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Update instructions in containers.rst
2020-12-10
M
agnus Lundbor
g
Im
p
roved variable names in
F
EP n
o
nbonded kernel
commit
|
commitdiff
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tree
2020-12-04
Mag
n
u
s Lundborg
Added s
c
alar fun
c
t
i
ons
c
brt as well
a
s masked R
c
p
commit
|
commitdiff
|
tree
2020-11-23
Ma
g
nus
L
undborg
P
r
operly ch
e
ck if th
e
r
e
are per
t
u
rbed constraints or
.
.
.
commit
|
commitdiff
|
tree
2020-11-05
Ma
g
nus Lundborg
Set
pbc
a
tom
_
input in order to pass later checks
commit
|
commitdiff
|
tree
2020-11-03
Magnus Lund
b
o
rg
Remove T
O
D
O reg
a
rding
A
W
H cov
e
r thres
h
old along
lamb
d
a
.
.
.
commit
|
commitdiff
|
tree
2020-10-16
Magn
u
s Lundborg
W
h
en loadi
n
g
AWH
user data d
o
not conv
o
lve th
e
bias
.
.
.
commit
|
commitdiff
|
tree
2020-10-09
M
agnus
Lundborg
A
WH:
Rem
o
v
e
random term from FEP tests
commit
|
commitdiff
|
tree
2020-09-21
Mag
n
us Lund
b
org
AWH avoid constr
u
ct
o
r
s only differ
i
ng in parame
t
er
.
.
.
commit
|
commitdiff
|
tree
2020-09-03
M
ag
n
us
L
u
ndborg
Pr
i
nt
l
ambda s
t
at
e
to log file
i
f using
A
WH fo
r
FEP
.
commit
|
commitdiff
|
tree
2020-08-25
M
agnus Lundb
o
rg
Avoid
l
og(0) if probabilit
y
is too
low
commit
|
commitdiff
|
tree
2020-08-20
Magnus Lundborg
Make it
possible to use FEP la
m
bd
a
states as a rea
c
t
i
on
.
.
.
commit
|
commitdiff
|
tree
2020-07-20
Magnus Lundb
o
r
g
Two
s
ets of coe
f
ficients for Co
u
lomb
FEP P
M
E on GP
U
commit
|
commitdiff
|
tree
2020-03-04
Magnus
L
und
b
org
S
e
parate AWH par
a
meter readi
n
g and checking
commit
|
commitdiff
|
tree
2020-03-03
Mag
n
us Lundbor
g
Store dHdL for all neighb
o
r lambdas
commit
|
commitdiff
|
tree
2020-02-25
M
a
gnus
Lundborg
Fix ou
t
of s
y
nc checkp
o
int files in simula
t
i
o
n
s shari
n
g
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Magnus
Lundborg
M
o
re SIMD prepar
a
tion
s
in t
h
e FE calculat
i
o
ns
commit
|
commitdiff
|
tree
2020-01-24
M
a
gnus Lundborg
R
e
m
oved SC RPower 48
f
rom FE
P
kernel
commit
|
commitdiff
|
tree
2020-01-23
Magn
u
s
Lundborg
Minor cosmetic im
p
rovements
i
n A
W
H
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|
commitdiff
|
tree
2019-09-24
Magnu
s
L
undbo
r
g
A
d
d
.
pa
r
t0001
.
to
f
i
l
es from th
e
first run with -noappen
d
.
commit
|
commitdiff
|
tree
2019-09-11
Magnus Lundborg
Tidy u
p
t
h
e FE kernel
commit
|
commitdiff
|
tree
2019-09-10
Magnu
s
Lundborg
More tem
p
la
t
ing of gmx_nb_free_energy_kernel()
commit
|
commitdiff
|
tree
2019-09-04
Magnus Lundb
o
rg
I
nline functions
o
f calculations of FE in
t
eraction
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
Magnus
Lun
d
borg
Change
d
som
e
variables
f
rom SCReal
to real
in FE kernel
.
commit
|
commitdiff
|
tree
2019-07-03
Magn
u
s Lundborg
Vectorize GPU bond
e
d da
t
a
.
