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Fix CG minimization with DD
2019-09-28
Be
r
k Hess
F
ix CG
minimiz
a
tion with DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Extract g
m
x::Range
commit
|
commitdiff
|
tree
2019-09-27
Berk Hes
s
Fix
loca
t
ion
o
f angle
in
vsite figure
commit
|
commitdiff
|
tree
2019-09-26
Berk Hess
Made
mdrun appending work ag
a
i
n
commit
|
commitdiff
|
tree
2019-09-24
Berk H
e
ss
Remove ob
s
ole
t
e dd_get_ns_ra
n
ges()
commit
|
commitdiff
|
tree
2019-09-23
Berk Hess
L
i
mit
Z
en nbnxm kernel choice
to Zen 1
commit
|
commitdiff
|
tree
2019-09-22
Berk Hess
Remove cgs_gl fro
m
gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-21
Berk
H
ess
Fix incorrect shift forces f
o
r CMAP
commit
|
commitdiff
|
tree
2019-09-20
Berk
H
ess
Fix
DD 1 pul
s
e
checks w
i
thout
D
LB
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Rem
o
ve bLoca
l
CG from DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
R
e
move obsolete
m
ake_exclusions_
z
o
ne_cg()
commit
|
commitdiff
|
tree
2019-09-19
Ber
k
Hess
Rem
o
ve charge
g
rou
p
data from
t
_
f
orcerec
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
A
dd haveFr
e
eE
n
ergyWork to
DomainLi
f
e
timeWorkload flags
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Added free-energy kerne
l
performance note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
F
ix
i
n
c
orrect D
D
ndim
a
s
se
r
t
ion
commit
|
commitdiff
|
tree
2019-09-17
B
erk Hess
Remo
v
e spurious newline
from log file
commit
|
commitdiff
|
tree
2019-09-17
B
erk Hess
Fix todos for
u
pdate gr
o
ups
commit
|
commitdiff
|
tree
2019-09-16
Ber
k
Hess
Remove obsolet
e
m
d
p
op
t
i
on n
s
-type
commit
|
commitdiff
|
tree
2019-09-16
Berk
H
ess
A
dd virtual sit
e
t
ype 2FD
commit
|
commitdiff
|
tree
2019-09-16
Berk H
e
ss
Remove cut-o
f
f sc
h
emes from manual
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add opti
o
n request
1
D DD with
1
p
ulse
commit
|
commitdiff
|
tree
2019-09-13
Berk Hes
s
Fi
x
nonbonded-be
n
ch compila
t
ion issue
commit
|
commitdiff
|
tree
2019-09-13
Ber
k
He
s
s
Add nbnxm ker
n
el
benchmark t
o
ol
commit
|
commitdiff
|
tree
2019-09-12
B
e
rk
H
e
s
s
Updated md
p
d
ocumenta
t
ion for group
s
cheme removal
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Fix mast
e
r not compiling
commit
|
commitdiff
|
tree
2019-09-12
Berk He
s
s
E
nable
T
PI wit
h
the Verlet
cut-off scheme
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Remove incorrect check with
r
f-zer
o
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Ex
t
r
act
Cartesian dat
a
fro
m
DDRankSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Rename DDSetup to
DDGridSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk
H
ess
Clean up
PM
E
rank
va
r
iables
commit
|
commitdiff
|
tree
2019-09-09
B
erk Hess
Refac
t
o
r
in
i
t_domain_decomposition()
commit
|
commitdiff
|
tree
2019-09-06
Be
r
k H
e
ss
Extrac
t
get
t
ing of DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
Ber
k
Hess
Add PP grid in
f
o to DDRankSetup
commit
|
commitdiff
|
tree
2019-09-05
Ber
k
Hess
Extrac
t
DDRankSetup fro
m
g
m
x
_
domdec
_
c
o
mm_t
commit
|
commitdiff
|
tree
2019-09-05
Ber
k
Hess
Sp
l
i
