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Use gmx::Range in domdec
2019-10-01
Berk Hess
Use
g
mx::Rang
e
in domdec
commit
|
commitdiff
|
tree
2019-10-01
B
e
r
k
Hess
Com
p
l
etely remove ch
a
rge groups
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Simpli
f
y DD exclusion coun
t
i
n
g
commit
|
commitdiff
|
tree
2019-09-30
Ber
k
He
s
s
Remove charg
e
grou
p
c
o
de from forcerec
commit
|
commitdiff
|
tree
2019-09-29
Berk Hess
Increase ti
3
p
5 minimization test tolerance
commit
|
commitdiff
|
tree
2019-09-28
Berk He
s
s
Fix CG minimization with
DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Extract gmx::R
a
nge
commit
|
commitdiff
|
tree
2019-09-27
Berk Hes
s
Fix loc
a
t
ion of
a
ngle
i
n vsite figure
commit
|
commitdiff
|
tree
2019-09-26
Berk
He
s
s
Made mdrun appending w
o
rk
a
ga
i
n
commit
|
commitdiff
|
tree
2019-09-24
Berk Hes
s
Remo
v
e obso
l
et
e
dd_get_ns_rang
e
s()
commit
|
commitdiff
|
tree
2019-09-23
Berk Hess
Li
m
i
t
Ze
n
nbnxm kernel choic
e
to Zen 1
commit
|
commitdiff
|
tree
2019-09-22
Berk
He
s
s
Remo
v
e cgs_gl f
r
om g
m
x_domdec_com
m
_t
commit
|
commitdiff
|
tree
2019-09-21
Berk
H
ess
Fi
x
i
n
correct shift forces for CMAP
commit
|
commitdiff
|
tree
2019-09-20
B
e
rk
Hess
F
ix DD 1 pulse checks
w
ithout DLB
commit
|
commitdiff
|
tree
2019-09-19
B
e
rk Hess
Remove bLocalCG from
D
D
c
od
e
commit
|
commitdiff
|
tree
2019-09-19
Ber
k
H
e
ss
R
em
o
ve obsolete make_exclusions_zo
n
e
_
cg()
commit
|
commitdiff
|
tree
2019-09-19
B
erk H
e
ss
Remove charge gro
u
p data fro
m
t_forcere
c
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Add haveFr
e
e
EnergyWork to Do
m
ainLif
e
timeWorkload
flags
commit
|
commitdiff
|
tree
2019-09-18
B
e
rk Hess
Added
free-
e
nergy
k
er
n
e
l performan
c
e note
commit
|
commitdiff
|
tree
2019-09-18
B
e
rk H
e
ss
Fix
i
ncorrect DD ndim a
s
sertion
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Re
m
o
ve
s
purio
u
s n
e
wline f
r
om log
f
ile
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Fix
t
odos for update group
s
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remove obsolete m
d
p
opt
i
o
n
ns-t
y
pe
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hess
Add
v
irtual site type 2FD
commit
|
commitdiff
|
tree
2019-09-16
B
erk Hess
R
e
move cut-off
sc
h
e
mes from manual
commit
|
commitdiff
|
tree
2019-09-16
B
e
rk Hess
A
dd
option request 1D DD with
1 pulse
commit
|
commitdiff
|
tree
2019-09-13
Berk
Hess
F
ix nonbonded-b
e
nch compilation issue
commit
|
commitdiff
|
tree
2019-09-13
Berk Hess
Add nbnxm ke
r
n
e
l benchmark too
l
commit
|
commitdiff
|
tree
2019-09-12
Berk
H
e
ss
Updated md
p
docume
n
tation for group scheme removal
commit
|
commitdiff
|
tree
2019-09-12
Ber
k
Hess
Fix master not comp
i
li
n
g
commit
|
commitdiff
|
tree
2019-09-12
Berk He
s
s
Enable TPI with
the
V
erlet cut-o
f
f scheme
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
R
e
m
ove incorrect check with rf-zero
commit
|
commitdiff
|
tree
2019-09-09
B
erk He
s
s
E
xtract
C
artesian data from DDRank
S
etup
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Rename DDSetup to
D
DGri
d
S
etu
p
commit
|
commitdiff
|
tree
2019-09-09
Berk
