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Update instructions in containers.rst
2020-12-10
Magnus
L
undb
o
rg
I
m
proved variable na
m
es in FE
P
n
o
nbonded kernel
commit
|
commitdiff
|
tree
2020-12-04
Magnus Lu
n
dborg
Added
s
calar func
t
ions cbrt as well as
m
asked
R
cp
commit
|
commitdiff
|
tree
2020-11-23
Magnus Lundborg
P
roperly ch
e
ck i
f
there are perturbed constraints or
.
.
.
commit
|
commitdiff
|
tree
2020-11-05
Mag
n
us Lu
n
dborg
Set
pbc
a
t
o
m
_
input in order
t
o pass later checks
commit
|
commitdiff
|
tree
2020-11-03
M
ag
n
u
s Lundborg
Remove TO
D
O regarding AWH co
v
er threshold
alon
g
lambda
.
.
.
commit
|
commitdiff
|
tree
2020-10-16
Magnus Lundborg
When loadin
g
AWH use
r
data do not convolve
the bias
.
.
.
commit
|
commitdiff
|
tree
2020-10-09
Magnus
Lundb
o
rg
AWH: Re
m
ove random term from FEP tests
commit
|
commitdiff
|
tree
2020-09-21
M
agnus Lundborg
AWH avoid constructors only diffe
r
in
g
in paramet
e
r
.
.
.
commit
|
commitdiff
|
tree
2020-09-03
Magnus Lundborg
Print lambda state to log fi
l
e if using AWH for
FEP
.
commit
|
commitdiff
|
tree
2020-08-25
M
agn
u
s Lu
n
db
o
rg
Avoi
d
log
(
0) if prob
a
bilit
y
is t
o
o low
commit
|
commitdiff
|
tree
2020-08-20
Magnus Lundb
o
rg
Ma
k
e
i
t pos
s
ible to use
FEP lambda st
a
tes as a reaction
.
.
.
commit
|
commitdiff
|
tree
2020-07-20
M
a
gn
u
s Lun
d
borg
Two sets of coeffi
c
ients
f
o
r
Coulomb FEP
P
ME
o
n
GPU
commit
|
commitdiff
|
tree
2020-03-04
M
agnus L
u
n
dborg
Separate AWH parameter read
i
ng and checking
commit
|
commitdiff
|
tree
2020-03-03
Ma
g
nus
L
undborg
Store dHdL for all neighbor lamb
d
as
commit
|
commitdiff
|
tree
2020-02-25
Ma
g
nus Lu
n
dborg
Fix out of sync checkpo
i
nt files in s
i
mu
l
ations sharing
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Magnus Lun
d
borg
M
ore SIMD preparatio
n
s
i
n the FE
c
alcu
l
ations
commit
|
commitdiff
|
tree
2020-01-24
Magnu
s
Lundborg
Remov
e
d SC
R
P
ower 48 from
F
E
P
kerne
l
commit
|
commitdiff
|
tree
2020-01-23
Magnus L
u
nd
b
org
M
inor cosmetic improvemen
t
s in
AW
H
commit
|
commitdiff
|
tree
2019-09-24
Magn
u
s Lundbor
g
Add
.
part0001
.
t
o
files
f
r
o
m
the first run with -noappend
.
commit
|
commitdiff
|
tree
2019-09-11
M
agnu
s
L
u
n
dborg
Tidy up the FE kernel
commit
|
commitdiff
|
tree
2019-09-10
Magnus Lundborg
More te
m
plat
i
ng of gmx_
n
b_free_en
e
rgy_kernel()
commit
|
commitdiff
|
tree
2019-09-04
M
agnus Lundborg
Inlin
e
functions
of
c
a
lculati
o
ns of FE interaction
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
Ma
g
nus Lundborg
Changed some variables from SCRe
a
l to
r
eal in FE kernel
.
commit
|
commitdiff
|
tree
2019-07-03
M
agnus Lundborg
Vectorize GPU bonded data
.
