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Fix cpuinfo on clang + non-x86
2017-10-12
Berk H
e
ss
S
implify virial h
a
ndling
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disable
A
RM N
e
on na
t
ive
rsqr
t
iteration
commit
|
commitdiff
|
tree
2017-10-06
Berk H
e
ss
A
d
d acceleration correction VCM mode
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Fix max
_
size
(
) in allocato
r
.
h
commit
|
commitdiff
|
tree
2017-10-06
B
erk H
e
s
s
Add
S
IMD intrinsics
version of simple update
commit
|
commitdiff
|
tree
2017-10-06
B
e
r
k Hes
s
I
m
prove P
a
d
dedRVec
V
ector resizi
n
g
commit
|
commitdiff
|
tree
2017-10-05
Berk
Hess
Make SIMD ambiguous t
e
st work
w
i
t
h float/double
o
nly
commit
|
commitdiff
|
tree
2017-10-04
B
e
rk Hess
R
e
move a f
o
rce
b
uffe
r
argument from I
F
orcePro
v
i
d
e
r
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
M
ove calling of spec
i
al forc
e
f
u
ncti
o
ns
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Re
m
ov
e
hybrid gpu+c
p
u nonbo
n
ded mode
commit
|
commitdiff
|
tree
2017-09-25
Berk Hess
Put rerun state
p
r
e
paration
i
n a function
commit
|
commitdiff
|
tree
2017-09-25
Berk Hess
Set gl
o
bal
s
tate on maste
r
rank
o
nly
commit
|
commitdiff
|
tree
2017-09-20
B
e
rk He
s
s
Ch
a
nge
nbnxn indexing
t
o
templates
commit
|
commitdiff
|
tree
2017-09-15
B
e
rk Hess
Rem
o
ve nb-paramet
e
r
s
f
rom
t_forcerec
commit
|
commitdiff
|
tree
2017-09-14
Berk Hess
Fix n
b
nxn SIMD 2xN
N
PME tabulated ker
n
e
l
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Fix exceptio
n
in
S
IMD LJ
P
ME solve
commit
|
commitdiff
|
tree
2017-09-12
Be
r
k Hess
Do not pass state to init_replica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Berk Hess
Fix PBC
bugs i
n
the swap code
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
Avo
i
d
i
n
f in SIMD double sq
r
t()
commit
|
commitdiff
|
tree
2017-09-07
Berk
Hess
Fix FEP stat
e
with rerun
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Fix
t
wo nbnxn search indexing bugs
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Consol
i
date
arch
i
t
ect
u
r
e booleans
commit
|
commitdiff
|
tree
2017-09-03
B
erk Hes
s
P
ut mdru
n
o
p
tio
n
s
in s
t
ructs
commit
|
commitdiff
|
tree
2017-09-02
Berk
Hess
Put a
l
l domdec op
t
ions i
n
a struct
commit
|
commitdiff
|
tree
2017-09-02
Berk Hess
Fix mdru
n
-
n
b
option point
e
r
commit
|
commitdiff
|
tree
2017-09-01
Berk Hess
Fi
x
md
r
un -nb op
t
ion pointer
commit
|
commitdiff
|
tree
2017-08-29
Berk
H
ess
Make pull p
o
tenti
a
l registr
a
tion thr
e
ad-s
a
f
e
commit
|
commitdiff
|
tree
2017-08-29
Berk
H
ess
Set de
f
a
u
lt GMX_O
P
EN
M
P_MAX_THR
E
ADS
t
o 64
commit
|
commitdiff
|
tree
2017-08-28
Berk Hess
Avoid bonded forces loops/timer
s
on i
n
put
s
w
i
th no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Be
r
k H
e
ss
E
n
able d
y
namic
p
air list pruning
commit
|
commitdiff
|
tree
2017-08-18
B
e
rk Hess
Add CPU
r
eferen
c
e and S
I
MD pruning k
e
r
n
el
s
commit
|
commitdiff
|
tree
2017-08-16
Berk Hess
Add dy
n
amic pa
i
r-list pruning framework
commit
|
commitdiff
|
tree
2017-08-16
Berk
H
ess
C
lean
u
p
nbnxn clust
e
r
pai
r
addition c
o
de
commit
|
commitdiff
|
tree
2017-08-15
Ber
k
Hess
Ad
d
OpenMP f
o
r orientation rest
r
aints
commit
|
commitdiff
|
tree
2017-08-15
B
e
rk Hess
Use
g
r
a
ph with orien
t
ati
o
n restraints
commit
|
commitdiff
|
tree
2017-08-12
Ber
k
Hes
s
Remo
v
e loop over all
atoms in
i
n
it_mdatoms
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fix
o
rienta
t
ion
r
e
stra
i
nt reference
commit
|
commitdiff
|
tree
2017-08-03
Be
r
k Hess
Add check for nr of orient
a
tion
restrai
n
ts
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fix bugs with orientation res
t
r
aints
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Clea
n
up matrix inversion
commit
|
commitdiff
|
tree
2017-08-02
Berk Hes
s
Fix orie
n
tati
o
n restra
i
nt r
e
ference
commit
|
commitdiff
|
tree
2017-08-02
Berk H
e
s
s
Make loop varia
b
le
s
in
o
rires
.
