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Fix log file flag output
2019-09-24
Berk Hess
Remove obsolet
e
dd_get_ns_ra
n
ges()
commit
|
commitdiff
|
tree
2019-09-22
Berk Hess
Remov
e
cgs_gl from gmx_
d
omdec_co
m
m_t
commit
|
commitdiff
|
tree
2019-09-21
B
erk He
s
s
Fix inc
o
rrect
s
hift fo
r
ce
s
for
CMAP
commit
|
commitdiff
|
tree
2019-09-20
Be
r
k H
e
ss
Fix DD 1 pulse checks without DLB
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove bL
o
calCG from DD code
commit
|
commitdiff
|
tree
2019-09-19
Ber
k
H
e
ss
R
e
move ob
s
o
l
et
e
m
ake_ex
c
lusi
o
ns_
z
one_cg()
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove ch
a
r
ge group data from t_forcerec
commit
|
commitdiff
|
tree
2019-09-19
Be
r
k
Hess
A
dd haveFr
e
e
EnergyWo
r
k to
D
omainLifetime
W
orkload flags
commit
|
commitdiff
|
tree
2019-09-18
B
erk Hess
A
d
de
d
free-energy ke
r
ne
l
performa
n
c
e
n
ote
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fix incorrect
D
D n
d
im as
s
ertion
commit
|
commitdiff
|
tree
2019-09-17
B
e
rk H
e
ss
Re
m
o
ve spurious n
e
wline
from log
file
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Fix to
d
os for update
groups
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
R
e
move obsolete mdp option n
s
-t
y
pe
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add virtual site type 2FD
commit
|
commitdiff
|
tree
2019-09-16
B
er
k
Hess
Remove cut-off
s
chemes from ma
n
u
a
l
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add opti
o
n r
e
quest 1D DD
w
i
th 1 pulse
commit
|
commitdiff
|
tree
2019-09-13
Berk
He
s
s
F
i
x nonbonded-bench compila
t
ion
issue
commit
|
commitdiff
|
tree
2019-09-13
Berk H
e
ss
Add nbnxm
kernel
be
n
chmark too
l
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Updated mdp document
a
tion for group schem
e
removal
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Fix master not compiling
commit
|
commitdiff
|
tree
2019-09-12
Berk
H
ess
Enable TP
I
w
i
th the Verlet cut-of
f
schem
e
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
R
e
move
inc
o
rrect check wi
t
h rf-zero
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
E
x
t
ract Carte
s
ian
d
ata from DDRankSetup
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
Hess
Rename DDSetup to DDGrid
S
etup
commit
|
commitdiff
|
tree
2019-09-09
Berk
H
ess
Clean up PME ran
k
v
a
riables
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Refact
o
r init_domain
_
decomposition()
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Ex
t
r
a
ct getting of DDR
a
nkSetup
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Add PP grid i
n
fo to D
D
RankSe
t
up
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Ex
t
ract
D
DRa
n
k
Setup from gm
x
_domd
e
c_comm_t
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Spl
i
t off g
e
tting of the DD setup
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Collect
settings for D
D
in D
D
S
e
tting
s
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
E
xt
r
act getting
o
f D
D
SystemInfo
commit
|
commitdiff
|
tree
2019-09-04
B
erk
Hess
S
i
mpl
i
f
y h
a
ndling of DD bon
d
ed distances
commit
|
commitdiff
|
tree
2019-09-04
B
erk H
e
ss
Move constra
i
n
t and bon
d
ed filtering info into D
D
Sy
s
te
m
Info
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hess
Move upda
t
e
grouping to
D
DSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Change DD p
m
e
f
orce buffer to std::
v
ector
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Initialize all membe
r
s of gmx_
d
omdec_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Extract DDSyst
e
m
I
nfo
from gmx_domdec_comm_
t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Unify manual an
d
auto D
D
g
r
id
c
hoices
commit
|
commitdiff
|
tree
2019-09-03
Berk Hes
s
R
emove gmx_domdec_t
f
rom dd_choos
e
_
g
r
id()
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Extact UnitCellInfo from
g
mx_domd
e
c_t
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Fix incorr
e
ct rvdw on GPU with rvdw<rcoulomb
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
O
n
l
y use fshift
w
hen
n
eeded
commit
|
commitdiff
|
tree
2019-08-26
Berk Hess
Fix g
r
ompp c
o
nstraints=
a
ll
-
a
n
gle
s
wit
h
c
o
nstr
a
ints
commit
|
commitdiff
|
tree
2019-08-22
Berk
H
e
ss
Fix perturbed
b
onded bug
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Merge
t
w
o dih
e
dral function
s
commit
|
commitdiff
|
tree
2019-08-20
Ber
k
Hess
Use shiftForces in ForceO
u
puts
commit
|
commitdiff
|
tree
2019-08-20
Ber
k
He
s
s
Make bonded v
i
rial c
o
m
p
utation conditional
commit
|
commitdiff
|
tree
2019-08-20
Berk Hes
s
Fix missing
b
o
nd
e
d
f
o
rce
s
with
C
U
DA GPUs an
d
DD
commit
|
commitdiff
|
tree
2019-08-15
Berk Hess
Template bond
e
d interactions
o
n
k
ernel
flav
o
r
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
