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Fix genion charge summation accuracy
2013-04-26
Berk Hess
PME l
o
ad
b
alancing no
w
checks for PM
E
grid restrictions
commit
|
commitdiff
|
tree
2013-04-18
Berk Hess
c
h
a
n
ged mdrun -nsteps to g
m
x_large_int_t
commit
|
commitdiff
|
tree
2013-04-12
Berk
Hess
i
m
pr
o
v
ed
load balanci
n
g with Verlet cut
-
off scheme
commit
|
commitdiff
|
tree
2013-03-27
Berk Hess
r
emoved x86 sp
e
cif
i
c
s from nbnxn SIMD kernels
commit
|
commitdiff
|
tree
2013-03-27
Berk He
s
s
co
r
rected log file
w
all
t
ime breakdown
commit
|
commitdiff
|
tree
2013-03-21
Berk H
e
ss
m
a
de PM
E
work wi
t
h a mix of 1 and more threads
commit
|
commitdiff
|
tree
2013-03-14
B
e
rk Hess
corrected
grompp rvdw ch
a
r
ge
-
group radii check
commit
|
commitdiff
|
tree
2013-02-26
B
e
r
k
Hess
fixed PME
ti
m
e print w
i
t
h -ntomp_
p
me
!
= -ntomp
commit
|
commitdiff
|
tree
2013-02-20
B
erk Hess
added
m
drun chec
k
for Ve
r
let+p
e
rtur
b
e
d atoms
commit
|
commitdiff
|
tree
2013-02-06
Berk He
s
s
fixed bug with sd i
n
t
egrato
r
and OpenMP threading
commit
|
commitdiff
|
tree
2013-02-05
Berk
H
ess
i
mprove
d
load
ba
l
ancing on the GPU
commit
|
commitdiff
|
tree
2013-02-04
Be
r
k Hess
fix
e
d segv in init_forcerec wit
h
fr->hwinfo=NULL
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
improve
d
CUDA kernel performance by
pre-loading cj
commit
|
commitdiff
|
tree
2013-01-16
Carsten Kutzne
r
Made g_tune_
p
me work corre
c
tly again wi
t
h thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Berk Hes
s
mad
e
SHAKE
w
or
k
again with parti
c
le deco
m
postion
commit
|
commitdiff
|
tree
2013-01-10
Berk Hes
s
fixed
b
u
g with Verlet + D
D
+ bonded atom
co
m
munication
commit
|
commitdiff
|
tree
2013-01-10
E
r
ik Lindahl
Rev
e
rt
d
efault rlist
/
rv
d
w/rco
u
lomb to valid values
.
.
.
commit
|
commitdiff
|
tree
2013-01-02
B
e
rk Hess
m
inor speed-up a
n
d cod
e
clean-up
i
n nbnxn kernels
commit
|
commitdiff
|
tree
2012-12-20
B
erk
H
e
s
s
fixed
r
e
cent bugs in LINC
S
f
o
r
deriva
t
i
v
es
commit
|
commitdiff
|
tree
2012-12-18
B
e
r
k Hess
r
e
n
amed
g
mx
_
x
86_simd_mac
r
os
.
h to
g
mx_s
i
md_macros
.
