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Pull group count for coords stored in tpr
2015-12-01
Berk Hess
P
ull
group count for coo
r
ds stored
i
n
tpr
commit
|
commitdiff
|
tree
2015-11-25
Mark
A
b
raham
Fix logic of d
d
_print_missing_i
n
teractions e
x
it
commit
|
commitdiff
|
tree
2015-11-18
Berk Hess
Removed Reaction-Field-nec
commit
|
commitdiff
|
tree
2015-11-11
B
erk Hess
Fixed (harmless) fp exception in wallcycle_
s
um
commit
|
commitdiff
|
tree
2015-11-09
Berk Hess
Cor
r
ect LINC
S
dHdl
c
o
ntri
b
ution
commit
|
commitdiff
|
tree
2015-11-05
V
e
dran Miletić
Upd
a
te explanation of re
p
li
c
a
exc
h
ange output
commit
|
commitdiff
|
tree
2015-11-03
Mark Abraham
Merge branch re
l
ea
s
e-
5
-1
commit
|
commitdiff
|
tree
2015-09-16
Berk
Hess
Split nbnxn_gri
d
.
c of
f
from n
b
nxn_search
.
c
commit
|
commitdiff
|
tree
2015-09-15
Ber
k
He
s
s
Detec
t
incorrect cycl
e
c
o
unti
n
g
commit
|
commitdiff
|
tree
2015-08-25
B
er
k
H
e
ss
Simp
l
ify changing t
h
e tpx
_
version
commit
|
commitdiff
|
tree
2015-08-12
Berk H
e
ss
Added const quali
f
iers t
o
core MD routines
commit
|
commitdiff
|
tree
2015-06-30
Berk He
s
s
Fix incons
i
stent OpenMP aut
o
mation
commit
|
commitdiff
|
tree
2015-06-26
Alexey Shvetsov
F
i
x rece
n
t compilatio
n
is
s
u
e
i
n
p
u
llcode
commit
|
commitdiff
|
tree
2015-06-22
Ber
k
Hess
F
i
x g_
e
nergy average/RMSD bug
commit
|
commitdiff
|
tree
2015-05-23
Be
r
k Hes
s
Remove
d
static from variables in gmx_l
a
pack
commit
|
commitdiff
|
tree
2015-05-13
Ber
k
Hess
Fixed CUD
A
error with empty domains
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
Changed FFTW war
n
ing from
AVX to no SS
E
commit
|
commitdiff
|
tree
2015-05-07
B
erk Hess
R
e
m
oved
non-
f
f atomtypes fro
m
opl
s
aa and charmm27
commit
|
commitdiff
|
tree
2015-05-04
Berk
H
ess
Fixe
d
GPU non-loc
a
l F
c
opy local conditio
n
a
l
commit
|
commitdiff
|
tree
2015-04-28
B
er
k
Hes
s
Re-
e
nabled FMA for AV
X
-128-F
M
A
commit
|
commitdiff
|
tree
2015-04-22
Berk
He
s
s
M
er
g
e
bran
c
h 'releas
e
-
5
-0'
commit
|
commitdiff
|
tree
2015-04-17
Berk
H
ess
C
orrect -ntmpi auto for
i
ntel
n
ehal
e
m
and
olde
r
commit
|
commitdiff
|
tree
2015-03-05
Berk
H
e
ss
Made
D
D exclusion pro
c
ess
i
ng mor
e
efficient
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
R
e
-fixed
P
M
E
