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Enable TPI with the Verlet cut-off scheme
2019-09-12
Berk
Hess
Enable TPI with the Verlet
cut-
o
ff
s
cheme
commit
|
commitdiff
|
tree
2019-09-09
Be
r
k Hess
Remove incorrect check with
rf-z
e
ro
commit
|
commitdiff
|
tree
2019-09-09
Berk He
s
s
E
x
tract Car
t
esian data from DDR
a
nkSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Ren
a
me
DDS
e
tup to DDGri
d
Setup
commit
|
commitdiff
|
tree
2019-09-09
Berk H
e
ss
Clean up PME r
a
nk vari
a
bles
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Refactor init_domain_decomposition()
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
E
x
tract g
e
tting of
DDRankSet
u
p
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
A
d
d PP
g
r
i
d info to DDRank
S
etup
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Extrac
t
DDR
a
nkSetup fr
o
m g
m
x_domdec_
c
omm_t
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Split o
f
f ge
t
t
ing o
f
the DD setup
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Co
l
lect settin
g
s for DD
in DDSettings
commit
|
commitdiff
|
tree
2019-09-04
Berk
H
ess
Extract gett
i
ng of DDSystemI
n
fo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
S
i
mplify handling of DD bonded distances
commit
|
commitdiff
|
tree
2019-09-04
Berk He
s
s
M
o
ve constraint and bonded filter
i
ng i
n
fo into DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move update groupi
n
g to DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk He
s
s
Change DD pme force buffer to std::vector
commit
|
commitdiff
|
tree
2019-09-04
B
e
rk Hess
In
i
tial
i
ze
a
l
l
m
e
mbers of g
m
x_domdec_
t
commit
|
commitdiff
|
tree
2019-09-03
Be
r
k Hess
Extra
c
t DDSystemInf
o
fr
o
m gmx
_
do
m
d
ec_comm
_
t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Un
i
fy manual and auto DD grid choices
commit
|
commitdiff
|
tree
2019-09-03
Berk
H
ess
Remove gmx_dom
d
ec_t
f
rom
dd_choo
s
e_g
r
id()
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Exta
c
t UnitCellInfo from g
m
x
_
domdec_t
commit
|
commitdiff
|
tree
2019-09-02
B
erk
Hess
Only use fshift when ne
e
ded
commit
|
commitdiff
|
tree
2019-08-22
Berk Hess
Fix pert
u
rbed
b
onded bug
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Merge two dihed
r
al
f
unc
t
ions
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
U
s
e
shif
t
F
orces
in ForceOuputs
commit
|
commitdiff
|
tree
2019-08-20
Berk
H
ess
Ma
k
e bonded virial computatio
n
conditional
commit
|
commitdiff
|
tree
2019-08-20
Berk
He
s
s
Fix missing bonded force
s
with CUDA GPUs and D
D
commit
|
commitdiff
|
tree
2019-08-15
Berk
H
ess
T
emplate bonded
i
n
teractions on kernel flavor
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
Mo
v
e bon
d
e
d
functi
o
n
table into
bon
d
ed
.
