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Moved pull params to mdtypes/pull-params.h
2014-11-12
Berk Hess
Corrected para
m
eter for
s
orting o
n
sear
c
h grid
commit
|
commitdiff
|
tree
2014-11-12
Berk H
e
ss
F
ix DD bon
d
ed i
n
ter
a
ction range print
commit
|
commitdiff
|
tree
2014-10-20
Berk Hess
Removed f_n
o
virsum reduc
t
ion in
V
erl
e
t scheme
commit
|
commitdiff
|
tree
2014-10-07
Berk H
e
ss
Fixes issue with vsiten a
n
d V
e
rlet
buffers
commit
|
commitdiff
|
tree
2014-09-30
B
e
rk Hess
Avoid DLB wi
t
h o
v
e
r
loade
d
P
M
E ranks
commit
|
commitdiff
|
tree
2014-09-30
Berk
He
s
s
A
d
d
e
d
GPU
local wait to load balancing
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
Domain decomposition n
o
w ch
e
c
k
s the rlist buffer
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
SIMD accel
e
ration
for RB dihe
d
rals
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
Avoid P
M
E tuning
dec
r
easing rcoulomb
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
Fix calc
_
grid avoiding PME g
r
i
d
fa
c
tor 84
commit
|
commitdiff
|
tree
2014-09-09
Berk Hess
Fixed DD state collec
t
ion
issue
commit
|
commitdiff
|
tree
2014-09-08
Berk Hes
s
Check for implici
t
solvent + Verlet sch
e
me
commit
|
commitdiff
|
tree
2014-08-28
B
e
r
k
Hess
Fixed
t
wo PME issues w
i
t
h MPI+Open
M
P
commit
|
commitdiff
|
tree
2014-08-25
Berk
H
ess
Fixed bugs i
n
vsite
N
w
i
th OpenMP
commit
|
commitdiff
|
tree
2014-08-24
B
e
rk Hess
Initia
l
i
ze unused velo
c
ity constraint c
o
mponen
t
s
commit
|
commitdiff
|
tree
2014-08-17
Berk Hess
Halved the cost of
the
p
ull communic
a
t
ion
commit
|
commitdiff
|
tree
2014-08-14
Berk He
s
s
Corrected SI
M
D math overflow do
c
umentation
commit
|
commitdiff
|
tree
2014-08-10
Be
r
k Hess
Added checks for TPI +
Verlet scheme
commit
|
commitdiff
|
tree
2014-08-05
Be
r
k
H
ess
Fix han
g
with LJ-PME and empty domains
commit
|
commitdiff
|
tree
2014-08-02
B
e
rk Hess
Fi
x
ed PME
bu
g
with h
i
gh OpenMP th
r
ead
count
commit
|
commitdiff
|
tree
2014-07-31
B
erk Hess
Avoid divis
i
on by 0
i
n
nbn
x
n
_
sear
c
h
commit
|
commitdiff
|
tree
2014-06-29
B
erk Hess
Take
L
J-PME into account for table spacing
commit
|
commitdiff
|
tree
2014-06-29
B
e
rk
Hess
Updated
L
J
-
PME d
o
cumentati
o
n
commit
|
commitdiff
|
tree
2014-06-24
Berk Hess
Fixed the sig
n
o
f mass perturbed
c
ontributio
n
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
Fix g_mindist with pbc=XY
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
Fixed shells with particle decomposition
commit
|
commitdiff
|
tree
2014-06-18
Berk Hess
F
i
xed sign e
r
ro
r
in po
s
r
e
s dvdl
commit
|
commitdiff
|
tree
2014-06-17
Berk Hess
Updated mdr
u
n -npme docu
m
e
n
t
ation
commit
|
commitdiff
|
tree
2014-06-17
Be
r
k
Hess
Removed rounding issue in nbnxn Ewald table
commit
|
commitdiff
|
tree
2014-06-14
Ber
k
Hess
Fixed
PME
bug wit
h
#Open
M
P
-
thre
a
d
s
a large pr
i
me
commit
|
commitdiff
|
tree
2014-06-13
B
e
rk He
s
s
Ch
a
n
g
ed appending file name
error message
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
Made shells work with t
h
e Verlet scheme
commit
|
commitdiff
|
tree
2014-06-12
Berk Hess
Fixed
p
erturbed wall
inte
r
ac
t
ions
commit
|
commitdiff
|
tree
2014-06-12
B
e
r
k He
s
s
Made gmxcheck -
r
msd work again with f
o
rces
commit
|
commitdiff
|
tree