commit
|
commitdiff
|
tree
2019-06-30
Magnus Lundborg
Cl
e
a
n
ing up
the GPU bon
d
ed kernel
commit
|
commitdiff
|
tree
2019-06-28
M
a
g
nus Lun
d
borg
Fused GPU bon
d
ed
k
ernels
commit
|
commitdiff
|
tree
2018-12-14
Magnus Lundbo
r
g
Set HAVE_LMFIT p
r
o
perly
commit
|
commitdiff
|
tree
2018-11-29
Ma
g
nus Lu
n
dborg
Make p
u
ll with COM
from previous st
e
p
w
or
k
w
i
th MPI
commit
|
commitdiff
|
tree
2018-10-16
Magnus Lu
n
db
o
r
g
Move gm
x
_ffparams
_
t
t
o fo
r
cef
i
eldparameters
commit
|
commitdiff
|
tree
2018-10-15
Ma
g
nus Lundborg
Enable output
o
f
a
verag
e
pul
l
force an
d
p
o
s
i
tions
.
commit
|
commitdiff
|
tree
2018-10-03
Magnus Lundborg
Allow using COM of previous
s
tep as
PBC reference
commit
|
commitdiff
|
tree
2018-09-26
M
a
gnus Lundborg
Added pullChe
c
kPb
c
WithinGroup() to check one group
commit
|
commitdiff
|
tree
2018-09-25
Magnus Lu
n
dborg
A
d
d ma
r
gin as inpu
t
to pullGroupObeysPbcRestricti
o
ns
commit
|
commitdiff
|
tree
2018-09-21
Magnus
L
u
ndb
o
rg
F
ixes a bug in pull group size
c
alculation
commit
|
commitdiff
|
tree
2018-09-07
M
a
gnus L
u
ndborg
Chec
k
q
p
erturbation whe
n
PME on GPU is
t
ested
commit
|
commitdiff
|
tree
2018-06-04
Mag
n
us Lu
n
dborg
Write lambdas and bo
x
t
o
TNG at cor
r
ect i
n
terv
a
ls
commit
|
commitdiff
|
tree
2018-03-29
M
a
g
n
u
s Lundb
o
rg
Improved check
o
f
i
f only
for
c
es are
comput
e
d in
d
o_pairs
(
)
commit
|
commitdiff
|
tree
2017-12-05
Mag
n
us
Lundborg
SI
M
D acceler
a
ted Urey-Bradley
commit
|
commitdiff
|
tree
2017-11-18
Magnus Lundborg
Added M
a
gnus
L
undborg as contr
i
butor
i
n
the manual
.
Added
Magnus Lundborg
as contributor in the manual.
commit
|
commitdiff
|
tree
2017-11-08
Mag
n
us Lun
d
bo
r
g
U
p
d
ate t
o
TNG
v
1
.
8
.
1
commit
|
commitdiff
|
tree
2017-10-13
M
a
gnus Lundborg
Do not includ
e
h
e
aders related t
o
ObservablesHistory
commit
|
commitdiff
|
tree
2017-10-03
Magnus Lun
d
b
org
Write atom ma
s
ses and partial charges to TNG
commit
|
commitdiff
|
tree
2017-06-11
Ma
g
nus
L
undborg
Updated TNG to ve
r
sion 1
.
8
commit
|
commitdiff
|
tree
2015-12-05
Mag
n
u
s Lun
d
borg
W
rite forces and velociti
e
s
t
o co
m
pressed TNG
.
commit
|
commitdiff
|
tree
2015-11-30
Magnu
s
Lund
b
org
F
ix
e
d typos
i
n outp
u
t
.
commit
|
commitdiff
|
tree
2015-11-25
M
a
gnus
Lundborg
Use loca
l
vari
a
ble
s
instead of th
o
s
e in *ir
.
commit
|
commitdiff
|
tree
2015-06-24
Magnu
s
Lundborg
U
pdat
e
header when appending to TNG file
.
commit
|
commitdiff
|
tree
2015-06-12
Magnus Lundborg
T
NG version 1
.
7
.
6
commit
|
commitdiff
|
tree
2015-05-16
Magnu
s
Lundbor
g
TNG ve
r
sion 1
.
7
.
