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Improve Verlet buffer constraint estimate
2017-05-26
Be
r
k Hess
Imp
r
ove Verlet buffer co
n
straint estimate
commit
|
commitdiff
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tree
2017-05-23
Be
r
k He
s
s
A
dd conserved q
u
a
n
tity
fo
r
Berendsen P-couple
commit
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commitdiff
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tree
2017-05-23
Berk Hess
Add conserved q
.
fo
r
P
R and Berendsen T-couple
commit
|
commitdiff
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tree
2017-05-23
Berk Hess
M
a
ke
D
D setup
o
be
y
PME
r
estriction
s
commit
|
commitdiff
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tree
2017-05-22
Berk Hess
Introduce O
b
serva
b
lesHist
o
ry contai
n
e
r
commit
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commitdiff
|
tree
2017-05-16
Berk
Hess
Fix conf
o
ut
.
gro with e
n
ergy minimiz
a
tion
commit
|
commitdiff
|
tree
2017-04-21
Be
r
k Hess
F
i
x bugs
in double AVX(2)_256 Simd4
commit
|
commitdiff
|
tree
2017-04-19
Be
r
k Hes
s
Fix
u
nused
S
IM
D
P
ME table ke
r
nel
commit
|
commitdiff
|
tree
2017-04-18
Berk Hess
Suppre
s
s
t
w
o compiler warnings
commit
|
commitdiff
|
tree
2017-03-16
Berk Hess
Repla
c
e instance of grou
p
b
y
coord in pu
l
l
mdp
docs
commit
|
commitdiff
|
tree
2017-03-14
Berk Hes
s
Mak
e
grompp -r o
b
ligatory w
i
th posres
commit
|
commitdiff
|
tree
2017-02-28
Berk He
s
s
Add loa
d
balance
f
r
a
ction to DLB pr
i
nt
commit
|
commitdiff
|
tree
2017-02-07
Berk Hess
Add mdp option ch
e
c
k
wit
h
decoupled m
o
des
commit
|
commitdiff
|
tree
2017-02-02
Berk Hess
R
eally fix ar
r
a
y of com
p
lex in c
r
oss_c
o
rr
commit
|
commitdiff
|
tree
2017-02-02
Berk
Hess
Fix
ar
r
ay of
complex in
c
ross
_
corr
commit
|
commitdiff
|
tree
2017-01-20
B
erk Hess
Disa
l
low overwriting of dihe
d
ral typ
e
9
commit
|
commitdiff
|
tree
2017-01-20
Berk H
e
ss
Only predi
c
t s
h
e
lls with velocities
commit
|
commitdiff
|
tree
2017-01-19
Berk He
s
s
Fi
x
P
ME order
a
nd
g
ri
d
si
z
e checks
commit
|
commitdiff
|
tree
2017-01-17
Berk Hess
Correct assert
o
n pme-
o
rd
e
r
commit
|
commitdiff
|
tree
2017-01-05
Berk Hess
Fix
flat-botto
m
position restraints + DD +
OpenMP
commit
|
commitdiff
|
tree
2016-12-14
Berk
Hess
Ad
d
bonded #t
h
r
e
ad runtime
c
heck
commit
|
commitdiff
|
tree
2016-12-08
Be
r
k
H
e
s
s
Ma
d
e mdrun
-
pforc
e
termi
n
a
t
e with non-finite f
o
rc
e
s
commit
|
commitdiff
|
tree
2016-11-24
Berk Hess
Chang
e
spline m
o
duli calc
u
lation
to double
commit
|
commitdiff
|
tree
2016-11-23
Berk Hess
C
onvert energyhistory_t to use s
t
d::ve
c
t
o
r
commit
|
commitdiff
|
tree
2016-11-23
Ber
k
Hess
U
se tem
p
lat
i
ng in checkpoint
.
c
p
p
commit
|
commitdiff
|
tree
2016-11-01
Berk Hess
Fix
time label print in gmx vanhove
commit
|
commitdiff
|
tree
2016-10-29
Berk Hess
Add gmx dump option for printing par
a
m
e
t
e
rs
commit
|
commitdiff
|
tree
2016-10-28
Berk He
s
s
DL
B
c
an now
t
urn o
f
f
, when slower
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
Fix
D
LB timing wit
h
CUDA and OpenC
L
commit
|
commitdiff
|
tree
2016-10-15
Berk
H
ess
Move energyhis
t
ory_t
o
ut of t_state
commit
|
commitdiff
|
tree
2016-10-14
Berk Hess
Apply Ber
e
ndsen
P-couple at nstpcouple steps
commit
|
commitdiff
|
tree
2016-10-13
B
er
k
Hess
E
xtend mtop
_
looku
p
.