cpp
local
commit
|
commitdiff
|
tree
2017-08-02
B
er
k
H
ess
Add chec
k
for nr of
o
r
i
ent
a
tion restraints
commit
|
commitdiff
|
tree
2017-07-25
Berk Hess
Fix bugs with orienta
t
ion re
s
t
ra
i
n
ts
commit
|
commitdiff
|
tree
2017-07-09
Berk
Hess
Restruc
t
ure the
load bal
a
ncing t
i
ming
commit
|
commitdiff
|
tree
2017-07-04
B
erk
H
ess
Unify nbnxn kernel dis
p
a
tchers
commit
|
commitdiff
|
tree
2017-07-03
Berk Hess
Remove
g
mx_constexpr
commit
|
commitdiff
|
tree
2017-06-17
Berk Hess
Add to
l
erance to ca
l
c_v
e
rletbuf t
e
st
commit
|
commitdiff
|
tree
2017-06-12
B
e
rk Hess
Disable
P
M
E
tu
n
ing with th
e
g
r
o
u
p scheme
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
Fix nu
l
l poi
n
ter print in D
D
commit
|
commitdiff
|
tree
2017-06-10
Berk Hess
P
u
t replica ex
c
h
ang
e
parameters in a struct
commit
|
commitdiff
|
tree
2017-06-09
Ber
k
Hess
Replace iso
b
y in
s
t
ead of
commit
|
commitdiff
|
tree
2017-06-08
Berk Hess
F
i
x COM
p
u
ll
f
orce with SD
commit
|
commitdiff
|
tree
2017-06-07
Berk
H
ess
Avoid gr
o
mpp cha
r
ge warning wit
h
rounding
commit
|
commitdiff
|
tree
2017-06-04
Berk
Hess
Fix checkpoin
t
reading
w
ithout energy
h
isto
r
y
commit
|
commitdiff
|
tree
2017-06-02
B
erk
H
e
s
s
Fix i
n
itia
l
t
e
mperatur
e
reporting
commit
|
commitdiff
|
tree
2017-05-27
Be
r
k Hess
Made
d
uplicate a
t
oms
in bondeds a
n
e
rror
commit
|
commitdiff
|
tree
2017-05-26
B
e
rk Hess
Improve V
e
rl
e
t bu
f
fer c
o
n
s
traint estimate
commit
|
commitdiff
|
tree
2017-05-23
Berk Hess
Add con
s
er
v
e
d
quantity for Be
r
e
nds
e
n P-coupl
e
commit
|
commitdiff
|
tree
2017-05-23
Berk Hess
Add conse
r
v
ed q
.
for PR an
d
Berendsen T-
c
ou
p
l
e
commit
|
commitdiff
|
tree
2017-05-23
Be
r
k Hess
Mak
e
DD setup obey P
M
E restrictions
commit
|
commitdiff
|
tree
2017-05-22
Berk
H
ess
I
n
tro
d
uce Obse
r
vablesHistory con
t
aine
r
commit
|
commitdiff
|
tree
2017-05-16
Ber
k
Hess
Fix confout
.