h
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
i
m
pl
e
ment
e
d nbnxn AVX-25
6
2
x
(
N+N) kernels
commit
|
commitdiff
|
tree
2012-12-11
Berk Hess
r
e
d
uced PLINCS communicat
i
on
wi
t
h H-b
o
nd co
n
straints
commit
|
commitdiff
|
tree
2012-12-07
Berk Hess
fixed GPU pair-search with GMX_CPU_ACCELERATION=None
commit
|
commitdiff
|
tree
2012-12-05
Berk He
s
s
fix
e
d
i
ncorrect virial with virtua
l
s
ites and Ope
n
MP
commit
|
commitdiff
|
tree
2012-12-05
B
e
r
k
H
e
ss
fixed segv
in Verlet pair-sear
c
h with
t
r
ilinic DD
commit
|
commitdiff
|
tree
2012-11-30
Berk Hess
f
i
xed issu
e
wit
h
-multi and GPUs
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
f
ixed thread pinning with mdr
u
n
-
multi
commit
|
commitdiff
|
tree
2012-11-28
Szilard Pa
l
l
enable G
P
U
e
mulation
witho
u
t GPU su
p
p
o
rt
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
exten
d
ed nbnxn x86 S
I
MD kernel b
l
endv support
commit
|
commitdiff
|
tree
2012-11-27
B
e
rk Hess
fixed
b
u
g in nbnxn OpenMP non-b
o
nded forc
e
r
e
d
u
ction
commit
|
commitdiff
|
tree
2012-11-26
B
e
r
k
Hess
made nbnxn
analytic
a
l Ewald consis
t
ent
commit
|
commitdiff
|
tree
2012-11-26
Berk Hess
a
dded n
b
nxn ana
l
yt
i
c
al Ewald correctio
n
kernels
commit
|
commitdiff
|
tree
2012-11-15
Berk Hess
fixed
i
n
c
orrect 1-4 energie
s
with OpenMP
+ energy gro
u
ps
commit
|
commitdiff
|
tree
2012-11-14
Berk Hes
s
fixed nbnxn x86 SIM
D
non-bonded performanc
e
re
g
ression
commit
|
commitdiff
|
tree
2012-11-12
Ber
k
Hess
nbnxn CPU force b
u
ffer redu
c
tion now us
e
s
SI
M
D
commit
|
commitdiff
|
tree
2012-11-05
Berk
H
ess
updated seve
r
al things re
l
a
ted
with OpenM
P
thre
a
d co
u
nt
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
fi
x
ed incorrect PME load balancin
g
lim
i
tation
commit
|
commitdiff
|
tree
2012-10-26
Berk H
e
ss
set the default fo
r
ns
t
dhdl to 100
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
f
ixed inc
o
r
rect group
e
ne
r
gies wi
t
h
nbnxn
C
PU kernels
commit
|
commitdiff
|
tree
2012-10-22
R
oland Schulz
Fi
x
clang
3
.
2 unin
t
ia
l
ized va
r
iable warnin
g
s
commit
|
commitdiff
|
tree
2012-10-18
Berk Hess
ren
a
med constraint va
r
iables rmdr
to
v
ir
_
r_m_dr
commit
|
commitdiff
|
tree
2012-10-17
Berk Hess
r
e
na
m
ed pme_
s
witch
.
.
.
t
o
pme_loa
d
ba
l
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
B
e
rk He
s
s
made pair-searc
h
with GPU 20% f
a
ster
commit
|
commitdiff
|
tree
2012-10-08
Berk Hess
made non-b
o
nded
p
otent
i
al shifts mdp options
commit
|
commitdiff
|
tree
2012-10-03
Berk Hess
impro
v
ed the energy cons
e
rva
t
io
n
w
ith
S
ETTLE
commit
|
commitdiff
|
tree
2012-09-13
B
erk Hess
fixed recent bug with grompp c
h
eck for P-R P-
c
ou
p
ling
commit
|
commitdiff
|
tree
2012-08-29
Berk Hess
bug fix for pme
.