5
commit
|
commitdiff
|
tree
2015-04-21
Mag
n
us Lundborg
T
N
G ve
r
sio
n
1
.
7
.
3
commit
|
commitdiff
|
tree
2014-11-24
Mag
n
us L
u
ndborg
When writing
T
NG the input must contain
m
olecule data
.
commit
|
commitdiff
|
tree
2014-09-02
Magnus
Lundborg
TNG Fix for GMX
_
D
OUBLE b
u
i
lds an
d
where ZLIB is not
.
.
.
commit
|
commitdiff
|
tree
2014-09-02
Magnus Lu
n
dborg
Fix
d
a
ta block le
n
g
t
h
when unc
o
mpressing TNG data
.
commit
|
commitdiff
|
tree
2014-09-01
M
a
gnus
L
undborg
TNG
:
Hand
l
e
large
files o
n
3
2 bi
t
systems
.
commit
|
commitdiff
|
tree
2014-09-01
Magnus
L
u
n
dborg
When writing TNG include
file closing in wallcycle
.
commit
|
commitdiff
|
tree
2014-08-21
Magnus
Lundborg
Fixe
d
TNG memory
alignment problem an
d
reset p
o
inters
.
commit
|
commitdiff
|
tree
2014-07-05
Magn
u
s Lund
b
org
Fix bug causing reading ne
x
t frame not to stop
.
commit
|
commitdiff
|
tree
2014-07-05
Magnus Lundbo
r
g
Fix tng_num_frame
_
se
t
s
_get() with
n
o
f
r
a
m
e
sets
.
commit
|
commitdiff
|
tree
2014-06-28
M
a
gnus Lundbo
r
g
Update TNG build system
commit
|
commitdiff
|
tree
2014-06-24
Mag
n
us Lun
d
bor
g
Improved check to decide
if to add chain
/
res
i
due
.
commit
|
commitdiff
|
tree
2014-06-19
Ma
g
n
u
s Lundborg
Bumped the TNG library to
t
he latest v
e
rsion
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundborg
Fix
b
ug writing TNG o
u
tput f
r
om
dump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundborg
Bug fix
i
n
t
he TNG library to
impr
o
ve reading
.
commit
|
commitdiff
|
tree
2014-04-24
M
a
gnus Lundborg
More effici
e
nt TN
G
selection group cr
e
ation
commit
|
commitdiff
|
tree
2014-04-16
Magn
u
s Lundborg
Fixed bug invertin
g
compression pr
e
cision
.
commit
|
commitdiff
|
tree
2014-03-01
Magnus Lund
b
org
B
umped TNG to latest versio
n
.
commit
|
commitdiff
|
tree
2014-02-13
Magnus Lundb
o
rg
O
n
e more
bump of the
TNG
version
.
commit
|
commitdiff
|
tree
2014-02-13
Magnus L
u
n
dborg
Removed o
p
tion
t
o use OpenMP with the TNG libra
r
y
.
commit
|
commitdiff
|
tree
2014-02-12
M
a
gnus Lundborg
Enable
TNG bui
l
ds on Window
s
by default
.
commit
|
commitdiff
|
tree
2014-02-12
Magnus
L
u
n
dborg
Bumped
T
NG to latest
v
ersion
.
commit
|
commitdiff
|
tree
2014-02-11
Mag
n
u
s
Lundb
o
rg
A
dded information about h
o
w to cite t
h
e
TNG paper
.
commit
|
commitdiff
|
tree
2014-01-20
Magnus
Lund
b
org
Add TNG writing and
r
e
ading support
commit
|
commitdiff
|
tree
2013-10-29
Magnu
s
L
u
n
d
bor
g
Fix
e
d mem
o
ry leak in gmxd
u
mp
.
commit
|
commitdiff
|
tree
2013-09-02
Magnus L
u
n
d
borg
Set upper case
o
f FFTW
v
ariable at
t
he right place
.
commit
|
commitdiff
|
tree
2013-04-29
Magnu
s
L
u
n
dborg
Fixes "Function type U-B not imp
l
e
me
n
ted in ip_p
e
r
t
.
"
commit
|
commitdiff
|
tree