bug with
h
igh Op
e
nMP th
r
ead co
u
nt
commit
|
commitdiff
|
tree
2015-01-21
B
e
r
k Hess
C
or
r
ected RDTSCP warning text
commit
|
commitdiff
|
tree
2014-12-11
Berk Hess
Added
g
rompp error for
pul
l
ing to negative d
i
stance
commit
|
commitdiff
|
tree
2014-12-09
Berk Hess
Fix recent bug with t
r
ilinic 1D DD
commit
|
commitdiff
|
tree
2014-11-24
D
avi
d
van der Spoel
Added warnings for ewal
d
-g
e
o
metry and sur
f
a
c
e-epsilo
n
commit
|
commitdiff
|
tree
2014-10-07
B
e
rk H
e
s
s
Fixes
i
ssue with vsiten and Verlet buffers
commit
|
commitdiff
|
tree
2014-09-09
Be
r
k He
s
s
Fixed DD state c
o
llection
i
s
sue
commit
|
commitdiff
|
tree
2014-09-08
Berk
H
e
ss
Ch
e
c
k
for implicit sol
v
ent + Verlet s
c
heme
commit
|
commitdiff
|
tree
2014-08-25
Berk Hess
Fixed bugs
in vsite
N
with OpenM
P
commit
|
commitdiff
|
tree
2014-08-02
Berk H
e
s
s
F
ixed PME
bug with h
i
gh OpenMP t
h
read count
commit
|
commitdiff
|
tree
2014-07-31
Berk Hess
Avoid
d
iv
i
sion by 0 in
nbn
x
n_search
commit
|
commitdiff
|
tree
2014-07-28
Ch
r
istian We
n
nberg
F
i
x ov
e
rflow
in LJ-PME nbnxn kernels
commit
|
commitdiff
|
tree
2014-06-20
Berk He
s
s
Fixed
s
hell
s
with
p
arti
c
l
e
decomposition
commit
|
commitdiff
|
tree
2014-06-10
Berk
Hess
Replaced gmx_host
n
ame_num by gmx_ph
y
sical
n
od
e
_id_hash
commit
|
commitdiff
|
tree
2014-06-02
Berk Hess
Fixed g_ener
g
y
E
i
n
s
tein viscosi
t
y
commit
|
commitdiff
|
tree
2014-03-24
Berk Hess
Add
s
c
u
t
-off checks fo
r
t
riclin
i
c domain
decompos
i
tion
commit
|
commitdiff
|
tree
2013-12-03
Berk H
e
ss
Removed restrict
i
on of one ref
e
rence pull group
commit
|
commitdiff
|
tree
2013-11-15
Ber
k
He
s
s
corrected potenti
a
l nb
n
xn
SIMD memory is
s
ue
commit
|
commitdiff
|
tree
2013-11-08
Ber
k
Hes
s
f
ix nbnxn atom sorti
n
g
with distant bondeds
commit
|
commitdiff
|
tree
2013-11-06
Szilar
d
P
all
ena
b
le GPU s
h
a
r
i
ng among tMPI ra
n
ks
commit
|
commitdiff
|
tree
2013-10-31
Berk
Hess
reorg
a
nized
G
P
U
d
etection and selection
commit
|
commitdiff
|
tree
2013-10-22
Berk H
e
s
s
fixed re
c
ent bug with
C
U
DA t
e
xture
ob
j
ects
commit
|
commitdiff
|
tree
2013-10-22
Be
r
k
H
ess
fixed
O
penMP thr
e
ads
being pinn
e
d to the same
c
ores
commit
|
commitdiff
|
tree
2013-10-10
B
erk Hess
fixe
d
nb
n
xn
4
x8 pair se
a
rch wi
t
h
o
ut AVX
commit
|