h
commit
|
commitdiff
|
tree
2016-10-12
Berk
Hess
F
i
xed exception in usus
e
d result
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
Fixed print bug
in gmx wham
commit
|
commitdiff
|
tree
2016-10-12
B
erk Hess
R
e
f
a
c
t
o
r NPT e
n
er
g
y calculation
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
R
estructure lea
p
-frog integrators
commit
|
commitdiff
|
tree
2016-10-11
Berk Hess
S
p
eed u
p
mtop_util
a
tom lookup
commit
|
commitdiff
|
tree
2016-10-08
Berk Hess
Add
r
eadConfAnd
T
o
p
ology
commit
|
commitdiff
|
tree
2016-10-07
Berk Hess
C
h
anged fr
-
>f_n
o
virsum to PaddedRV
e
cVecto
r
commit
|
commitdiff
|
tree
2016-10-01
Berk Hess
Fi
x
input
r
ec
initializatio
n
in
4
tool
s
commit
|
commitdiff
|
tree
2016-09-29
B
e
r
k
Hess
Use
std::vector
in
t_s
t
ate
commit
|
commitdiff
|
tree
2016-09-29
B
e
rk Hess
Ad
d
flag
s
for op
t
ional
t
_atoms
e
ntrie
s
commit
|
commitdiff
|
tree
2016-09-22
B
e
r
k Hess
F
i
x gc
c
w
a
rn
i
ng in Ali
g
n
edAllocato
r
commit
|
commitdiff
|
tree
2016-09-20
Berk H
e
ss
Rem
o
ve st
a
te d
u
plic
a
t
i
on in seri
a
l
ru
n
s
commit
|
commitdiff
|
tree
2016-09-16
B
e
rk Hess
Fixed unuse
d
variab
l
e
s in domdec
.
c
p
p
commit
|
commitdiff
|
tree
2016-09-16
Berk He
s
s
Mer
g
e
b
ranch r
e
l
eas
e
-2016
commit
|
commitdiff
|
tree
2016-09-16
Berk Hess
Made
d
istance res
t
raints work with t
h
r
e
a
ds and DD
commit
|
commitdiff
|
tree
2016-09-13
B
e
r
k Hess
M
ov
e
d expa
n
ded
e
nsemble hi
s
tory to poi
n
ter in t_
s
tate
commit
|
commitdiff
|
tree
2016-09-13
Be
r
k Hess
C
h
ange ED and swapstate to p
o
inters in t
_
s
t
ate
commit
|
commitdiff
|
tree
2016-09-12
Berk Hess
Add co
n
st t
o
thread-MPI
f
un
c
t
ions
commit
|
commitdiff
|
tree
2016-09-10
B
e
rk He
s
s
R
e
move
c
o
ntinuation from convert_tpr
commit
|
commitdiff
|
tree
2016-09-06
Berk H
e
s
s
Fix bug w
i
th conjugate-gradient and
O
penMP
commit
|
commitdiff
|
tree
2016-09-06
Berk Hess
Consolidate MD algor
i
t
hm a
t
om setup
commit
|
commitdiff
|
tree
2016-09-05
Berk Hess
Re-enable flexib
l
e con
s
train
t
s
w
i
t
h
DD
commit
|
commitdiff
|
tree
2016-09-04
Berk Hess
Me
r
ge branch releas
e
-2016
commit
|
commitdiff
|
tree
2016-09-03
Berk Hess
Clean up PM
E
flag
s
variable use
commit
|
commitdiff
|
tree
2016-09-02
Ber
k
Hess
Merge
b
ranch
r
elea
s
e-5-1 into release-
2
016
commit
|
commitdiff
|
tree
2016-09-02
B
e
rk Hes
s
Fix Parrinello-Rahman with n
s
tpcouple>1
commit
|
commitdiff
|
tree
2016-08-30
Berk Hess
Mak
e
virial
r
e
producible
commit
|
commitdiff
|
tree
2016-08-27
Berk Hess
R
educe r
o
undi
n
g error
s
in S
E
TTLE
commit
|
commitdiff
|
tree
2016-08-24
Ber
k
H
e
ss
Fix E
w
a
ld surface+3D
C
c
orrections
commit
|
commitdiff
|
tree
2016-08-24
Berk H
e
ss
Merge branch releas
e
-5-
1
i
n
t
o release-2016
commit
|
commitdiff
|
tree
2016-08-23
Be
r
k
H
ess
R
e
move varia
b
l
e
precis
i
on gro w
r
iting
commit
|
commitdiff
|
tree
2016-08-17
B
erk Hess
Fixed opening
o
f
wall table files
commit
|
commitdiff
|
tree
2016-08-15
Berk Hess
Reduce FE pair-lis
t
m
e
mory usage
commit
|
commitdiff
|
tree
2016-08-10
Berk
H
ess
Fix de
a
dlock wit
h
thread-MPI
commit
|
commitdiff
|
tree
2016-08-09
B
e
r
k