gro with
e
nergy
m
inimizati
o
n
commit
|
commitdiff
|
tree
2017-05-15
Berk
Hess
Fix LJPME + switch grompp
error
commit
|
commitdiff
|
tree
2017-05-14
Be
r
k
Hess
F
i
x bugs
in double Simd4 implementations
commit
|
commitdiff
|
tree
2017-04-21
Berk Hess
Fix b
u
gs in do
u
ble
A
VX(2)_256 Simd4
commit
|
commitdiff
|
tree
2017-04-19
Be
r
k
Hess
Fix unused SI
M
D PME table kernel
commit
|
commitdiff
|
tree
2017-04-18
B
erk Hess
Suppres
s
two compil
e
r warni
n
gs
commit
|
commitdiff
|
tree
2017-03-16
Berk Hes
s
Replace instance
of group by
c
o
ord
i
n
p
u
ll
m
d
p
docs
commit
|
commitdiff
|
tree
2017-03-14
Berk Hess
Make grompp -r
obligatory with po
s
res
commit
|
commitdiff
|
tree
2017-02-28
Berk
Hess
Add load balance fraction to DLB pr
i
nt
commit
|
commitdiff
|
tree
2017-02-07
B
e
r
k Hess
Ad
d
mdp
o
ption chec
k
w
i
t
h deco
u
pled modes
commit
|
commitdiff
|
tree
2017-02-02
Berk Hess
Really fix
a
r
ray of complex in c
r
o
ss_corr
commit
|
commitdiff
|
tree
2017-02-02
B
e
r
k
Hess
Fix arr
a
y of comp
l
ex
i
n
cross_corr
commit
|
commitdiff
|
tree
2017-01-20
Berk Hes
s
Dis
a
llow overwriting of
d
ihedral type 9
commit
|
commitdiff
|
tree
2017-01-20
Ber
k
Hess
Only
predict s
h
ells with velocities
commit
|
commitdiff
|
tree
2017-01-19
B
erk Hess
Fix PME order and grid size ch
e
cks
commit
|
commitdiff
|
tree
2017-01-17
Berk Hess
Correct
a
s
s
ert on pme-order
commit
|
commitdiff
|
tree
2017-01-05
Berk
Hess
Fix fl
a
t-bottom posit
i
on restraints + D
D
+ OpenMP
commit
|
commitdiff
|
tree
2016-12-14
Berk Hess
A
dd bon
d
ed #thre
a
d
runt
i
me ch
e
ck
commit
|
commitdiff
|
tree
2016-12-08
Berk Hess
Made mdrun -p
f
or
c
e
termi
n
ate with non-finite fo
r
ces
commit
|
commitdiff
|
tree
2016-11-24
Berk H
e
ss
Chang
e
spl
i
ne m
o
d
u
li ca
l
culation to do
u
ble
commit
|
commitdiff
|
tree
2016-11-23
Berk
H
ess
Convert energ
y
history_t
to use
std
:
:ve
c
tor
commit
|
commitdiff
|
tree
2016-11-23
Be
r
k
H
ess
Use templating in
c
h
e
ckpoint
.
cpp
commit
|
commitdiff
|
tree
2016-11-01
Berk He
s
s
Fix
t
i
m
e label print in gmx
v
anhove
commit
|
commitdiff
|
tree
2016-10-29
Berk Hess
A
dd
gm
x
dump option for printing paramete
r
s
commit
|
commitdiff
|
tree
2016-10-28
B
e
rk Hess
DLB ca
n
n
ow turn off, when slower
commit
|
commitdiff
|
tree
2016-10-28
Berk
He
s
s
Fix DLB tim
i
ng with CUDA and OpenCL
commit
|
commitdiff
|
tree
2016-10-15
Be
r
k Hess
Move energ
y
histor
y
_t
o
ut of t_sta
t
e
commit
|
commitdiff
|
tree
2016-10-14
B
e
r
k Hess
Apply Berendsen P-
c
ou
p
le at nstp
c
ouple ste
p
s
commit
|
commitdiff
|
tree
2016-10-13
Be
r
k H
e
ss
E
xtend mto
p
_l
o
o
k
up
.
h
commit
|
commitdiff
|
tree
2016-10-12
Berk He
s
s
Fixed ex
c
ept
i
on i
n
usu
s
e
d res
u
lt
commit
|
commitdiff
|
tree
2016-10-12
Berk He
s
s
F
i
xed print bug in gmx wham
commit
|
commitdiff
|
tree
2016-10-12
Ber
k
He
s
s
Re
f
actor NPT en
e
rg
y
calculation
commit
|
commitdiff
|
tree
2016-10-12
Ber
k
Hes
s
Restruct
u
re leap-
f
rog integ
r
ators
commit
|
commitdiff
|
tree
2016-10-11
Berk Hess
Speed
up mtop
_
util at
o
m lookup
commit
|
commitdiff
|
tree
2016-10-08
B
e
r
k Hess
A
dd readConfAndTo
p
ology
commit
|
commitdiff
|
tree
2016-10-07
Berk Hes
s
C
h
anged
f
r->f_no
v
irsum to
Padde
d
RVecVector
commit
|
commitdiff
|
tree
2016-10-01
B
e
rk
Hess
Fi
x
inp
u
trec
i
n
i
tializat
i
on in 4 tools
commit
|
commitdiff
|
tree
2016-09-29
Berk
Hess
Use s
t
d::v
e
ctor
i
n t_state
commit
|
commitdiff
|
tree
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