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Convert gmx_mtop_t to C++
2017-10-05
Berk Hess
Mak
e
SIMD ambiguous test
work w
i
th flo
a
t/double only
commit
|
commitdiff
|
tree
2017-10-04
Be
r
k
H
ess
R
e
move a forc
e
buf
f
er argument from IForceProvider
commit
|
commitdiff
|
tree
2017-10-03
Berk Hess
Move calling o
f
s
p
e
cial force functions
commit
|
commitdiff
|
tree
2017-10-02
Berk Hess
Remove hybrid gpu+cpu
n
onbonded mode
commit
|
commitdiff
|
tree
2017-09-25
Berk He
s
s
Put rer
u
n state p
r
epar
a
tio
n
in a function
commit
|
commitdiff
|
tree
2017-09-25
Berk
He
s
s
Set global
state on
m
aster r
a
n
k o
n
ly
commit
|
commitdiff
|
tree
2017-09-23
Berk Hess
Fix grompp with Andersen mass
i
ve
a
nd no CO
M
removal
commit
|
commitdiff
|
tree
2017-09-20
Be
r
k
H
ess
Cha
n
ge nb
n
xn indexing to templates
commit
|
commitdiff
|
tree
2017-09-15
Berk He
s
s
Remove
n
b-par
a
me
t
e
r
s fr
o
m t_forcerec
commit
|
commitdiff
|
tree
2017-09-14
Berk Hess
Fix
nbnxn SIMD 2
x
NN PM
E
ta
b
ulated kernel
commit
|
commitdiff
|
tree
2017-09-12
Berk He
s
s
Fix exc
e
pti
o
n in
S
IM
D
L
J PME solve
commit
|
commitdiff
|
tree
2017-09-12
Ber
k
Hess
Do not pass st
a
te to init_replica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Ber
k
He
s
s
F
ix PBC bugs in the
s
wap code
commit
|
commitdiff
|
tree
2017-09-09
Berk He
s
s
Avoid inf
i
n SIMD double sqrt()
commit
|
commitdiff
|
tree
2017-09-07
Ber
k
Hess
F
ix FEP state wit
h
rerun
commit
|
commitdiff
|
tree
2017-09-04
Berk Hess
Fix t
w
o nbnxn sea
r
c
h
inde
x
i
ng bugs
commit
|
commitdiff
|
tree
2017-09-04
Berk
Hess
C
o
nsoli
d
a
t
e
ar
c
h
itecture boolean
s
commit
|
commitdiff
|
tree
2017-09-03
Berk Hess
Put mdrun options in st
r
ucts
commit
|
commitdiff
|
tree
2017-09-02
B
erk Hess
P
u
t all domde
c
options in a stru
c
t
commit
|
commitdiff
|
tree
2017-09-02
Berk
Hess
Fix mdrun -nb op
t
ion point
e
r
commit
|
commitdiff
|
tree
2017-09-01
B
e
rk
He
s
s
Fix md
r
un -n
b
o
p
tion po
i
n
ter
commit
|
commitdiff
|
tree
2017-08-29
Ber
k
H
es
s
Make
pull potenti
a
l
r
e
g
istration threa
d
-safe
commit
|
commitdiff
|
tree
2017-08-29
Berk Hess
Set
d
efault GMX_OPENMP_MAX_TH
R
E
A
DS
t
o
6
4
commit
|
commitdiff
|
tree
2017-08-28
Berk Hess
Av
o
i
d bonded forc
e
s loop
s
/ti
m
e
r
s on inputs with no
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Ber
k
Hess
Enabl
e
d
y
nam
i
c pair li
s
t pruning
commit
|
commitdiff
|
tree
2017-08-18
Ber
k
H
e
s
s
A
dd CPU refer
e
nce and
SIMD pruning kernels
commit
|
commitdiff
|
tree
2017-08-16
Berk H
e
ss
Add dynam
i
c p
a
i
r-list p
r
uning framework
commit
|
commitdiff
|
tree
2017-08-16
Berk Hess
Cle
a
n
u
p
n
bnxn c
l
ust
e
r pair
a
ddition code
commit
|
commitdiff
|
tree
2017-08-15
Berk Hess
Add Ope
n
MP for orientation restraints
commit
|
commitdiff
|
tree
2017-08-15
Berk Hes
s
U
se
g
raph
with
orie
n
ta
t
ion
r
e
straint
s
commit
|
commitdiff
|
tree
2017-08-12
B
erk Hess
Remove loo
p
over all atoms in
i
nit
_
mdatoms
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fix orientation r
e
stra
i
n
t refe
r
e
n
ce
commit
|
commitdiff
|
tree
2017-08-03
B
e
rk Hess
A
d
d c
h
eck for nr of orientation rest
r
aints
commit
|
commitdiff
|
tree
2017-08-03
Ber
k
Hes
s
Fi
x
bugs with orientation restra
i
nts
commit
|
commitdiff
|
tree
2017-08-02
Berk
H
ess
Clean
up matrix inversion
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Fix orientation restraint reference
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Make loop variables in ori
r
es
.
