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Re-enabled SIMD for angles and dihedrals
2015-02-06
B
erk Hess
Re-ena
b
led SIMD for an
g
les an
d
dihedrals
commit
|
commitdiff
|
tree
2015-01-21
Berk Hess
Corrected RDTSCP warning
t
ext
commit
|
commitdiff
|
tree
2015-01-15
Berk Hess
Fi
x
allocati
o
n issue with
V
V
integrat
o
r
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
F
i
xed pb
c
=xy + 2 wa
l
l
s + V
e
rlet sch
e
me
commit
|
commitdiff
|
tree
2014-12-22
Be
r
k Hess
Fix bug FE + GPU
+ 2/3D domain
decomposition
commit
|
commitdiff
|
tree
2014-12-11
Berk
Hess
Added grompp e
r
ror
for pulling t
o
neg
a
t
i
ve
distance
commit
|
commitdiff
|
tree
2014-12-09
Berk H
e
ss
Fix
recent bug
w
ith trilinic 1D DD
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Fi
x
ed pull
coord init with rate!=0, t_s
t
a
rt!=0
commit
|
commitdiff
|
tree
2014-12-08
B
e
rk Hess
Ad
d
ed P
B
C no
t
e to comm-mode=ang
u
l
ar warning
commit
|
commitdiff
|
tree
2014-12-05
Berk
Hess
Ma
k
e do
m
d
e
c a
p
roper module
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Clari
f
ied grompp p
u
ll
e
rro
r
me
s
sages
commit
|
commitdiff
|
tree
2014-12-05
Berk Hes
s
Avoid race
on d
v
dl with Ve
r
le
t
+Op
e
nM
P
+LINCS+FE+VV
commit
|
commitdiff
|
tree
2014-12-01
Berk
He
s
s
Added warning for
unneces
s
ary
s
oft-core
commit
|
commitdiff
|
tree
2014-11-26
Berk Hess
Fixed triclinic 1xNx1 do
m
ain decompositi
o
n
commit
|
commitdiff
|
tree
2014-11-25
B
erk
Hess
Fix
e
d twin-range
+ freeze
+
constraints
commit
|
commitdiff
|
tree
2014-11-24
Ber
k
Hess
Avo
i
d NaN i
n
rlist b
u
ffer calcula
t
i
o
n
commit
|
commitdiff
|
tree
2014-11-12
Ber
k
Hess
Corr
e
cted parameter
f
o
r
s
o
rt
i
ng on search gri
d
commit
|
commitdiff
|
tree
2014-11-12
Ber
k
H
e
ss
F
i
x D
D
bon
d
e
d int
e
ractio
n
range print
commit
|
commitdiff
|
tree
2014-10-20
Berk Hess
R
e
move
d
f_novirsum
reduct
i
o
n i
n
Verl
e
t sc
h
eme
commit
|
commitdiff
|
tree
2014-10-07
Berk Hess
Fixes issue with vsiten and Verlet b
u
ffers
commit
|
commitdiff
|
tree
2014-09-30
B
erk Hess
Avoid
DLB with overloaded
PME ra
n
ks
commit
|
commitdiff
|
tree
2014-09-30
Berk Hess
Added GPU
l
ocal
wait to load balancing
commit
|
commitdiff
|
tree
2014-09-29
Berk
Hess
Dom
a
in decomposition now c
h
ecks
the rlist buff
e
r
commit
|
commitdiff
|
tree
2014-09-29
Berk
H
ess
SIMD acc
e
l
e
ration for RB dih
e
drals
commit
|
commitdiff
|
tree
2014-09-29
Berk
H
ess
A
v
oi
d
P
ME tuning
decreasi
n
g
rcoulomb
commit
|
commitdiff
|
tree
2014-09-29
Berk
Hess
Fix calc_g
r
id
a
voidin
g
P
M
E
grid factor 8
4
commit
|
commitdiff
|
tree
2014-09-09
B
e
r
k Hess
F
i
xed DD state col
l
e
cti
o
n issue
commit
|
commitdiff
|
tree
2014-09-08
B
e
r
k Hess
Check fo
r
implicit
s
ol
v
ent + Ve
r
let scheme
commit
|
commitdiff
|
tree
2014-08-28
Berk Hess
Fixed two PME is
s
ues wit
h
MPI+OpenMP
commit
|
commitdiff
|
tree
2014-08-25
Berk
H
ess
Fi
x
ed bugs
i
n vsi
t
eN with O
p
enMP
commit
|
commitdiff
|
tree
2014-08-24
Berk Hess
Initialize unused velocity constraint components
commit
|
commitdiff
|
tree
2014-08-17
Berk H
e
s
s
H
al
v
ed the cost of
the pull co
m
muni
c
ation
commit
|
commitdiff
|
tree
2014-08-14
Berk Hess
Co
r
rec
t
e
d
SIMD
math overflow
docum
e
ntation
commit
|
commitdiff
|
tree
2014-08-10
Be
r
k
H
e
ss
Added ch
e