commit
|
commitdiff
|
tree
2019-06-30
Magnus Lundborg
C
leaning u
p
the GP
U
bonded kernel
commit
|
commitdiff
|
tree
2019-06-28
M
agnus Lun
d
borg
Fused GPU bonded kernels
commit
|
commitdiff
|
tree
2018-12-14
Ma
g
nus
L
undborg
Set HAV
E
_LMFIT pr
o
per
l
y
commit
|
commitdiff
|
tree
2018-11-29
Magnus
L
u
n
d
b
o
rg
Make
p
ull with C
O
M from previo
u
s step work with MPI
commit
|
commitdiff
|
tree
2018-10-16
Magnus Lundborg
Move gmx_ffpa
r
ams
_
t to forcefieldparameters
commit
|
commitdiff
|
tree
2018-10-15
Magnus
Lundb
o
rg
Enable outpu
t
o
f average pull for
c
e and positions
.
commit
|
commitdiff
|
tree
2018-10-03
M
a
gn
u
s
Lu
n
dbo
r
g
A
llow using COM of
previous step a
s
PBC refer
e
nce
commit
|
commitdiff
|
tree
2018-09-26
Magn
u
s Lu
n
dborg
Added p
u
ll
C
hec
k
PbcW
i
thinGroup() to
c
heck one group
commit
|
commitdiff
|
tree
2018-09-25
Magnus Lun
d
borg
Add mar
g
in
as input to pullGroupObeysP
b
c
R
est
r
ic
t
ions
commit
|
commitdiff
|
tree
2018-09-21
Magnus Lundborg
Fixes a bug in pull group
s
ize calculat
i
on
commit
|
commitdiff
|
tree
2018-09-07
Magnus Lundborg
Check
q pertur
b
ation when
PME on GPU i
s
tested
commit
|
commitdiff
|
tree
2018-06-04
Magn
u
s Lundborg
Writ
e
lambdas and b
o
x to TNG at corr
e
ct intervals
commit
|
commitdiff
|
tree
2018-03-29
Magnus Lundborg
Im
p
roved
c
heck of if only fo
r
ces are
c
ompute
d
in
d
o
_
pairs()
commit
|
commitdiff
|
tree
2017-12-05
M
a
gnu
s
Lundborg
SIMD a
c
c
elerated Urey-Bradley
commit
|
commitdiff
|
tree
2017-11-18
Magnus Lun
d
bo
r
g
Added Magnus L
u
ndbor
g
as
c
ontributor
i
n
the manual
.
Added
Magnus Lundborg
as contributor in the manual.
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|
commitdiff
|
tree
2017-11-08
Magnus L
u
n
dborg
Upda
t
e to TNG v 1
.
8
.
1
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|
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|
tree
2017-10-13
Mag
n
us
Lundborg
Do
n
o
t
in
c
lude
h
eaders related to
O
b
serva
b
lesHisto
r
y
commit
|
commitdiff
|
tree
2017-10-03
M
a
g
n
u
s
Lundbor
g
Write at
o
m masses and
p
artial
charges to TNG
commit
|
commitdiff
|
tree
2017-06-11
Magnus
L
u
n
dborg
Update
d
TNG to versio
n
1
.
8
commit
|
commitdiff
|
tree
2015-12-05
Ma
g
nus
Lund
b
org
Write forces and vel
o
citi
e
s
to
compre
s
sed TNG
.
commit
|
commitdiff
|
tree
2015-11-30
Magn
u
s Lun
d
b
org
Fixed
ty
p
o
s i
n
output
.
commit
|
commitdiff
|
tree
2015-11-25
Magn
u
s Lundborg
U
s
e local
variables instead of those in *ir
.
commit
|
commitdiff
|
tree
2015-06-24
M
a
gn
u
s Lundborg
Up
d
ate
h
eade
r
w
hen append
i
ng to TNG file
.
commit
|
commitdiff
|
tree
2015-06-12
M
a
gnus Lun
d
borg
TNG version
1
.
7
.
6
commit
|
commitdiff
|
tree
2015-05-16
Magnu
s
Lundborg
TN
G
version 1
.
7
.
5
commit
|
commitdiff
|
tree
2015-04-21
Magnus L
u
ndborg
TNG ver
s
i
o
n 1
.
7
.