commitdiff
|
tree
2013-06-03
Berk
Hess
f
ixe
d
dead
l
o
ck with repli
c
a ex
c
hange a
n
d -
m
axh
commit
|
commitdiff
|
tree
2013-05-08
Berk
Hes
s
fixed i
n
correct scaling of cos-a
c
celerat
i
on viscosity
commit
|
commitdiff
|
tree
2013-04-26
Berk Hess
P
ME load balancing now checks for PME gri
d
res
t
ric
t
i
ons
commit
|
commitdiff
|
tree
2013-04-18
Berk Hess
c
h
anged mdrun
-nsteps to gmx_large_
i
nt
_
t
commit
|
commitdiff
|
tree
2013-04-12
B
erk H
e
ss
improved loa
d
b
a
lancin
g
w
ith Verlet cu
t
-off
s
c
heme
commit
|
commitdiff
|
tree
2013-03-27
Berk Hess
removed x86
s
pecif
i
cs f
r
om nbnxn SI
M
D kernels
commit
|
commitdiff
|
tree
2013-03-27
Berk
H
ess
c
o
rrec
t
e
d log
f
ile wall time breakdown
commit
|
commitdiff
|
tree
2013-03-21
Be
r
k Hess
made
P
M
E
work with a mix of 1
a
nd more threads
commit
|
commitdiff
|
tree
2013-03-14
Berk H
e
ss
correc
t
ed gr
o
mpp rvdw
c
harge-g
r
oup
r
a
dii check
commit
|
commitdiff
|
tree
2013-02-26
Berk Hess
fixed PME time print with -ntomp_pme != -ntomp
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
added md
r
u
n check for Verlet+pe
r
turbed atoms
commit
|
commitdiff
|
tree
2013-02-06
Berk Hess
fixed bug with sd integrator and
O
p
e
nMP threading
commit
|
commitdiff
|
tree
2013-02-05
Berk H
e
ss
i
m
proved load
bal
a
ncing
o
n t
h
e GPU
commit
|
commitdiff
|
tree
2013-02-04
Berk Hess
f
ixed segv in
i
n
i
t_forcerec
with fr->hwi
n
fo=NULL
commit
|
commitdiff
|
tree
2013-01-17
Berk Hes
s
improved CUDA kernel perfor
m
ance by pre-
l
oading cj
commit
|
commitdiff
|
tree
2013-01-16
Car
s
ten Kutzner
Made g_
t
une_pme
w
o
rk co
r
rectly
ag
a
in with thread-MP
I
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Be
r
k Hess
m
a
d
e SHAK
E
work again with partic
l
e
d
ecompostion
commit
|
commitdiff
|
tree
2013-01-10
Be
r
k Hess
fixed bug wit
h
Verlet
+
DD + bon
d
e
d ato
m
c
omm
u
n
ication
commit
|
commitdiff
|
tree
2013-01-10
E
r
ik Lind
a
hl
R
ever
t
d
e
fault rl
i
st/rvdw/
r
coulomb
to
v
alid values
.
.
.
commit
|
commitdiff
|
tree
2013-01-02
Berk Hess
minor spe
e
d-up and code clean-up in nbnxn kernels
commit
|
commitdiff
|
tree
2012-12-20
Berk
H
ess
f
ixed recent bug
s
in LIN
C
S
for
d
e
r
i
vatives
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
rename
d
gmx_x86_si
m
d_macr
o
s
.
h to gmx_
s
imd_macr
o
s
.