2014-06-11
Berk
H
ess
Deco
u
pled
r
epl
_
ex_nst f
r
om
nstca
l
cenergy
commit
|
commitdiff
|
tree
2014-06-11
Ber
k
Hess
Made
r
ep
l
_ex
t
ime
s
tep
more readable
commit
|
commitdiff
|
tree
2014-06-10
Be
r
k Hess
Replaced gmx_hostname_
n
um
by gmx_physicalnod
e
_id_hash
commit
|
commitdiff
|
tree
2014-06-09
B
erk Hess
S
e
t make_ndx max name
l
e
ngth
a
nd count to 1024
commit
|
commitdiff
|
tree
2014-06-05
Berk Hess
Fi
x
ed shif
t
and
s
witch m
o
d
ifiers, particular
l
y for
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
B
e
rk Hess
F
i
x
const
r
a
int virial with
m
ultiple time
s
tepping
commit
|
commitdiff
|
tree
2014-06-02
B
e
rk Hess
Fi
x
ed g_energy Ei
n
stein viscosity
commit
|
commitdiff
|
tree
2014-05-22
Berk Hess
Avoid energy dr
i
ft with verlet-buffer-tolerance
commit
|
commitdiff
|
tree
2014-05-09
B
e
r
k Hess
Minor tweak
s
to
t
h
e DD setup
commit
|
commitdiff
|
tree
2014-04-29
Berk He
s
s
Remove
d
truncati
o
n
o
f
nrdf in v-resc
a
le thermos
t
at
commit
|
commitdiff
|
tree
2014-04-23
Berk Hess
Fix
e
d nbnxn FE lis
t
allocation is
s
ue
commit
|
commitdiff
|
tree
2014-04-02
B
e
rk Hess
Added LJ-
P
ME a
n
d
LJ Pot-switch
to PME
l
o
a
d estimate
commit
|
commitdiff
|
tree
2014-03-24
Berk Hes
s
Ad
d
s cut-off c
h
ecks for tricli
n
ic d
o
main decomposition
commit
|
commitdiff
|
tree
2014-03-23
Berk He
s
s
F
i
xed bug in p
a
r
allel v/f
constraining
commit
|
commitdiff
|
tree
2014-03-23
Berk Hess
CUDA cut-off kernels
n
o
w shift
exclusion energies
commit
|
commitdiff
|
tree
2014-03-11
Berk
H
ess
PME load
balan
c
ing
now work
s
with
L
J-PME
commit
|
commitdiff
|
tree
2014-03-06
B
erk
H
ess
Fixed
e
xit with FEP with PME nodes wit
h
out L
J
-PME
commit
|
commitdiff
|
tree
2014-03-05
B
erk
Hess
B
uffer estimate now w
o
r
ks with rvd-switch=
0
commit
|
commitdiff
|
tree
2014-02-26
Berk Hess
Fre
e
-energy no
w
works
with th
e
Verlet
s
cheme
commit
|
commitdiff
|
tree
2014-02-25
Berk Hess
F
i
xes
s
eperat
e
PME nodes wi
t
hout
L
J
-
PME
commit
|
commitdiff
|
tree
2014-02-24
Ber
k
Hess
Impl
e
mented
L
J-PME
n
bnx
n
k
e
rnels
commit
|
commitdiff
|
tree
2014-02-24
Berk H
e
ss
F
i
xed bug
w
i
t
h LJ pot-s
w
itch in 4xN kerne
l
s
commit
|
commitdiff
|
tree
2014-02-19
Berk Hess
Implemented nbnxn
LJ switch fun
c
tions
commit
|
commitdiff
|
tree
2014-01-30
Berk Hes
s
M
ad
e
referen
c
e SIMD work
a
gain
commit
|
commitdiff
|
tree
2014-01-29
Berk
H
ess
Automated
Verlet r
l
i
s
t for
NVE simula
t
i
ons
commit
|
commitdiff
|
tree
2013-12-03
Berk He
s
s
Remo
v
ed restri
c
ti
o
n of one
reference pull group
commit
|
commitdiff
|
tree
2013-12-02
Ber
k
He
s
s
Made
c
u
tof
f
-s
c
heme=Verlet the defaul
t
commit
|
commitdiff
|
tree
2013-12-02
Berk Hess
Renamed verlet-b
u
ff
e
r-drift to
v
erlet-buffer-tolerance
commit
|
commitdiff
|
tree
2013-12-01
Ber
k
Hess
Fixed zero h
a
rdw
a
re thr
e
ad count
commit
|
commitdiff
|
tree
2013-11-29
Berk Hess
Creat
e
d SI
M
D modul
e
commit
|
commitdiff
|
tree
2013-11-26
Be
r
k
H
es
s
F
i
x
ed return val
u
e of
gmx_mtop_bonded
s
_free_energ
y
commit
|
commitdiff
|
tree
2013-11-15
Berk H
e
ss
corre
c
ted potential nbnxn SIM
D
m
emory issue
commit
|
commitdiff
|
tree
2013-11-08
Berk Hess
fix nbnxn atom s
o
rting with dis
t
ant bo
n
deds
commit
|
commitdiff
|
tree
2013-11-07
B
e
rk Hess
corr
e
cted
d
ynamic load balancing when
s
haring GPUs
commit