Hess
Clean up PME rank variables
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
H
e
ss
Re
f
actor init
_
domain_decomposit
i
on()
commit
|
commitdiff
|
tree
2019-09-06
B
erk Hess
Extrac
t
g
etting
o
f
DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
Berk H
e
ss
Add PP g
r
id info to DD
R
ank
S
etup
commit
|
commitdiff
|
tree
2019-09-05
Be
r
k
Hess
Ext
r
act DDRan
k
Setup from gmx_domdec_comm_
t
commit
|
commitdiff
|
tree
2019-09-05
Be
r
k H
e
ss
Split off
g
e
tting of the DD
setup
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Collect
settings for DD in DDSett
i
ngs
commit
|
commitdiff
|
tree
2019-09-04
Berk H
e
ss
Ex
t
ract get
t
ing
of DDSystem
I
nfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Simplify handlin
g
of DD
b
onded di
s
tances
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k
Hess
Move cons
t
raint and bonded f
i
ltering i
n
fo into DDSystem
I
nfo
commit
|
commitdiff
|
tree
2019-09-04
Berk He
s
s
Move update gr
o
uping to DDSyst
e
mInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk H
e
ss
Change
D
D pme force b
u
ffer
t
o std::v
e
ctor
commit
|
commitdiff
|
tree
2019-09-04
Berk
H
ess
Initialize all membe
r
s
of gmx_domde
c
_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hes
s
Extr
a
c
t DDSystemInfo from
gmx_d
o
m
d
ec_comm_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Unify
m
a
nual and auto DD gri
d
choices
commit
|
commitdiff
|
tree
2019-09-03
B
e
rk
H
e
ss
Remove
g
mx
_
domdec_t fr
o
m dd
_
cho
o
se_
g
rid()
commit
|
commitdiff
|
tree
2019-09-03
Berk
Hess
E
x
t
act UnitC
e
llIn
f
o
f
r
om gmx_domde
c
_t
commit
|
commitdiff
|
tree
2019-09-02
Ber
k
H
e
s
s
Fix
incorrect rvdw on G
P
U with rv
d
w<
r
coulomb
commit
|
commitdiff
|
tree
2019-09-02
Be
r
k
Hess
O
n
ly
u
se fshift wh
e
n
needed
commit
|
commitdiff
|
tree
2019-08-26
Berk H
e
ss
Fi
x
grompp constr
a
int
s
=all-angles with co
n
strai
n
ts
commit
|
commitdiff
|
tree
2019-08-22
Berk Hess
F
ix perturbed bonded bug
commit
|
commitdiff
|
tree
2019-08-20
Be
r
k Hess
M
e
r
g
e
t
w
o dihedral functio
n
s
commit
|
commitdiff
|
tree
2019-08-20
Be
r
k Hess
Use s
h
iftFor
c
e
s
i
n
F
o
rceOu
p
uts
commit
|
commitdiff
|
tree
2019-08-20
B
e
rk Hess
Make
bonded
viri
a
l computation condi
t
i
onal
commit
|
commitdiff
|
tree
2019-08-20
B
e
rk Hess
Fix missing bo
n
ded f
o
r
c
es w
i
th CUDA GPUs and DD
commit
|
commitdiff
|
tree
2019-08-15
Berk Hess
Templ
a
te b
o
n
d
ed interactions on kernel flavor
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
Mov
e
b
o
nded
f
unction tabl
e
into bonded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
Ber
k
Hess
S
I
MD acceleratio
n
for F_FOURDIHS an
d
F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-06
Berk H
e
ss
Ad
d
Fo
r
ceWithShi
f
tForces cl
a
ss
commit
|
commitdiff
|
tree
2019-08-06
Be
r
k Hess
Fix l
a
tex fo
r
m
ula in
r
efe
r
enc
e
manual
commit
|
commitdiff
|
tree
2019-08-05
Berk H
e
ss
Make box cons
t
in
d
o_for
c
e()
commit
|
commitdiff
|
tree
2019-08-05
Berk Hess
Change
F
orceOutp
u
ts t
o
a class
commit
|
commitdiff
|
tree
2019-08-03
Be
r
k He
s
s
Remove
semicolon fr
o
m GPU T
E
RM
macros
commit
|
commitdiff
|
tree
2019-08-02
Berk Hess
