-25
Berk Hess
S
pl
i
t
can
D
e
t
ectGpus()
commit
|
commitdiff
|
tree
2019-07-08
B
erk Hess
Store nbnxm gridSe
t
data in GridSetDat
a
commit
|
commitdiff
|
tree
2019-07-05
Be
r
k Hess
Change affinity enum
to enum class
commit
|
commitdiff
|
tree
2019-07-02
B
e
rk
Hess
Refactor thr
e
a
d
a
f
f
inity checking
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Re-e
n
able affinity diagonostics w
i
th MP
I
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
F
i
x MPI deadlock in af
f
inity set
t
i
ng
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Template free
-
e
nergy kernel on di
f
fering co
u
l/vdw sof
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Ber
k
H
e
ss
Remov
e
tabul
a
tion f
r
om fr
e
e
-
e
nergy ker
n
el
commit
|
commitdiff
|
tree
2019-06-20
B
er
k
Hess
Rem
o
ve
unnecessary #if
G
MX_
M
PI in pme code
commit
|
commitdiff
|
tree
2019-06-20
Berk
Hess
Temp
l
at
e
free-energy kernel o
n
soft
-
core
commit
|
commitdiff
|
tree
2019-06-19
Berk He
s
s
R
e
factor PM
E
atom handling
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Removed
unused
code paths
i
n the NB FE kern
e
l
commit
|
commitdiff
|
tree
2019-06-18
Berk Hess
Make
forc
e
r
e
c
c
onst in dispatchNonbo
n
dedKer
n
el()
commit
|
commitdiff
|
tree
2019-06-17
Berk
H
ess
S
i
mpli
f
y GPU nbn
x
m x
conversi
o
n
commit
|
commitdiff
|
tree
2019-06-17
Berk
Hess
Remo
v
e unused nbnxm incl
u
de
files
commit
|
commitdiff
|
tree
2019-06-11
Berk Hess
A
llow AWH geometry '
d
irection' to be periodic
commit
|
commitdiff
|
tree
2019-06-10
B
e
rk Hess
Fix
gmx wham with
a
ng
l
e geo
m
etries
commit
|
commitdiff
|
tree
2019-06-05
Berk He
s
s
Fi
x
reference SIMD m
e
mory
alignment
commit
|
commitdiff
|
tree
2019-05-29
Berk Hess
Fix m
i
s
sing inte
r
molecular inter
a
ctio
n
s with DD
commit
|
commitdiff
|
tree
2019-05-27
Berk Hess
Wor
k
aroun
d
gcc 7 avx
5
12 bug
commit
|
commitdiff
|
tree
2019-05-23
Berk Hess
Fix SHAK
E
dH/dlambda con
t
ributions
commit
|
commitdiff
|
tree
2019-05-14
Be
r
k
Hess
Ma
k
e all d
o
_force
_
lowlev
e
l() input const
commit
|
commitdiff
|
tree
2019-05-14
B
e
rk
Hes
s
Correct user guide postion restraint virial
commit
|
commitdiff
|
tree
2019-05-04
Berk Hess
R
e
move P
M
E
e
xclusion c
o
rrection
commit
|
commitdiff
|
tree
2019-05-03
Berk
H
e
ss
Removed non-existent AWH mdp o
p
tion
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Convert manage_
t
hr
e
ading_t a
n
d g
m
x_enerda
t
a_
t
t
o C++
commit
|
commitdiff
|
tree
2019-05-02
Berk Hes
s
Change nbnxm
F
EP pointer to u
n
ique_ptr
commit
|
commitdiff
|
tree
2019-04-30
Berk Hess
A
d
d
con/destructor for t_
f
orcet
a
ble
commit
|
commitdiff
|
tree
2019-04-30
B
e
r
k Hess
C
o
nve
r
t DispersionCorrection to a cla
s
s
commit
|
commitdiff
|
tree
2019-04-18
Berk H
e
s
s
R
em
o
ve
n
bn
x
m kernel type
f
rom
p
air
l
i
s
t gene
r
ation
commit
|
commitdiff
|
tree
2019-04-18
Berk
He
s
s
Remove char
g
e groups from domde
c
and localtop
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
F
ix pdb-relate
d
issues
commit
|
commitdiff
|
tree
2019-04-17
Be
r
k Hes
s
Remove group
s
cheme search
c
ode
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
S
implify v
s
it
e
P
B
C
ha
n
dling
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
R
e
duc
e
nbnxm CPU kerne
l
arguments
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Si
m
plify nbnxm shift force handling
commit
|
commitdiff
|
tree
2019-04-16
Berk Hes
s
Simplify nbnxm bu
f
fer c
l
earing
commit
|
commitdiff
|
tree
2019-04-16
Berk He
s
s
Remove RF_excl_
c
orrecti
o
n()
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Ma
k
e mdrun -nsteps work
aga
i
n
.