c
p
p
commit
|
commitdiff
|
tree
2019-08-09
B
e
r
k Hess
SIMD accel
e
ration for F_FOURDIHS and F_
P
IDIHS
commit
|
commitdiff
|
tree
2019-08-06
Berk H
e
ss
Add For
c
eWithShiftForc
e
s class
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
F
i
x latex for
m
ula
i
n ref
e
rence manual
commit
|
commitdiff
|
tree
2019-08-05
Ber
k
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
H
ess
Rem
o
ve sem
i
colon from GPU TERM macros
commit
|
commitdiff
|
tree
2019-08-02
Be
r
k
H
ess
Made g
m
x disre work
with non-
c
onse
c
utively labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
B
erk Hess
R
e
m
o
ve a pointe
r
in t_forcere
c
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Fix nbnxm
G
PU me
m
ory reservation issue
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Remove unuse
d
CGLO_INITIALIZATION
commit
|
commitdiff
|
tree
2019-07-31
B
e
r
k Hess
Re
m
o
v
e vcm r
e
moval from compute_globals()
commit
|
commitdiff
|
tree
2019-07-31
Ber
k
Hess
Add grompp
w
arning wit
h
use
o
f GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
B
e
r
k
Hess
R
e
m
o
ve need f
o
r GROMOS FF in
t
est
commit
|
commitdiff
|
tree
2019-07-30
Berk H
e
ss
Use invsq
r
t and cbrt in f
r
ee
ene
r
gy
k
ernel
commit
|
commitdiff
|
tree
2019-07-29
B
e
rk Hes
s
Remove
LJ Ewal
d
correction tables
commit
|
commitdiff
|
tree
2019-07-29
Berk He
s
s
Add init
i
alization
to t_nrnb
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Fix
segm
e
ntat
i
o
n fault with cosi
n
e pul
l
in
g
commit
|
commitdiff
|
tree
2019-07-28
Berk Hess
R
e
m
o
ved generalized reaction-fi
e
l
d
commit
|
commitdiff
|
tree
2019-07-28
B
erk
Hes
s
Convert Ewald correct
i
o
n
t
ables
t
o
C
+
+
commit
|
commitdiff
|
tree
2019-07-26
Berk
H
e
ss
Add de
f
au
l
t
i
niti
a
l
i
zation to interacti
o
n_cons
t
_t
commit
|
commitdiff
|
tree
2019-07-26
Be
r
k He
s
s
Remove sh_
i
nvrc6 fro
m
interac
t
i
o
n
_const_t
commit
|
commitdiff
|
tree
2019-07-25
B
e
r
k Hess
Split canDetectGpus()
commit
|
commitdiff
|
tree
2019-07-08
Berk Hess
St
o
r
e
nbnxm gridSet data in
GridSe
t
Data
commit
|
commitdiff
|
tree
2019-07-05
Berk
Hess
Change
a
f
f
ini
t
y enum to enum
cl
a
ss
commit
|
commitdiff
|
tree
2019-07-02
Ber
k
He
s
s
Refactor thread affinit
y
ch
e
ckin
g
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
R
e
-enable affin
i
ty dia
g
onostics with MPI
commit
|
commitdiff
|
tree
2019-07-01
B
erk Hess
Fix M
P
I
d
eadlock
in af
f
inity
se
t
t
i
ng
commit
|
commitdiff
|
tree
2019-07-01
Berk
Hess
T
e
mplate free-en
e
rgy kernel on
d
ifferi
n
g
c
oul/vdw so
f
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Berk Hess
R
emov
e
tabula
t
ion
f
rom free-en
e
rgy kernel
commit
|
commitdiff
|
tree
2019-06-20
B
erk Hess
Remov
e
u
nnecess
a
ry #if GMX_MP
I
in
p
m
e code
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
T
emplat
e
free-ener
g
y
kerne
l
on soft-co
r
e
commit
|
commitdiff
|
tree
2019-06-19
B
erk Hess
Refact
o
r
P
M
E atom han
d
ling
commit
|
commitdiff
|
tree
2019-06-19
Ber
k
Hes
s
Rem
o
ved unused c
o
d
e
paths in the N
B
F
E kernel
commit
|
commitdiff
|
tree
2019-06-18
Berk Hess
Ma
k
e forc
e
rec co
n
st in
d
i
s
patchNo
n
bondedKernel()
commit
|
commitdiff
|
tree
2019-06-17
Ber
k
Hess
Simplif
y
G
P
U nbnxm x conversion
commit
|
commitdiff
|
tree
2019-06-17
Be
r
k He
s
s
Remo
v
e unused
nbn
x
m