cks for TPI +
V
erlet
sche
m
e
commit
|
commitdiff
|
tree
2014-08-05
Ber
k
Hess
Fix ha
n
g
w
i
t
h LJ
-
PM
E
a
n
d empty domains
commit
|
commitdiff
|
tree
2014-08-02
Berk Hess
Fixed PME bug with high Op
e
n
M
P thread count
commit
|
commitdiff
|
tree
2014-07-31
Berk Hess
Avoid di
v
ision
b
y
0
in nb
n
xn_s
e
arch
commit
|
commitdiff
|
tree
2014-06-29
Berk H
e
ss
Take LJ-PME into account
f
or
table spa
c
ing
commit
|
commitdiff
|
tree
2014-06-29
B
e
rk
H
ess
Updated LJ
-
PM
E
d
o
c
ument
a
tion
commit
|
commitdiff
|
tree
2014-06-24
Berk Hess
Fixed the sign of mass pertur
b
ed contribut
i
on
commit
|
commitdiff
|
tree
2014-06-20
Berk
Hess
Fix g_m
i
ndist with
p
b
c
=
XY
commit
|
commitdiff
|
tree
2014-06-20
Berk
Hess
Fixed sh
e
lls with
par
t
icle decom
p
osition
commit
|
commitdiff
|
tree
2014-06-18
Berk Hes
s
Fixed
s
ign error in posre
s
dvdl
commit
|
commitdiff
|
tree
2014-06-17
Berk Hess
Updated mdr
u
n -npme
d
ocu
m
entation
commit
|
commitdiff
|
tree
2014-06-17
Berk
H
ess
Removed rou
n
d
ing issu
e
i
n nbnxn Ewald table
commit
|
commitdiff
|
tree
2014-06-14
Berk
Hess
Fixed PME bug
w
ith #OpenMP-threads a
l
arge p
r
ime
commit
|
commitdiff
|
tree
2014-06-13
Berk
H
e
s
s
Chang
e
d append
i
ng file nam
e
e
rror m
e
ssage
commit
|
commitdiff
|
tree
2014-06-13
Be
r
k Hess
Ma
d
e sh
e
lls work
w
i
th the V
e
rlet
scheme
commit
|
commitdiff
|
tree
2014-06-12
Berk Hess
Fix
e
d
perturb
e
d wall int
e
ra
c
tions
commit
|
commitdiff
|
tree
2014-06-12
Be
r
k
H
ess
Made gmx
c
heck -rmsd work again with fo
r
c
es
commit
|
commitdiff
|
tree
2014-06-11
B
erk
Hess
D
e
coupled r
e
pl_ex_nst
f
r
o
m nstcalcenergy
commit
|
commitdiff
|
tree
2014-06-11
B
erk
Hess
Made
repl_ex time step more re
a
dable
commit
|
commitdiff
|
tree
2014-06-10
Be
r
k
H
e
ss
Replaced
g
mx_hostname_num by gmx_physic
a
ln
o
d
e_id_hash
commit
|
commitdiff
|
tree
2014-06-09
B
e
rk Hess
Set make_ndx ma
x
name l
e
ngth and count
to 1024
commit
|
commitdiff
|
tree
2014-06-05
Berk Hess
F
i
xed
shift and switch modifiers, particula
r
l
y
f
or
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
Ber
k
H
e
ss
Fix constraint
virial with multi
p
le time stepping
commit
|
commitdiff
|
tree
2014-06-02
Ber
k
He
s
s
Fixed g_ener
g
y Einstein
v
iscosity
commit
|
commitdiff
|
tree
2014-05-22
Berk
H
ess
A
void energy drift wi
t
h ve
r
let-buffer-tolerance
commit
|
commitdiff
|
tree
2014-05-09
Berk H
e
ss
Min
o
r
tweaks
t
o
t
h
e
DD setup
commit
|
commitdiff
|
tree
2014-04-29
Berk Hess
Removed trun
c
ation of n
r
df in
v-rescale thermostat
commit
|
commitdiff
|
tree
2014-04-23
Berk Hess
Fixed nbnxn FE
l
i
s
t alloc
a
t
i
on i
s
sue
commit
|
commitdiff
|
tree
2014-04-02
Berk Hess
Added LJ-PME and LJ Po
t
-switch to PME load estimate
commit
|
commitdiff
|
tree
2014-03-24
Berk H
e
s
s
A
dd
s
cut-o
f
f c
h
ec
k
s for tric
l
inic domain decomposit
i
on
commit
|
commitdiff
|
tree
2014-03-23
Berk Hess
Fixe
d
b
u
g
i
n parallel v/f
constraining
commit
|
commitdiff
|
tree
2014-03-23
Berk Hess
CUDA cut-of
f
kernels now shift exclusion energies
commit
|
commitdiff
|
tree
2014-03-11
Berk Hess
P
M
E load balancing n
o
w works
with LJ-
P
ME
commit
|
commitdiff
|
tree
2014-03-06
Berk Hess
Fixed exi
t
wi
t
h
FEP wi
t
h PME nodes wit
h
out LJ
-
PME
commit
|
commitdiff
|
tree
2014-03-05
Berk Hess