t
off
g
etting of the DD
s
e
t
u
p
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Collec
t
s
e
ttings
f
o
r DD
in DDSett
i
ngs
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
E
x
t
r
act gettin
g
of D
D
SystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Berk
He
s
s
Simplify
handling of DD bonde
d
distances
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Mo
v
e
con
s
t
r
aint and bon
d
ed filteri
n
g in
f
o
into DD
S
y
s
temI
n
fo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Move update grouping to DDSyst
e
mIn
f
o
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
C
h
ange D
D
pme force
b
uffer t
o
std::vect
o
r
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Initialize all members of gmx_d
o
mdec_t
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Extract DDSystemInfo from gmx_domdec_c
o
mm_t
commit
|
commitdiff
|
tree
2019-09-03
Berk H
e
s
s
Unify manual
a
nd
a
u
to DD grid choices
commit
|
commitdiff
|
tree
2019-09-03
Berk
Hess
Remove g
m
x
_domdec_t from dd_choo
s
e_grid()
commit
|
commitdiff
|
tree
2019-09-03
Be
r
k He
s
s
E
x
tac
t
UnitC
e
llInfo f
r
om gmx_d
o
mdec_t
commit
|
commitdiff
|
tree
2019-09-02
B
erk
H
ess
F
i
x
inc
o
rrect rvd
w
on
GPU wi
t
h rvd
w
<rcoulomb
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Only us
e
f
shift when needed
commit
|
commitdiff
|
tree
2019-08-26
Ber
k
Hess
Fix
grompp
c
onstraints=a
l
l-angles with const
r
aints
commit
|
commitdiff
|
tree
2019-08-22
Berk
H
e
ss
Fi
x
perturbed bonded bug
commit
|
commitdiff
|
tree
2019-08-20
Berk
Hess
Me
r
ge two dihe
d
r
a
l fu
n
ctions
commit
|
commitdiff
|
tree
2019-08-20
B
erk Hess
Use shiftForces in ForceOuputs
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Make bonded
v
i
r
ial computation
c
ondition
a
l
commit
|
commitdiff
|
tree
2019-08-20
Berk H
e
ss
Fix missing bonded f
o
rces
w
ith C
U
DA GPUs an
d
DD
commit
|
commitdiff
|
tree
2019-08-15
Berk Hess
Templat
e
bo
n
d
ed interactio
n
s on kernel flavor
commit
|
commitdiff
|
tree
2019-08-09
Ber
k
Hess
Mov
e
b
o
nded function
t
ab
l
e into bon
d
e
d
.
c
pp
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
S
I
MD acceleration for
F
_FOURDIHS
a
nd
F
_PIDIHS
commit
|
commitdiff
|
tree
2019-08-06
B
e
rk Hess
Add
ForceWi
t
hShif
t
Forces c
l
ass
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
Fix lat
e
x formula in reference manual
commit
|
commitdiff
|
tree
2019-08-05
Be
r
k
H
ess
Make box const
in
do_force()
commit
|
commitdiff
|
tree
2019-08-05
B
erk Hess
Ch
a
n
ge Forc
e
Outputs to a c
l
ass
commit
|
commitdiff
|
tree
2019-08-03
Berk Hess
Remov
e
se
m
i
c
olon fro
m
GPU TERM macros
commit
|
commitdiff
|
tree
2019-08-02
Ber
k
H
es
s
Made gmx dis
r
e work
with no
n
-consecuti
v
e
ly labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk He
s
s
Remo
v
e a poin
t
e
r
in t_f
o
r
cerec
commit
|
commitdiff
|
tree
2019-08-01
Berk
Hess
Fix nb
n
xm GPU
m
emory res
e
rvation
i
ss
u
e
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Remove unused CGLO_INITI
A
LI
Z
A
TION
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
R
emove vcm
r
emoval from compute_globa
l
s(
)
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Add grompp