|
commitdiff
|
tree
2013-11-05
Berk Hess
GPU detection is don
e
o
nce per physica
l
nod
e
commit
|
commitdiff
|
tree
2013-11-05
Berk Hes
s
removed (h
a
rmless) l
e
ft
-
over in nbnxn SIMD ke
r
n
e
ls
commit
|
commitdiff
|
tree
2013-10-31
Berk Hess
r
eorganized GPU
d
etection and se
l
ectio
n
commit
|
commitdiff
|
tree
2013-10-29
Berk Hess
corr
e
cte
d
v
o
lume with serial N
P
T replica ex
c
hange
commit
|
commitdiff
|
tree
2013-10-28
B
erk Hess
impro
v
e
d the
n
b
n
x
n bu
f
fer si
z
e estimate with G
P
Us
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
fixed r
e
cen
t
bu
g
with CUDA text
u
re obje
c
ts
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
f
ixed OpenMP t
h
reads
b
eing
pinn
e
d to the same cores
commit
|
commitdiff
|
tree
2013-10-16
Berk
H
ess
avoid divisio
n
by zero in SI
M
D
a
n
gl
e
s
a
nd dihedrals
commit
|
commitdiff
|
tree
2013-10-16
Berk Hess
f
i
x
ed a half bin misa
l
i
gnment in
g
m
x_vanhove -or
commit
|
commitdiff
|
tree
2013-10-11
Berk Hess
in
t
r
o
du
c
ed general 4-wide
S
IMD supp
o
r
t
commit
|
commitdiff
|
tree
2013-10-10
Berk Hess
fixed nbnxn
4
x
8 pair
s
earch w
i
thout AVX
commit
|
commitdiff
|
tree
2013-10-02
Be
r
k Hes
s
Fi
x
es react
i
on field free ener
g
y bug
commit
|
commitdiff
|
tree
2013-09-24
Berk Hess
optimized gener
i
c S
I
MD invsqrt
commit
|
commitdiff
|
tree
2013-09-21
Be
r
k
Hess
fixed m
u
ltiple dista
n
ce
r
estr
a
ints with
O
penMP
commit
|
commitdiff
|
tree
2013-09-18
Berk Hess
made free energy
P
ME
k
ernel 40% faster
commit
|
commitdiff
|
tree
2013-09-16
Ber
k
He
s
s
md
r
un
without Open
M
P with thread-MPI now u
s
e
s all c
o
res
commit
|
commitdiff
|
tree
2013-09-13
Berk Hess
corrected grom
p
p constraint/
D
O
F
warning with vsites
commit
|
commitdiff
|
tree
2013-08-25
Berk Hess
i
ntr
o
duced nbnxn d
a
ta s
t
ructure for bounding boxes
commit
|
commitdiff
|
tree
2013-08-20
Berk Hess
fix
e
d
p
aralle
l
normal modes with PM
E
commit
|
commitdiff
|
tree
2013-07-24
Berk H
e
ss
impleme
n
t
e
d
plain-C SIMD mac
r
os for referen
c
e
commit
|
commitdiff
|
tree
2013-06-20
Ber
k
Hess
f
i
xed SD and BD integra
t
or Op
e
nMP performance
commit
|
commitdiff
|
tree
2013-06-20
Ber
k
Hess
f
l
op
s
table now
r
e
po
r
t
s CUDA analytical
Ewald
commit
|
commitdiff
|
tree
2013-06-14
Berk Hess
fixe
d
minor g_bar output i
s
sues
commit
|
commitdiff
|
tree
2013-06-05
B
e
rk Hess
fixe
d
DD internal
s
tate corruption w
i
th ene
r
gy minim
i
zat
i
on
commit
|
commitdiff
|
tree
2013-06-03
Berk Hess
fixed deadlock with
r
e
plica
e
x
change and -maxh
commit
|
commitdiff
|
tree
2013-05-08
B
e
r
k Hess
fixed incorrec
t
sca
l
ing of cos-acceleration viscosity
commit
|
commitdiff
|
tree
2013-04-29
B
erk Hess
general SIMD accelera
t
ion
for angles+dihedrals
commit
|
commitdiff
|
tree
2013-04-26
B
e
rk Hess
PME load balancing
n
ow ch
e
cks for PME gr
i
d r
e
st
r
ictions
commit
|
commitdiff
|
tree
2013-04-18
B
er
k
Hess
changed mdrun
-
n
steps to gmx_large_
i
nt_t
commit
|
commitdiff
|
tree
2013-04-12
Berk Hess
improved
load balancing w
i
th
V
erlet cut-off
s
che
m
e
commit
|
commitdiff
|
tree
2013-03-27
Berk H
e
ss
removed
x
8
6 specifics from nb
n
xn SIMD kernels
commit
|
commitdiff
|
tree
2013-03-27
Berk Hess
corr
e
cted log file
wall
t
ime breakdown
commit
|
commitdiff
|
tree
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