H
ess
F
i
x twin-cutoff
for GPU LJ pot-switch
commit
|
commitdiff
|
tree
2016-07-07
B
e
rk Hes
s
Relax pull PBC check
commit
|
commitdiff
|
tree
2016-07-05
B
e
rk Hes
s
A
d
d
checks for too much m
e
mory in g_nm
e
i
g
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add grompp check fo
r
pull grou
p
commit
|
commitdiff
|
tree
2016-06-28
Berk Hess
P
roper
l
y reset CUDA applicati
o
n c
l
ocks
commit
|
commitdiff
|
tree
2016-06-27
Berk Hess
Use sysconf(_SC_NPROCES
S
ORS_ON
L
N)
commit
|
commitdiff
|
tree
2016-06-26
Berk Hes
s
Fix
v
site bug with MPI+
O
penMP
commit
|
commitdiff
|
tree
2016-06-24
B
e
r
k Hess
Fix Verlet
b
uf
f
er calculation with nstli
s
t=1
commit
|
commitdiff
|
tree
2016-06-23
Berk Hes
s
More accurate GPU
l
i
st
s
p
li
t
ting
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Upd
a
ted O
p
enC
L
TODOL
i
s
t
.
txt
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Add
n
b
nxn p
a
ir-list r
e
balancing
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
Remove Ope
n
MP ove
r
h
e
ad at high p
a
rallel
i
z
a
t
i
on
commit
|
commitdiff
|
tree
2016-06-22
B
erk
Hess
Corre
c
t GPU pair estimate for list
s
p
l
itti
n
g
commit
|
commitdiff
|
tree
2016-06-21
Berk H
e
ss
Fix bug with fbposres+
M
PI+OpenMP
commit
|
commitdiff
|
tree
2016-06-20
B
erk
H
es
s
Increase
d
tpx_incom
p
ati
b
le_version to 30
commit
|
commitdiff
|
tree
2016-06-19
Be
r
k Hess
R
emove warnin
g
s on checkpoint mismatch
commit
|
commitdiff
|
tree
2016-06-17
Berk H
e
ss
Remove std
:
:thr
e
ad::hardware_co
n
currenc
y
()
commit
|
commitdiff
|
tree
2016-06-14
Berk H
e
ss
F
i
x Op
e
nCL error with empty domain
s
commit
|
commitdiff
|
tree
2016-06-13
Berk He
s
s
H
andle constraint error
s
with
E
M
commit
|
commitdiff
|
tree
2016-06-07
Berk Hess
F
i
x dat
a
race in hwinfo with
t
hr
e
a
d
-MPI
commit
|
commitdiff
|
tree
2016-06-03
Berk H
e
ss
Handl
e
par
t
iall
y
f
rozen and
c
onstrained atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk
H
es
s
Reposition nbnxn f
i
ller particles
commit
|
commitdiff
|
tree
2016-05-31
Berk
Hess
Avoi
d
numerical overflow
w
ith overlapping atom
s
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Add
c
hec
k
f
o
r f
i
nite en
e
r
g
i
es
commit
|
commitdiff
|
tree
2016-05-30
Berk Hes
s
Add grompp che
c
k for unbound atoms
commit
|
commitdiff
|
tree
2016-05-23
B
e
r
k H
e
ss
Fix bug in v-rescale thermostat & re
p
lica exc
h
a
n
g
e
commit
|
commitdiff
|
tree
2016-05-10
B
e
rk H
e
ss
Optimized
t
h
e vsite threading
commit
|
commitdiff
|
tree
2016-05-10
B
erk H
e
ss
Fix CUDA shmem bug
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Support cmap
w
ith QMMM
commit
|
commitdiff
|
tree
2016-05-08
B
e
rk Hess
Update mdrun
t
e
rmination info
commit
|
commitdiff
|
tree
2016-05-06
Berk Hess
OpenMP
parallelization fo
r
pull
commit
|
commitdiff
|
tree
2016-04-20
Berk Hess
Fi
x
pu
l
l
l
e
g
e
nd wit
h
e
x
ternal
p
o
tential
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Allow rcoulomb>
r
v
dw with PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Broadcast pull external potenti
a
l
p
ro
v
ider
s
tring
commit
|
commitdiff
|
tree
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