c
pp
l
oc
a
l
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Add c
h
e
c
k for nr of orie
n
tatio
n
restraints
commit
|
commitdiff
|
tree
2017-07-25
Berk H
e
ss
Fix bugs with
o
rientation
r
e
s
train
t
s
commit
|
commitdiff
|
tree
2017-07-09
Ber
k
H
e
ss
Re
s
t
r
uc
t
u
r
e
t
he loa
d
balancing t
i
ming
commit
|
commitdiff
|
tree
2017-07-04
B
e
r
k Hes
s
Unify
n
bnxn ker
n
el dispatchers
commit
|
commitdiff
|
tree
2017-07-03
B
e
r
k
He
s
s
Remove gmx_constexpr
commit
|
commitdiff
|
tree
2017-06-17
Berk Hess
Ad
d
tolera
n
ce to ca
l
c
_
v
e
r
letbuf
test
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
D
isable
PME
t
uning with th
e
group sche
m
e
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
Fix
n
u
l
l pointer
print
i
n DD
commit
|
commitdiff
|
tree
2017-06-10
Berk
Hess
Put replica
e
x
change pa
r
a
m
e
te
r
s in a struc
t
commit
|
commitdiff
|
tree
2017-06-09
Berk
H
ess
Repla
c
e
iso by in
s
t
e
a
d of
commit
|
commitdiff
|
tree
2017-06-08
Berk H
e
ss
Fi
x
COM
p
ull force
w
ith SD
commit
|
commitdiff
|
tree
2017-06-07
Berk Hess
Avoid
grom
p
p charge warning w
i
th rounding
commit
|
commitdiff
|
tree
2017-06-04
Berk Hess
Fix
c
h
e
ckpoint
r
e
a
ding wit
h
out
energy histo
r
y
commit
|
commitdiff
|
tree
2017-06-02
Berk
Hess
Fix initial te
m
perature reporting
commit
|
commitdiff
|
tree
2017-05-27
Berk Hess
Made
duplicate
atoms
i
n
b
o
n
d
eds an error
commit
|
commitdiff
|
tree
2017-05-26
Berk Hes
s
Improve Verlet buffer constraint e
s
ti
m
a
t
e
commit
|
commitdiff
|
tree
2017-05-23
Berk
Hess
A
d
d conserved quan
t
ity for Berendsen P-couple
commit
|
commitdiff
|
tree
2017-05-23
Ber
k
H
e
ss
Add
conserved q
.
for
PR
a
nd Berendsen T-cou
p
le
commit
|
commitdiff
|
tree
2017-05-23
Berk
H
e
ss
Make DD setup obey PME
r
estrictions
commit
|
commitdiff
|
tree
2017-05-22
B
erk He
s
s
Introduce Observabl
e
s
Hi
s
t
ory contai
n
er
commit
|
commitdiff
|
tree
2017-05-16
Berk Hess
Fix confout
.