warning w
i
th use
o
f GR
O
MO
S
FF
commit
|
commitdiff
|
tree
2019-07-31
Ber
k
Hess
Remove n
e
ed for GROMOS FF in test
commit
|
commitdiff
|
tree
2019-07-30
Berk Hess
Use invsqrt and cbrt in free
energ
y
kernel
commit
|
commitdiff
|
tree
2019-07-29
Ber
k
Hess
R
emove LJ Ew
a
l
d
corre
c
t
i
on
t
ables
commit
|
commitdiff
|
tree
2019-07-29
Berk Hes
s
Add in
i
tialization to t_n
r
nb
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Fix segmentat
i
on fault
w
i
t
h cosine
p
ulling
commit
|
commitdiff
|
tree
2019-07-28
Be
r
k
Hess
Re
m
ove
d
g
e
neralized reaction-f
i
e
l
d
commit
|
commitdiff
|
tree
2019-07-28
Ber
k
Hess
Conve
r
t Ewald correct
i
o
n
t
a
bles to C++
commit
|
commitdiff
|
tree
2019-07-26
B
erk H
e
s
s
Add default initial
i
zation to
interac
t
i
on_c
o
ns
t
_t
commit
|
commitdiff
|
tree
2019-07-26
Berk
Hess
Rem
o
ve sh_invrc6 f
r
om interact
i
on_const_t
commit
|
commitdiff
|
tree
2019-07-25
Berk Hess
Split
c
anDetectGpus()
commit
|
commitdiff
|
tree
2019-07-08
B
e
rk He
s
s
Store n
b
nxm gridSet
dat
a
in
G
ridSetData
commit
|
commitdiff
|
tree
2019-07-05
B
e
rk Hess
Change affini
t
y enum to enum
c
lass
commit
|
commitdiff
|
tree
2019-07-02
Berk He
s
s
Refa
c
tor
t
hr
e
ad
a
ffinity
checking
commit
|
commitdiff
|
tree
2019-07-02
Berk
H
e
ss
Re-enabl
e
a
ffini
t
y dia
g
onostics with
M
PI
commit
|
commitdiff
|
tree
2019-07-01
Berk
H
es
s
Fix MPI
deadlock in a
f
fin
i
ty s
e
t
t
ing
commit
|
commitdiff
|
tree
2019-07-01
Be
r
k
Hess
Template free-
e
nergy kernel on di
f
f
e
ring coul/vd
w
soft
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Berk
Hess
Remov
e
tabulation from free-en
e
rgy ker
n
el
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Remove u
n
n
ecessary #i
f
GMX_MPI in pme code
commit
|
commitdiff
|
tree
2019-06-20
Berk H
e
ss
Template fr
e
e
-energy k
e
rnel on s
o
f
t-core
commit
|
commitdiff
|
tree
2019-06-19
Berk He
s
s
R
e
fac
t
o
r PME atom handling
commit
|
commitdiff
|
tree
2019-06-19
B
erk Hes
s
R
e
m
o
ved unuse
d
code paths in the NB
F
E kernel
commit
|
commitdiff
|
tree
2019-06-18
Berk He
s
s
Make forcerec
c
onst in
dispatc
h
N
onb
o
ndedKe
r
nel
(
)
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
S
impli
f
y GPU nbnxm x conversion
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
R
emove
u
nus
e
d nbn
x
m i
n
clude
files
commit
|
commitdiff
|
tree
2019-06-11
Berk Hess
A
llow A
W
H
geom
e
try 'direct
i
on'
t
o be p
e
ri
o
d
i
c
commit
|
commitdiff
|
tree
2019-06-10
Berk Hess
Fix gmx wham with angle geometri
e
s
commit
|
commitdiff
|
tree
2019-06-05
Berk Hess
Fix ref
e
rence SIMD mem
o
ry al
i
gnm
e
nt
commit
|
commitdiff
|
tree
2019-05-29
Berk Hess
Fix missing intermolecul
a
r inte
r
actions w
i
th
D
D
commit
|
commitdiff
|
tree
2019-05-27
Berk
H
ess
Work arou
n
d
g
c
c 7 av
x
5
12 bug
commit
|
commitdiff
|
tree
2019-05-23
Berk H
e
ss
Fix SH
A
KE dH
/
dla
m
bda cont
r
ibutions
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
Make
all do_force_
l
o
w
level(
)
input const
commit
|
commitdiff
|
tree
2019-05-14
Ber
k
H
ess
C
o
rrect user
guide post
i
on restraint v
i
ria
l
commit
|
commitdiff
|
tree
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