Made gmx disre wo
r
k with non-consecut
i
vely labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk He
s
s
R
e
move a pointer
in t_forcerec
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Fix nbnxm GPU me
m
ory re
s
ervation issue
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Remove unused CGLO_IN
I
TIALIZATIO
N
commit
|
commitdiff
|
tree
2019-07-31
Ber
k
Hess
Re
m
ove vcm removal from com
p
ute_
g
l
o
bals()
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Add grompp war
n
i
ng wit
h
u
se of GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Berk
Hess
R
emove need for GROMOS FF in
test
commit
|
commitdiff
|
tree
2019-07-30
Berk Hess
Use in
v
sqr
t
and cbrt in free
e
nergy kernel
commit
|
commitdiff
|
tree
2019-07-29
Ber
k
Hess
Remove LJ Ewald correction tables
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Add
initialization to t_n
r
nb
commit
|
commitdiff
|
tree
2019-07-29
Be
r
k Hess
Fix
s
egmentation fault with cosine pulling
commit
|
commitdiff
|
tree
2019-07-28
Berk
Hess
Rem
o
ved
generaliz
e
d re
a
cti
o
n-field
commit
|
commitdiff
|
tree
2019-07-28
Berk Hess
Con
v
ert Ewald corr
e
ctio
n
t
ab
l
e
s to
C
++
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
A
d
d default initialization to interaction_cons
t
_t
commit
|
commitdiff
|
tree
2019-07-26
Berk H
e
ss
Remove sh_
i
nvrc6 from
i
n
t
e
raction_const_t
commit
|
commitdiff
|
tree
2019-07-25
Berk Hes
s
Split canDetectGpus
(
)
commit
|
commitdiff
|
tree
2019-07-08
Berk He
s
s
Stor
e
nbnxm
g
ridSet
d
at
a
in GridSetD
a
ta
commit
|
commitdiff
|
tree
2019-07-05
Berk
H
ess
C
h
a
nge affinity enu
m
to enum class
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Refac
t
or
t
hr
e
ad
a
f
fini
t
y checking
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Re-enable
affinit
y
diagonosti
c
s
with MPI
commit
|
commitdiff
|
tree
2019-07-01
Berk
H
ess
F
ix
M
P
I deadloc
k
in aff
i
n
i
t
y setting
commit
|
commitdiff
|
tree
2019-07-01
Berk He
s
s
Template
f
ree-en
e
rgy
k
ernel on differing
c
o
u
l
/vdw
s
oft
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Berk
H
ess
Remo
v
e tabulation f
r
om free-e
n
ergy kernel
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
R
e
mov
e
u
n
ne
c
essary #if
G
MX_MPI
in p
m
e code
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
T
empla
t
e
f
ree-
e
nergy kernel on soft-
c
ore
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Re
f
act
o
r PME at
o
m handlin
g
commit
|
commitdiff
|
tree
2019-06-19
Berk H
e
s
s
R
emoved
u
nused
code pat
h
s
in the
N
B F
E
k
e
rnel
commit
|
commitdiff
|
tree
2019-06-18
Berk Hess
Make
forcere
c
const in dispatchNonbonded
K
ernel()
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
Simplify GPU nbnxm x conversion
commit
|
commitdiff
|
tree
2019-06-17
Berk
Hess
Remov
e
unused
n
bnxm
include files
commit
|
commitdiff
|
tree
2019-06-11
Berk Hess
Allow
A
W
H
geomet
r
y 'dire
c
tion' to b
e
periodic
commit
|
commitdiff
|
tree
2019-06-10
Berk Hess
Fix gmx wha
m
wi
t
h angle ge
o
metries
commit
|
commitdiff
|
tree
2019-06-05
Be
r
k
H
e
ss
Fix refere
n
ce SIMD
memo
r
y alignme
n
t
commit
|
commitdiff
|
tree
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