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
Upd
a
te
2019 release notes
f
or
is
s
ue 2845
commit
|
commitdiff
|
tree
2019-04-15
B
er
k
Hess
Fix
p
db-re
l
ate
d
i
s
s
u
es
commit
|
commitdiff
|
tree
2019-04-15
Berk H
e
ss
Disa
l
l
o
w
pull g
e
ometry dire
c
tion-per
i
odi
c
w
ith
A
W
H
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Simplify nbnxm final force re
d
uc
t
ion
commit
|
commitdiff
|
tree
2019-03-28
B
e
r
k Hess
Move
e
a
r
ly re
t
ur
n
for nbnxm force red
u
ct
i
on
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Move
P
airli
s
tSet d
e
claration
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Move nbnx
m
domainSetup to
Gr
i
dSet
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Extract n
b
nxm Pairl
i
stS
e
t
s
commit
|
commitdiff
|
tree
2019-03-27
Berk Hess
Fix nbnxm OpenCL with cl
u
s
ter size 4
commit
|
commitdiff
|
tree
2019-03-25
Berk Hess
C
o
n
vert nbnxn_pairlist_set_t to class
PairlistSet
commit
|
commitdiff
|
tree
2019-03-20
Berk Hess
Move
ar
o
un
d
P
a
irSea
r
ch code
commit
|
commitdiff
|
tree
2019-03-19
Berk H
e
ss
R
e
duce dependenc
i
es of nbnxn_a
t
omdata_t
commit
|
commitdiff
|
tree
2019-03-15
Berk Hess
C
h
a
nge nbnxn_search t
o
class P
a
irSearch
commit
|
commitdiff
|
tree
2019-03-15
B
erk He
s
s
E
xtr
a
c
t
Dom
a
inSetup from nbnxn_searc
h
commit
|
commitdiff
|
tree
2019-03-14
Berk He
s
s
Change
n
bnxm macros to
constexpr
commit
|
commitdiff
|
tree
2019-03-14
B
e
rk Hess
M
ove fu
n
c
ti
o
n
s
to gridset
.
c
p
p
commit
|
commitdiff
|
tree
2019-03-14
B
erk Hess
Add nbnxm
G
r
i
dSet c
l
ass
commit
|
commitdiff
|
tree
2019-03-14
B
e
r
k Hess
F
i
x compilat
i
on issue
commit
|
commitdiff
|
tree
2019-03-12
B
erk H
e
ss
Move n
b
nxm atom macros to at
o
mda
t
a
.
h
commit
|
commitdiff
|
tree
2019-03-11
Ber
k
He
s
s
Add grom
p
p warni
n
g with use of GROMOS FF
commit
|
commitdiff
|
tree
2019-03-08
Berk Hess
Clean up c
a
l
c
_ver
l
et_buffer_size()
commit
|
commitdiff
|
tree
2019-03-06
Be
r
k
H
ess
Clean up nbn
x
m bounding box functions
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Clean u
p
nbnxm boundi
n
g boxes
commit
|
commitdiff
|
tree
2019-03-06
B
e
rk Hes
s
Convert nbnx
m
bounding bo
x
to a struct
commit
|
commitdiff
|
tree
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