include
f
iles
commit
|
commitdiff
|
tree
2019-06-11
Berk He
s
s
Al
l
ow AW
H
ge
o
metr
y
'direction' to be
pe
r
iodic
commit
|
commitdiff
|
tree
2019-06-10
Berk Hes
s
Fix gmx w
h
a
m w
i
t
h
a
ngle geometries
commit
|
commitdiff
|
tree
2019-06-05
Berk Hess
F
i
x referenc
e
SIMD memory alignment
commit
|
commitdiff
|
tree
2019-05-29
Berk Hess
Fix m
i
s
s
i
ng inte
r
molecular interacti
o
ns
w
ith DD
commit
|
commitdiff
|
tree
2019-05-27
Ber
k
Hess
W
ork a
r
ound gcc 7 avx5
1
2
b
ug
commit
|
commitdiff
|
tree
2019-05-23
B
e
r
k He
s
s
Fix SHAKE dH/dlambda cont
r
ibutions
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
M
a
ke
a
ll do_
f
orc
e
_lowlevel() input
const
commit
|
commitdiff
|
tree
2019-05-14
Ber
k
Hess
Correct use
r
guide pos
t
io
n
rest
r
aint
virial
commit
|
commitdiff
|
tree
2019-05-04
B
erk
Hess
Remove PME exclusi
o
n
c
o
rrection
commit
|
commitdiff
|
tree
2019-05-03
Ber
k
Hes
s
Re
m
ov
e
d n
o
n-ex
i
s
te
n
t
A
W
H
mdp option
commit
|
commitdiff
|
tree
2019-05-03
B
erk Hess
Conv
e
rt manage_threading_t and gmx_
e
n
erdata_t
to C+
+
commit
|
commitdiff
|
tree
2019-05-02
Berk He
s
s
Chan
g
e
nbnx
m
F
E
P pointer to unique_ptr
commit
|
commitdiff
|
tree
2019-04-30
Berk He
s
s
A
d
d
con/destruct
o
r for t_forcetable
commit
|
commitdiff
|
tree
2019-04-30
Berk Hess
Convert
D
ispe
r
s
ionCorrec
t
ion to a cla
s
s
commit
|
commitdiff
|
tree
2019-04-18
Berk
Hess
Re
m
ove nbn
x
m
kernel type fr
o
m
pairlist generation
commit
|
commitdiff
|
tree
2019-04-18
Berk Hes
s
R
emove charge gr
o
u
p
s f
r
om
d
omde
c
and localtop
commit
|
commitdiff
|
tree
2019-04-18
Be
r
k Hess
Fix
pdb-relate
d
issues
commit
|
commitdiff
|
tree
2019-04-17
Berk
H
es
s
R
e
m
ove group
scheme search code
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Simplify vsite PBC han
d
ling
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Reduce nbnxm
C
PU kernel argument
s
commit
|
commitdiff
|
tree
2019-04-17
Be
r
k
H
e
ss
Simplify nbnx
m
shif
t
for
c
e handling
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Simpli
f
y nbnxm buffer clearing
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Rem
o
ve
RF
_
excl_correc
t
i
o
n
()
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
M
a
ke mdrun -n
s
t
e
p
s
work
a
gain
.
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
Update
2019
r
elease notes fo
r
i
ssue
2
845
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
Fix pdb-related issues
commit
|
commitdiff
|
tree
2019-04-15
Be
r
k Hess
Disallo
w
pu
l
l geom
e
tr
y
di
r
ection-perio
d
ic with AW
H
commit
|
commitdiff
|
tree
2019-03-28
Berk
H
ess
Simpl
i
fy nb
n
xm final force r
e
du
c
ti
o
n
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Move earl
y
retu
r
n for nbnxm force reduction
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Move Pai
r
li
s
tS
e
t d
e
claration
commit
|
commitdiff
|
tree
2019-03-28
Be
r
k Hess
M
o
ve nbnxm doma
i
nSetup to GridSe
t
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Extract nbnxm Pairl
i
stSets
commit
|
commitdiff
|
tree
2019-03-27
Berk
Hess
Fix
n
b
n
x
m
Op
e
n
C
L wit
h
c
l
uster size 4
commit
|
commitdiff
|
tree
2019-03-25
Berk Hess
Convert
nbnxn_pai
r
l
ist_se
t
_t to class Pairlis
t
Set
commit
|
commitdiff
|
tree
2019-03-20
B
e
rk Hess
Move ar
o
u
nd PairSearch c
o
de
commit
|
commitdiff
|
tree
next