h
commit
|
commitdiff
|
tree
2012-12-18
B
e
rk Hess
implemented n
b
nxn AVX-2
5
6
2x(
N
+N
)
kerne
l
s
commit
|
commitdiff
|
tree
2012-12-11
Berk Hess
r
e
duced
PLINCS communication with H-bond constraints
commit
|
commitdiff
|
tree
2012-12-07
B
e
r
k Hess
fixed GPU p
a
ir-sear
c
h with GMX_CP
U
_A
C
CEL
E
RATION=None
commit
|
commitdiff
|
tree
2012-12-05
Berk Hess
fixed incorrec
t
virial with
virtual sites
a
n
d O
p
enMP
commit
|
commitdiff
|
tree
2012-12-05
Berk H
e
ss
f
i
x
ed s
e
g
v
in Ver
l
et pair-search
w
it
h
trilini
c
DD
commit
|
commitdiff
|
tree
2012-11-30
Berk H
e
ss
fixe
d
issu
e
with -multi and
G
PU
s
commit
|
commitdiff
|
tree
2012-11-28
Be
r
k Hess
fix
e
d thread pinning wit
h
mdrun -mu
l
ti
commit
|
commitdiff
|
tree
2012-11-28
S
zi
l
ard Pal
l
enable GPU emula
t
ion
wit
h
o
u
t
GPU suppor
t
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
e
xtended nbnxn x86 S
I
MD ke
r
nel
blendv support
commit
|
commitdiff
|
tree
2012-11-27
B
e
rk
Hess
f
i
x
ed bu
g
in nbnxn Ope
n
MP non-bon
d
e
d force re
d
uction
commit
|
commitdiff
|
tree
2012-11-26
Berk
Hess
made nbn
x
n a
n
alytical
E
wald consistent
commit
|
commitdiff
|
tree
2012-11-26
B
er
k
Hess
a
d
d
ed nbnxn analytical
Ew
a
ld
correc
t
ion kernels
commit
|
commitdiff
|
tree
2012-11-15
Berk Hes
s
f
ixed incorrect 1-
4
energi
e
s
with OpenMP + ener
g
y grou
p
s
commit
|
commitdiff
|
tree
2012-11-14
Berk H
e
ss
f
i
xed nbnxn x86 SIMD
non-bonded performa
n
c
e
regression
commit
|
commitdiff
|
tree
2012-11-12
Berk Hess
nbn
x
n
C
P
U force buffer
r
eduction now u
s
es SIM
D
commit
|
commitdiff
|
tree
2012-11-05
Berk
Hes
s
updated sev
e
r
a
l things rela
t
ed with OpenMP
t
hre
a
d count
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
f
ixe
d
inco
r
re
c
t P
M
E
load balanc
i
ng limitation
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
s
et t
h
e d
e
fault for
n
stdhdl
t
o 100
commit
|
commitdiff
|
tree
2012-10-26
Be
r
k Hess
fixed in
c
orrect group energies wit
h
nbnxn CPU kernels
commit
|
commitdiff
|
tree
2012-10-22
Ro
l
and Sc
h
u
lz
Fix
c
lang 3
.
2
uninti
a
lized v
a
riable
warni
n
gs
commit
|
commitdiff
|
tree
2012-10-18
Berk Hess
re
n
amed constraint variables rmdr
to vi
r
_r_m_dr
commit
|
commitdiff
|
tree
2012-10-17
Be
r
k
H
ess
renam
e
d
pme_switch
.
.
.
to pm
e
_loadbal
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Berk He
s
s
mad
e
pair-search
with GP
U
20%
f
aste
r
commit
|
commitdiff
|
tree
2012-10-08
Berk
He
s
s
made n
o
n-bon
d
ed
potential
s
hifts
m
dp opt
i
o
n
s
commit
|
commitdiff
|
tree
2012-10-03
Berk
H
ess
impr
o
ved
the energy conservation with
S
ETTLE
commit
|
commitdiff
|
tree
2012-09-13
Berk He
s
s
fixe
d
recent bug
with grompp ch
e
ck for P-R P-c
o
upling
commit
|
commitdiff
|
tree
2012-08-29
Berk Hess
bug fix for
p
me
.
c MPI_COMM_NULL fix d
c
f8b67e
commit
|
commitdiff
|
tree
2012-08-09
Berk
H
es
s
f
i
xed trjconv not writing velociti
e
s wit
h
cpt input
commit
|
commitdiff
|
tree
2012-08-06
Berk Hes
s
f
ixed incorrect TPI
r
es
u
lts
with dyn
a
mic b
o
x
commit
|
commitdiff
|
tree
2012-07-18
Berk Hess
fixed
D
D charge group
d
isplac
e
m
ent err
o
r
c
h
eck
commit
|
commitdiff
|
tree
2012-06-25
Berk H
e
ss
fixe
d
segv
/
hang wit
h
E
M and foreign lambda values
commit
|
commitdiff
|
tree
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