Buf
f
e
r estimate now wo
r
ks with
rvd-switc
h
=0
commit
|
commitdiff
|
tree
2014-02-26
B
erk Hess
Free-ene
r
g
y
now wor
k
s with the Verlet scheme
commit
|
commitdiff
|
tree
2014-02-25
Berk Hess
Fixes seperate
PME nodes without LJ-PME
commit
|
commitdiff
|
tree
2014-02-24
Berk Hess
Im
p
le
m
e
n
ted LJ-PME nbnxn
kernels
commit
|
commitdiff
|
tree
2014-02-24
Berk Hes
s
Fixed bug with LJ pot
-
switch in
4
xN k
e
rn
e
l
s
commit
|
commitdiff
|
tree
2014-02-19
Berk
Hess
I
m
p
l
ement
e
d nbn
x
n LJ switch func
t
io
n
s
commit
|
commitdiff
|
tree
2014-01-30
Be
r
k Hess
M
a
de
r
eferenc
e
SIMD work again
commit
|
commitdiff
|
tree
2014-01-29
B
erk Hess
Aut
o
mated Verl
e
t rlis
t
f
o
r NVE
s
imulat
i
ons
commit
|
commitdiff
|
tree
2013-12-03
Berk Hess
R
emove
d
restriction of one refere
n
ce pull group
commit
|
commitdiff
|
tree
2013-12-02
Berk Hes
s
Made cut
o
f
f-scheme=Ve
r
le
t
the
d
efault
commit
|
commitdiff
|
tree
2013-12-02
Berk Hess
Rena
m
ed verlet-buffer-drift to verlet
-
buf
f
er-
t
olera
n
ce
commit
|
commitdiff
|
tree
2013-12-01
Be
r
k
H
ess
Fi
x
e
d
z
e
ro hardware
thread
coun
t
commit
|
commitdiff
|
tree
2013-11-29
Ber
k
H
e
s
s
C
r
ea
t
ed SIMD module
commit
|
commitdiff
|
tree
2013-11-26
Berk Hess
Fixed retu
r
n value of
g
m
x_mto
p
_bonded
s
_free_energy
commit
|
commitdiff
|
tree
2013-11-15
Berk Hess
corrected
potential nbnxn SIMD mem
o
ry issue
commit
|
commitdiff
|
tree
2013-11-08
Ber
k
Hess
fi
x
nbn
x
n atom s
o
r
ting
w
ith distant bondeds
commit
|
commitdiff
|
tree
2013-11-07
B
e
rk Hess
correct
e
d dynamic load
balancing when shari
n
g GPUs
commit
|
commitdiff
|
tree
2013-11-05
Berk Hess
GPU detec
t
ion is done once p
e
r
physic
a
l node
commit
|
commitdiff
|
tree
2013-11-05
B
e
rk Hess
rem
o
ved (harmless)
left-
o
ver in nbnxn
SIMD kernels
commit
|
commitdiff
|
tree
2013-10-31
Berk Hess
r
eorganize
d
GPU de
t
ect
i
o
n and selection
commit
|
commitdiff
|
tree
2013-10-29
Berk Hess
cor
r
ected
volume
w
ith seri
a
l NPT rep
l
ica
exch
a
nge
commit
|
commitdiff
|
tree
2013-10-28
Be
r
k Hess
improved the
n
b
nxn
buffer size es
t
imate wi
t
h GPUs
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
fixed
recent
b
ug
w
i
t
h
CUDA texture objects
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
f
i
xed OpenMP
t
h
reads being pinned to th
e
same cores
commit
|
commitdiff
|
tree
2013-10-16
Be
r
k Hess
avoi
d
division by zero in SIMD a
n
gle
s
and di
h
ed
r
als
commit
|
commitdiff
|
tree
2013-10-16
B
erk Hess
fixed a half bin misalignment in gmx_van
h
o
v
e -or
commit
|
commitdiff
|
tree
2013-10-11
Berk
He
s
s
intr
o
duced general 4-wide SIMD su
p
port
commit
|
commitdiff
|
tree
2013-10-10
Be
r
k Hess
fi
x
ed nbnxn 4x8 pair
s
earch w
i
tho
u
t AVX
commit
|
commitdiff
|
tree
2013-10-02
Berk Hess
Fixes reaction
f
i
eld fre
e
energy bug
commit
|
commitdiff
|
tree
2013-09-24
B
e
r
k
H
ess
op
t
im
i
zed generic SIMD in
v
s
q
rt
commit
|
commitdiff
|
tree
2013-09-21
Berk Hess
fixed m
u
ltip
l
e di
s
tance restr
a
ints with Op
e
nM
P
commit
|
commitdiff
|
tree
2013-09-18
Berk
H
ess
made free en
e
rgy PME kernel 40% faster
commit
|
commitdiff
|
tree
2013-09-16
Berk
H
ess
mdrun without
Ope
n
MP with thread
-
MPI no
w
uses all cor
e
s
commit
|
commitdiff
|
tree
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