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Fix GPU atom data init timer issue
2019-10-03
Berk Hess
Fix
G
PU atom dat
a
init
timer issue
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Use gmx::Range f
o
r iZo
n
es in pair
s
e
a
r
c
h
commit
|
commitdiff
|
tree
2019-10-03
Berk H
e
ss
Fix setting max
N
umColumns in Nbnxm::Gr
i
dSet
commit
|
commitdiff
|
tree
2019-10-02
Berk H
e
ss
F
ix harmless OpenMP wr
i
te
r
ace
commit
|
commitdiff
|
tree
2019-10-01
B
e
rk Hess
Use
g
mx::Range in domd
e
c
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Completel
y
remove charge gro
u
ps
commit
|
commitdiff
|
tree
2019-10-01
Ber
k
Hess
Simpli
f
y DD exclusio
n
countin
g
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Remo
v
e charge gro
u
p code f
r
om force
r
ec
commit
|
commitdiff
|
tree
2019-09-29
Berk Hess
Increase ti3p5 minimiz
a
t
i
on test tolerance
commit
|
commitdiff
|
tree
2019-09-28
B
erk Hess
Fix
CG min
i
m
i
zat
i
on wit
h
DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hes
s
Extract gmx::Range
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Fix
l
oca
t
ion of angle in vsite fig
u
re
commit
|
commitdiff
|
tree
2019-09-26
Be
r
k Hess
M
a
de
m
dr
u
n appending
work again
commit
|
commitdiff
|
tree
2019-09-24
B
erk Hess
Remove obs
o
l
e
te dd_ge
t
_ns_ranges()
commit
|
commitdiff
|
tree
2019-09-23
Berk
H
ess
Limit Zen nbnx
m
kernel choic
e
t
o Zen 1
commit
|
commitdiff
|
tree
2019-09-22
Be
r
k He
s
s
Rem
o
v
e cgs_gl from gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-21
Berk Hess
Fix incorrect s
h
ift forc
e
s for CMAP
commit
|
commitdiff
|
tree
2019-09-20
Berk He
s
s
Fix DD 1
p
u
l
se che
c
ks wit
h
out DL
B
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove b
L
ocalCG from DD c
o
d
e
commit
|
commitdiff
|
tree
2019-09-19
B
e
r
k Hess
Remov
e
o
b
solete
make_exclusions_zo
n
e_cg()
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remo
v
e charg
e
group data from t_forcerec
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Add
ha
v
eFreeEn
e
rgyWork to DomainLifetimeWo
r
kload flags
commit
|
commitdiff
|
tree
2019-09-18
Berk H
e
ss
Add
e
d free-ener
g
y ke
r
nel performance
n
o
t
e
commit
|
commitdiff
|
tree
2019-09-18
Berk He
s
s
F
ix incorrect DD ndim assertion
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Remove spur
i
ous
newli
n
e
f
rom
log fil
e
commit
|
commitdiff
|
tree
2019-09-17
B
e
rk Hes
s
F
i
x todos for upd
a
te g
r
oup
s
commit
|
commitdiff
|
tree
2019-09-16
Berk He
s
s
Remov
e
obsolet
e
mdp o
p
tion n
s
-
t
ype
commit
|
commitdiff
|
tree
2019-09-16
B
erk Hess
A
d
d virtu
a
l s
i
te type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
R
e
move c
u
t-off schemes from manual
commit
|
commitdiff
|
tree
2019-09-16
B
e
r
k
Hess
Add op
t
ion request 1
D
DD wit
h
1
p
ulse
commit
|
commitdiff
|
tree
2019-09-13
Berk
H
e
s
s
Fix
n
onbond
e
d-benc
h
compi
l
ation is
s
ue
commit
|
commitdiff
|
tree
2019-09-13
Berk He
s
s
Add
nbnxm kern
e
l
b
enchm
a
rk
t
ool
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Updated mdp
d
o
cumentation for group schem
e
r
e
m
oval
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Fix ma
s
t
er
n
o
t