c MPI_COMM
_
NULL
fix dcf8b
6
7e
commit
|
commitdiff
|
tree
2012-08-09
Berk H
e
ss
fix
e
d trjco
n
v not writing velocities
w
ith
cpt input
commit
|
commitdiff
|
tree
2012-08-06
B
e
rk Hess
fixed
i
n
c
o
rrect TPI results with d
y
n
amic box
commit
|
commitdiff
|
tree
2012-07-18
Berk He
s
s
fix
e
d DD charge group
d
is
p
lacement erro
r
c
h
e
ck
commit
|
commitdiff
|
tree
2012-06-25
Be
r
k
Hess
fixed segv
/
hang with EM
and foreign
lambda
v
alue
s
commit
|
commitdiff
|
tree
2012-06-25
Berk Hess
added
check
for log fp!=N
U
LL when dis
a
bling
a
cceleration
commit
|
commitdiff
|
tree
2012-05-24
Be
r
k Hess
n
o
w mdrun alway
s
init
i
a
l
izes MPI
commit
|
commitdiff
|
tree
2012-05-21
Berk He
s
s
grompp now re
t
a
ins
the or
d
er of b
o
nds converted to
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
Berk Hess
re-in
t
roduced
f
i
x
for real/double i
s
sue
in gm
x
_densit
y
commit
|
commitdiff
|
tree
2012-05-08
Berk
H
ess
f
ixed m
d
run -cpi SD
and pc
o
upl initial
i
zat
i
on
commit
|
commitdiff
|
tree
2012-04-27
Berk Hess
fix
e
d segv in
T
PI w
i
th
P
ME, fixes #
9
27
commit
|
commitdiff
|
tree
2012-04-27
Berk Hess
changed PME MPI_Comm compa
r
isi
o
ns
t
o MPI
_
C
O
MM_NULL
.
.
.
commit
|
commitdiff
|
tree
2012-04-27
Berk
Hess
chang
e
d n
u
m
ber
o
f
i
atoms f
o
r F_SETTLE from 1 to 3
commit
|
commitdiff
|
tree
2012-04-26
Berk Hess
add
e
d suppor
t
for graphs no
t
s
t
arting at 0
commit
|
commitdiff
|
tree
2012-04-26
Be
r
k Hess
Mer
g
e r
e
l
e
ase-4-
5
-pa
t
che
s
i
n
t
o release-
4
-6
commit
|
commitdiff
|
tree
2012-04-26
Be
r
k Hess
fixed
t
he reported tempe
r
ature with B
r
ow
n
ian dynam
i
cs
commit
|
commitdiff
|
tree
2012-04-26
B
e
rk Hess
f
i
xed dispersion cor
r
ection with parallel EM
commit
|
commitdiff
|
tree
2012-04-25
Berk H
e
ss
replaced
P
P
PM
by P3
M
-
AD: a few
l
ines in pme
.
c
commit
|
commitdiff
|
tree
2012-04-25
Berk He
s
s
fixe
d
initial COM motion removal w
i
t
h multiple groups
commit
|
commitdiff
|
tree
2012-04-18
Berk Hess
fixed segfaul
t
in graph cod
e
wit
h
co
o
rdinate subs
e
ts
commit
|
commitdiff
|
tree
2012-04-18
B
e
rk H
e
ss
allow -append to
o
ver
r
ule unsupported file locking
commit
|
commitdiff
|
tree
2012-04-17
Berk H
e
ss
chang
e
d
m
d
run file l
o
cki
n
g not supported error to a
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
B
e
rk
H
ess
chang
e
d defaul
t
for nstxout, n
s
tvout
a
nd nstlog
commit
|
commitdiff
|
tree
2012-04-16
Berk
He
s
s
checkpoint files now con
t
ai
n
a double precis
i
on fl
a
g
commit
|
commitdiff
|
tree
2012-03-27
Ber
k
H
e
ss
added
correction for PME virial w
i
th non-linear vi
r
tual
.
.
.
commit
|
commitdiff
|
tree
2012-03-23
Berk Hess
fixed g_ba
r
x
vg readi
n
g
issue
commit
|
commitdiff
|
tree
2012-03-17
Be
r
k
H
ess
fixed increasing memory usage w
i
th S
H
AKE and DD
commit
|
commitdiff
|
tree
2012-03-13
Berk Hess
mdrun -npme wi
t
hout PME or with P
D
no
w
generates a
.
.
.
commit
|
commitdiff
|
tree
2012-03-05
Ber
k
Hess
fix
e
d g_anaeig inco
r
rect multiple extremes,
fixes #870
commit
|
commitdiff
|
tree
2012-03-05
Berk
H
ess
added check for mass-w
e
i
g
htin
g
with g_anaeig
-
e
n
t
ropy
.