g
r
o
w
i
th energy
m
inimization
commit
|
commitdiff
|
tree
2017-05-15
Berk Hess
F
i
x LJPME + switch
g
rompp
e
rror
commit
|
commitdiff
|
tree
2017-05-14
Berk Hess
Fix
b
u
g
s in double Simd4
imp
l
ementat
i
ons
commit
|
commitdiff
|
tree
2017-04-21
Ber
k
He
s
s
Fix
b
ugs
in double AVX(2)_256 Simd4
commit
|
commitdiff
|
tree
2017-04-19
Berk Hess
Fix unu
s
ed SIMD
P
M
E tabl
e
ker
n
el
commit
|
commitdiff
|
tree
2017-04-18
Berk He
s
s
Suppress two co
m
piler warnings
commit
|
commitdiff
|
tree
2017-03-16
Berk Hess
Replac
e
instan
c
e
of
group by coord in pull
m
dp
d
o
c
s
commit
|
commitdiff
|
tree
2017-03-14
B
e
rk Hess
M
a
k
e
grompp -r obligator
y
w
ith posres
commit
|
commitdiff
|
tree
2017-02-28
Ber
k
Hess
A
d
d l
o
ad bal
a
nce fraction to DLB print
commit
|
commitdiff
|
tree
2017-02-07
Berk Hess
Ad
d
mdp optio
n
check wi
t
h dec
o
upled modes
commit
|
commitdiff
|
tree
2017-02-02
Ber
k
Hess
R
e
ally fix arra
y
of complex in
c
ross_corr
commit
|
commitdiff
|
tree
2017-02-02
Berk Hess
Fi
x
arra
y
of
complex in cr
o
ss_cor
r
commit
|
commitdiff
|
tree
2017-01-20
Berk
Hess
Disallow
o
verwriting of dihedr
a
l type 9
commit
|
commitdiff
|
tree
2017-01-20
Berk He
s
s
Only predict shells with velocities
commit
|
commitdiff
|
tree
2017-01-19
B
e
rk Hess
F
i
x
PME or
d
er and grid si
z
e
check
s
commit
|
commitdiff
|
tree
2017-01-17
Berk Hess
Co
r
r
e
ct assert on pme-order
commit
|
commitdiff
|
tree
2017-01-05
Berk Hess
Fix
f
lat-bot
t
om po
s
ition restrai
n
ts
+
D
D
+ OpenMP
commit
|
commitdiff
|
tree
2016-12-14
Berk
H
ess
A
dd bonded #thread runtime
check
commit
|
commitdiff
|
tree
2016-12-08
B
er
k
He
s
s
Made
m
d
r
un
-
p
for
c
e terminate with non-finit
e
fo
r
ces
commit
|
commitdiff
|
tree
2016-11-24
Berk Hess
C
hange spline moduli calculation
to double
commit
|
commitdiff
|
tree
2016-11-23
Berk
H
ess
Co
n
ve
r
t e
n
ergyhistory_t to us
e
std::vector
commit
|
commitdiff
|
tree
2016-11-23
Berk Hess
U
se temp
l
at
i
ng in checkpoint
.
cpp
commit
|
commitdiff
|
tree
2016-11-01
Berk Hess
F
i
x time label print in
gmx vanhove
commit
|
commitdiff
|
tree
2016-10-29
Berk Hess
Add
g
mx
d
ump option for printing parameters
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
DLB can now tur
n
off, when slower
commit
|
commitdiff
|
tree
2016-10-28
Berk
Hes
s
Fix
DLB timing with
C
UDA
a
nd OpenCL
commit
|
commitdiff
|
tree
2016-10-15
B
erk
H
ess
Move energyhistory_t
o
u
t o
f
t_s
t
ate
commit
|
commitdiff
|
tree
2016-10-14
Be
r
k Hess
A
p
ply Be
r
e
n
dsen P-coupl
e
at nstpc
o
uple steps
commit
|
commitdiff
|
tree
2016-10-13
Berk
He
s
s
E
x
tend mtop_lo
o
kup
.
h
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
Fixed exceptio
n
in u
s
used result
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
Fi
x
ed print bug
i
n
gmx wham
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
Refactor NPT
e
ner
g
y calcul
a
tio
n
commit
|
commitdiff
|
tree
2016-10-12
Berk
H
es
s
Rest
r
ucture
l
e
ap-f
r
og integrators
commit
|
commitdiff
|
tree
2016-10-11
Be
r
k Hess
S
pee
d
up mtop_util atom lo
o
kup
commit
|
commitdiff
|
tree
2016-10-08
Berk
H
ess
A
d
d readC
o
nfAndTop
o
logy
commit
|
commitdiff
|
tree
2016-10-07
Berk
Hess
Ch
a
ng
e
d fr->f_novir
s
u
m
to PaddedRVecVect
o
r
commit
|
commitdiff
|
tree
2016-10-01
Berk Hess
Fix
i
nputrec initiali
z
ati
o
n i
n
4 tools
commit
|
commitdiff
|
tree
2016-09-29
Berk Hes
s
Use s
t
d::vector in t_stat
e
commit
|
commitdiff
|
tree
2016-09-29
B
e
rk He
s
s
Ad
d
flags for opti
o
nal t_atoms ent
r
i
e
s
commit
|
commitdiff
|
tree
2016-09-22
Berk
H
ess
Fix g
c
c war
n
i
n
g
i
n
A
l
ig
n
edAllocator
commit
|
commitdiff
|
tree
2016-09-20
Berk
H
e
ss
Remove state duplication in se
r
ial runs
commit
|
commitdiff
|
tree
2016-09-16
B
e
rk He
s
s
Fixed
u
nu
s
ed variabl
e
s in d
o
mdec
.
cpp
commit
|
commitdiff
|
tree
2016-09-16
Berk Hes
s
Merge bran
c
h
r
e
lea
s
e-2016
commit
|
commitdiff
|
tree
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