compiling
commit
|
commitdiff
|
tree
2019-09-12
Berk H
e
ss
Enable TP
I
w
ith th
e
Verlet cut-off schem
e
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
R
emove
i
ncor
r
e
c
t ch
e
ck
with rf-z
e
ro
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Extract
Carte
s
ian data fr
o
m
D
DR
a
nkSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk He
s
s
R
e
n
ame DDSetup to DDGridSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk
H
ess
C
l
ean up PME
r
ank va
r
iable
s
commit
|
commitdiff
|
tree
2019-09-09
Berk H
e
ss
Refactor init_domai
n
_decomposition()
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Extra
c
t
g
ettin
g
of DD
R
ankSetup
commit
|
commitdiff
|
tree
2019-09-06
B
erk He
s
s
Add PP grid inf
o
to DDRankSetup
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Extra
c
t
D
DRank
S
etup from gmx
_
domdec_comm_
t
commit
|
commitdiff
|
tree
2019-09-05
Berk He
s
s
Split
o
ff getting
o
f
the DD setup
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
C
ollec
t
setting
s
fo
r
DD
i
n DDSettings
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Extract getting of
DDSyst
e
m
I
nfo
commit
|
commitdiff
|
tree
2019-09-04
Ber
k
Hess
Simplify handli
n
g of DD bonded d
i
stances
commit
|
commitdiff
|
tree
2019-09-04
Berk
H
e
s
s
Mov
e
co
n
straint and
bonded filterin
g
info into DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move update
grouping
t
o DDS
y
stemIn
f
o
commit
|
commitdiff
|
tree
2019-09-04
B
erk Hess
Change
DD pme force
b
u
f
fer
t
o std::vector
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Ini
t
ialize
a
l
l
m
emb
e
rs of
g
mx_domdec_t
commit
|
commitdiff
|
tree
2019-09-03
Ber
k
Hess
Extract DDSyste
m
Info from g
m
x
_
domd
e
c_co
m
m_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Unify
m
anua
l
and
auto DD grid choices
commit
|
commitdiff
|
tree
2019-09-03
Berk
Hess
Remove gmx
_
domdec_t
f
rom dd_choose_gr
i
d()
commit
|
commitdiff
|
tree
2019-09-03
B
e
rk Hess
Extact UnitCellInfo
f
rom gmx
_
domdec_t
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Fix in
c
o
r
rect rvdw
o
n GPU wi
t
h rv
d
w
<
r
c
o
u
lom
b
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Only us
e
f
shift when ne
e
de
d
commit
|
commitdiff
|
tree
2019-08-26
Berk He
s
s
Fi
x
gr
o
m
p
p
constraints=all-
a
ngles with co
n
strain
t
s
commit
|
commitdiff
|
tree
2019-08-22
Berk Hess
Fix
p
erturbed b
o
nded
bug
commit
|
commitdiff
|
tree
2019-08-20
B
e
r
k
He
s
s
Merge two dihedral functions
commit
|
commitdiff
|
tree
2019-08-20
Berk
Hess
Use shif
t
Forces
in ForceOuputs
commit
|
commitdiff
|
tree
2019-08-20
Berk
H
ess
M
a
k
e b
o
n
d
ed vir
i
a
l comp
u
tation condit
i
ona
l
commit
|
commitdiff
|
tree
2019-08-20
Ber
k
Hess
Fix missing
bonded
forces
with CUDA GPUs and DD
commit
|
commitdiff
|
tree
2019-08-15
B
er
k
Hess
Template
bonded in
t
era
c
tions on kernel flavor
commit
|
commitdiff
|
tree
2019-08-09
Berk Hes
s
Move
b
onded function
t
able int
o
bonded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
SIMD accel
e
r
ati
o
n fo
r
F
_FOURDIHS and F_P
I
DIHS
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
A
dd ForceWit
h
ShiftForces c
l
ass
commit
|
commitdiff
|
tree