3
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|
commitdiff
|
tree
2014-11-24
Magnus
L
u
n
dborg
When wr
i
t
ing TNG
t
he input must contain
m
ol
e
cule data
.
commit
|
commitdiff
|
tree
2014-09-02
Magnu
s
L
u
ndbo
r
g
TNG Fix
fo
r
GMX
_
DOUBL
E
build
s
a
n
d
where ZL
I
B
is not
.
.
.
commit
|
commitdiff
|
tree
2014-09-02
Mag
n
u
s Lundb
o
rg
Fix data block length
when unco
m
pressing TNG data
.
commit
|
commitdiff
|
tree
2014-09-01
Mag
n
u
s
Lund
b
org
TN
G
: Handle
l
arge
f
i
les on 32 bit systems
.
commit
|
commitdiff
|
tree
2014-09-01
Magnus Lu
n
dborg
When writ
i
ng
TN
G
i
n
clu
d
e file closi
n
g in
wal
l
cy
c
l
e
.
commit
|
commitdiff
|
tree
2014-08-21
Ma
g
nu
s
Lundborg
F
ix
e
d TNG mem
o
ry alignment
p
roblem and reset pointers
.
commit
|
commitdiff
|
tree
2014-07-05
M
a
gnus Lundborg
Fix bug c
a
using reading next fr
a
me
n
ot to stop
.
commit
|
commitdiff
|
tree
2014-07-05
Magnus Lund
b
org
Fix tng_num_
f
rame_s
e
ts
_
get() w
i
th no
fram
e
sets
.
commit
|
commitdiff
|
tree
2014-06-28
Magn
u
s Lu
n
dborg
Update TNG build system
commit
|
commitdiff
|
tree
2014-06-24
M
a
g
n
u
s
L
u
ndbor
g
Impr
o
ved check to decide if to add
chain/resid
u
e
.
commit
|
commitdiff
|
tree
2014-06-19
M
agnus Lundborg
Bumped t
h
e
T
NG library to
t
he latest versi
o
n
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundbor
g
F
i
x bug
writin
g
TNG outp
u
t from
dump
.
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundborg
Bu
g
fix i
n
the TN
G
library to improve re
a
ding
.
commit
|
commitdiff
|
tree
2014-04-24
M
agnus Lundborg
More e
f
fi
c
ient TNG sele
c
tion group cr
e
ati
o
n
commit
|
commitdiff
|
tree
2014-04-16
Magnus Lu
n
dborg
Fi
x
ed bu
g
inverting
c
omp
r
ession pre
c
ision
.
commit
|
commitdiff
|
tree
2014-03-01
M
a
g
nus Lundborg
Bu
m
p
e
d
T
NG
to
la
t
est version
.
commit
|
commitdiff
|
tree
2014-02-13
Magn
u
s Lundborg
One mo
r
e bump of
the TN
G
version
.
commit
|
commitdiff
|
tree
2014-02-13
Magnus
Lundbo
r
g
Removed option
to u
s
e O
p
enMP with
the TNG
l
i
brary
.
commit
|
commitdiff
|
tree
2014-02-12
Magnus Lun
d
b
o
rg
E
nable TNG
b
uilds
o
n Windows
b
y defau
l
t
.
commit
|
commitdiff
|
tree
2014-02-12
Magnus Lun
d
borg
Bum
p
ed TNG to
l
a
t
e
s
t vers
i
on
.
commit
|
commitdiff
|
tree
2014-02-11
Magnus Lund
b
or
g
Added informa
t
ion about how to
c
ite the TNG pap
e
r
.
commit
|
commitdiff
|
tree
2014-01-20
Mag
n
us Lundborg
Add TNG writing an
d
r
e
ading
s
u
p
port
commit
|
commitdiff
|
tree
2013-10-29
Ma
g
nus Lundborg
Fixed memory
leak in gmxdum
p
.
commit
|
commitdiff
|
tree
2013-09-02
Magnu
s
Lundborg
Set upper case
o
f FFTW var
i
able at
t
h
e
r
i
ght place
.
commit
|
commitdiff
|
tree
2013-04-29
Ma
g
nus Lundborg
F
i
xes "Function ty
p
e U-B no
t
implement
e
d in ip_pert
.
"
commit
|
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|
tree