.
.
commit
|
commitdiff
|
tree
2012-03-05
Be
r
k He
s
s
r
emoved initial t
e
mperature w
i
t
h
O
pe
n
MM,
f
ixes #757
commit
|
commitdiff
|
tree
2012-02-28
B
erk
H
ess
f
ixed
a
rray index out
of bou
n
ds in EM for
c
e t
r
r storage
commit
|
commitdiff
|
tree
2012-02-26
Berk He
s
s
use separate PME no
d
es with #n
o
d
es>18
commit
|
commitdiff
|
tree
2012-02-23
Berk Hess
added
t
px file t
a
g string
commit
|
commitdiff
|
tree
2012-02-20
Berk Hess
ch
a
nged
default e
p
silo
n
-rf value to
0
commit
|
commitdiff
|
tree
2012-02-10
Berk Hess
fixed gmx
c
heck
segv wi
t
h
tp
r
fi
l
e
s without
AdResS
commit
|
commitdiff
|
tree
2012-02-06
Berk
Hess
Fixed bug with COM motion removal
o
n part of the system
commit
|
commitdiff
|
tree
2012-02-02
Berk Hess
Improved t
h
e accuracy of the sd1 integr
a
tor
commit
|
commitdiff
|
tree
2011-11-27
Berk Hess
fixed pull constraint periodic
i
ty consiste
n
c
y
check
.
.
.
commit
|
commitdiff
|
tree
2011-11-15
Berk Hess
fixed dd
l
o
a
d
print
f
requency with ns
t
eps=
-
1, fixes
.
.
.
commit
|
commitdiff
|
tree
2011-10-13
Be
r
k Hess
f
ixe
d
p
u
l
l constr
a
ining doin
g
nothing, fixes
#825
commit
|
commitdiff
|
tree
2011-10-06
Berk Hess
fixed
segv in parall
e
l
replica exchange
commit
|
commitdiff
|
tree
2011-09-19
Berk
H
e
ss
added
grompp che
c
k
f
o
r
p
o
sres+pcoup
l
+refcoo
r
d_s
c
alin
g
=no
commit
|
commitdiff
|
tree
2011-09-15
B
e
r
k
Hess
mdru
n
-multi -c
p
i now che
c
ks if simulation
s
p
a
rts are
.
.
.
commit
|
commitdiff
|
tree
2011-09-13
B
e
rk Hess
fixed grompp issue with decoupling and virtual si
t
es
commit
|
commitdiff
|
tree
2011-09-05
Berk Hes
s
m
a
de all
o
cati
o
n for LINCS with particle
d
e
c
o
m
position
.
.
.
commit
|
commitdiff
|
tree
2011-08-29
B
erk Hess
f
ixed in
c
orrect pV t
e
rm in the
e
nerg
y
file
commit
|
commitdiff
|
tree
2011-08-22
Be
r
k
H
ess
fixed op
e
ration
o
n clo
s
ed file struc
t
ure
i
n
g
m
x_rmsdist
.
.
.
commit
|
commitdiff
|
tree
2011-08-22
Be
r
k Hess
f
ixed pos
s
ible infini
t
e l
o
o
p
when r
e
adi
n
g atom types
.
.
.
commit
|
commitdiff
|
tree
2011-08-15
Berk Hess
fixed incor
r
ect
p
o
i
nter a
s
signment
i
n g_p
r
otonate
commit
|
commitdiff
|
tree
2011-08-12
Berk Hess
implemented f
u
ll exclu
s
ion support for t
h
e charge-group
.
.
.
commit
|
commitdiff
|
tree
2011-08-10
Berk H
e
ss
rem
o
ved
n
pm
e
nodes
mismatch warning in read_checkpoin
t
.
.
.
commit
|
commitdiff
|
tree
2011-08-10
Berk Hes
s
removed
f
atal_e
r
ror f
o
r p
r
ime number of nodes when
.
.
.
commit
|
commitdiff
|
tree