2019-08-06
Berk
Hess
Fix latex formula in ref
e
rence manual
commit
|
commitdiff
|
tree
2019-08-05
B
erk Hess
Make box
c
onst in do_force()
commit
|
commitdiff
|
tree
2019-08-05
B
erk Hes
s
Change ForceOutputs to a class
commit
|
commitdiff
|
tree
2019-08-03
Be
r
k Hess
Remove
s
emicolon
from GP
U
T
E
RM
macros
commit
|
commitdiff
|
tree
2019-08-02
B
e
r
k Hess
Made g
m
x di
s
re
w
or
k
with
n
on-consecutively l
a
beled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Remove a
pointer i
n
t
_forcerec
commit
|
commitdiff
|
tree
2019-08-01
Be
r
k Hess
Fix nbnx
m
G
P
U memory reservation i
s
sue
commit
|
commitdiff
|
tree
2019-07-31
Berk
Hess
Remove unused
C
G
L
O_INITIALIZATION
commit
|
commitdiff
|
tree
2019-07-31
Berk
H
ess
Remove vc
m
r
e
moval
f
ro
m
comp
u
te_globals()
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Add grompp warning with
use
o
f
GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
R
emo
v
e
n
e
e
d
for G
R
O
M
OS FF in tes
t
commit
|
commitdiff
|
tree
2019-07-30
Berk H
e
ss
Us
e
invsqrt a
n
d
cbrt in f
r
ee
e
nergy k
e
r
nel
commit
|
commitdiff
|
tree
2019-07-29
Ber
k
Hess
Remove LJ
Ewald c
o
r
rection tables
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Add initializa
t
ion to t_nrnb
commit
|
commitdiff
|
tree
2019-07-29
Berk He
s
s
F
ix segment
a
t
i
on fau
l
t
w
ith cos
i
ne
pulling
commit
|
commitdiff
|
tree
2019-07-28
Be
r
k
Hess
Re
m
oved generalized re
a
ction-field
commit
|
commitdiff
|
tree
2019-07-28
B
e
rk H
e
ss
Conv
e
r
t
E
wald
c
orrection ta
b
les
t
o C++
commit
|
commitdiff
|
tree
2019-07-26
B
e
r
k Hess
Add default ini
t
i
a
lizat
i
o
n to int
e
raction_const_t
commit
|
commitdiff
|
tree
2019-07-26
Be
r
k Hess
Remove sh_invrc6 from interaction_co
n
st_t
commit
|
commitdiff
|
tree
2019-07-25
Ber
k
He
s
s
Split canDetec
t
Gpus()
commit
|
commitdiff
|
tree
2019-07-08
Berk Hess
Store nbnxm
g
ridSet data
in G
r
id
S
etDa
t
a
commit
|
commitdiff
|
tree
2019-07-05
Berk Hes
s
C
hange affinity enum
to e
n
um
c
lass
commit
|
commitdiff
|
tree
2019-07-02
B
e
rk Hess
Re
f
a
c
tor thread affinit
y
che
c
kin
g
commit
|
commitdiff
|
tree
2019-07-02
B
e
rk He
s
s
Re-e
n
able affinity diagonostic
s
with
M
PI
commit
|
commitdiff
|
tree
2019-07-01
Be
r
k
H
ess
Fix MPI
deadlock in
a
ffin
i
ty setting
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
T
e
m
plate fr
e
e
-
energy k
e
rnel o
n
dif
f
ering cou
l
/vdw soft
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Berk Hess
Remo
v
e
tabulation from free
-
energy kernel
commit
|
commitdiff
|
tree
2019-06-20
B
erk Hess
Remove unne
c
e
ssary #
i
f GMX_MP
I
in pme
c
od
e
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Template
f
ree-e
n
e
r
g
y
kernel
on soft-core
commit
|
commitdiff
|
tree
2019-06-19
B
e
rk Hes
s
Refactor
PME at
o
m
handling
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
R
e
m
o
ved unus
e
d code paths in the
NB FE kerne
l
commit
|
commitdiff
|
tree
2019-06-18
B
e
rk H
e
ss
Make forcer
e
c c
o
nst in dispatchNonbondedKernel()
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
Simplify
G
PU nbnxm x conver
s
ion
commit
|
commitdiff
|
tree
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