Move
b
o
nded func
t
ion tab
l
e into bon
d
ed
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
Ber
k
He
s
s
SIMD accel
e
r
ation for F_FOURDIHS and F_PI
D
IHS
commit
|
commitdiff
|
tree
2019-08-06
Ber
k
Hes
s
Add ForceWithShiftForces cl
a
ss
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
Fix latex
f
or
m
ula
in
r
eference manua
l
commit
|
commitdiff
|
tree
2019-08-05
Berk H
e
ss
Make
b
ox const in do_force()
commit
|
commitdiff
|
tree
2019-08-05
Berk
He
s
s
Change
F
or
c
e
Outputs t
o
a class
commit
|
commitdiff
|
tree
2019-08-03
B
e
rk Hess
Remove
semicolon from GPU T
E
RM macros
commit
|
commitdiff
|
tree
2019-08-02
Berk Hess
Made gmx disre work with
n
on-co
n
s
ecu
t
ivel
y
l
a
beled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Remove a pointer
in t_f
o
rcerec
commit
|
commitdiff
|
tree
2019-08-01
B
e
rk
Hess
F
ix nbnxm G
P
U
memo
r
y
r
eservation
i
s
s
u
e
commit
|
commitdiff
|
tree
2019-07-31
B
e
rk
H
e
ss
Remove unused CGLO_INITIALIZATION
commit
|
commitdiff
|
tree
2019-07-31
Berk
Hess
Remove vcm removal from compute_globals()
commit
|
commitdiff
|
tree
2019-07-31
B
e
rk Hes
s
Add
grompp w
a
rning with use of
G
R
O
MOS
FF
commit
|
commitdiff
|
tree
2019-07-31
Be
r
k
Hess
Remove ne
e
d for GROMOS FF in test
commit
|
commitdiff
|
tree
2019-07-30
Berk
H
e
s
s
Use in
v
s
q
r
t
a
n
d cbrt in free energy k
e
r
n
e
l
commit
|
commitdiff
|
tree
2019-07-29
Berk He
s
s
Remove LJ Ewa
l
d correcti
o
n tables
commit
|
commitdiff
|
tree
2019-07-29
B
erk
He
s
s
Add initial
i
zati
o
n to t_nrnb
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Fi
x
segmentation fault with co
s
ine pulling
commit
|
commitdiff
|
tree
2019-07-28
Berk Hes
s
R
emoved genera
l
ized reaction-field
commit
|
commitdiff
|
tree
2019-07-28
B
e
rk Hess
Convert Ewald c
o
rr
e
ction tables to C++
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
Add defa
u
lt initialization
to interaction_const_t
commit
|
commitdiff
|
tree
2019-07-26
Berk Hes
s
Remove sh
_
inv
r
c6 from interac
t
i
o
n_const_t
commit
|
commitdiff
|
tree
2019-07-25
Ber
k
Hess
Split c
a
nDet
e
ctG
p
us()
commit
|
commitdiff
|
tree
2019-07-08
Berk Hess
Store nbnxm gridSet dat
a
in Gri
d
SetData
commit
|
commitdiff
|
tree
2019-07-05
Berk Hess
C
hang
e
affin
i
ty enum to
enum class
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Refactor thread
a
f
f
i
nity
c
he
c
k
i
n
g
commit
|
commitdiff
|
tree
2019-07-02
Berk
H
ess
R
e-
e
nable
a
f
f
inity diagon
o
stics
wi
t
h MPI
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Fix M
P
I deadlock
in af
f
inity setting
commit
|
commitdiff
|
tree
2019-07-01
Berk He
s
s
T
emplate free-energy
k
ernel o
n
differin
g
coul/vd
w
soft
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
B
erk Hess
Remove tabu
l
ation
from free-energ
y
k
ernel
commit
|
commitdiff
|
tree
2019-06-20
Berk Hes
s
R
emove unnecessary #i
f
GMX_MPI in
pme code
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Template free-en
e
rgy ke
r
nel on soft-core
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Refa
c
tor P
M
E a
t
o
m
handling
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Removed unused code p
a
ths in the NB FE kernel
commit
|
commitdiff
|
tree
2019-06-18
Berk
H
e
s
s
Make forcerec const in d
i
spat
c
hN
o
nbondedKernel()
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
S
implif
y
G
P
U nbnxm x
conversion
commit
|
commitdiff
|
tree
2019-06-17
Berk H
e
ss
Re
m
ove unused nbnxm in
c
lud
e
files
commit
|
commitdiff
|
tree
2019-06-11
Ber
k
Hess
Allow AWH geome
t
ry 'd
i
rection' to be periodic
commit
|
commitdiff
|
tree
2019-06-10
Berk Hess
F
i
x gmx
wha
m
wi
t
h angle geometrie
s
commit
|
commitdiff
|
tree
2019-06-05
B
e
rk Hess
F
i
x refer
e
nce SIMD me
m
ory alignment
commit
|
commitdiff
|
tree
2019-05-29
B
e
r
k Hess
Fix missing
intermolec
u
lar
int
e
ract
i
on
s
w
ith DD
commit
|
commitdiff
|
tree
2019-05-27
Be
r
k Hess
Work aro
u
nd gcc 7 avx
5
1
2
bug
commit
|
commitdiff
|
tree
2019-05-23
Ber
k
H
e
s
s
F
i
x SHAKE dH/dlambda contri
b
utions
commit
|
commitdiff
|
tree
2019-05-14
B
e
rk Hess
Make all do_force
_
lowle
v
el()
i
n
p
u
t
const
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
Corre
c
t user guid
e
p
ostion restrain
t
v
irial
commit
|
commitdiff
|
tree
2019-05-04
Berk He
s
s
Re
m
ove PME exclusion corr
e
ction
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Rem
o
ved
non-existent
A
W
H
m
d
p o
p
tion
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Co
n
vert m
a
nage_threading_t and g
m
x_ener
d
ata_t to C++
commit
|
commitdiff
|
tree
2019-05-02
Ber
k
Hess
Change nbnxm FEP pointer to unique
_
ptr
commit
|
commitdiff
|
tree
2019-04-30
B
e
rk Hess
A
d
d con/de
s
truct
o
r fo
r
t_for
c
etable
commit
|
commitdiff
|
tree
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