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Basic support for transforming KeyValueTrees
2016-07-11
Micha
e
l Shir
t
s
Fix
for incor
r
e
c
tly setting e
x
panded ensemble
w
hen
.
.
.
commit
|
commitdiff
|
tree
2016-01-07
M
icha
e
l Shirts
Fixe
s
two problems related
t
o restarts for
v
v
.
commit
|
commitdiff
|
tree
2015-10-12
M
i
chael
Shirts
F
ix for lack o
f
C
O
M
rem
o
val
for
m
d-vv
commit
|
commitdiff
|
tree
2015-08-18
M
ichael Shirts
Fix
f
or expanded en
s
e
mble
.
commit
|
commitdiff
|
tree
2015-04-30
Michael
Shirts
Fix for rare
l
y occur
i
ng replica exchan
g
e
e
rror
.
commit
|
commitdiff
|
tree
2014-06-29
Michael Shirts
Al
l
ow pri
n
ting potential
e
ner
g
ies
to d
h
dl
.
xvg file
commit
|
commitdiff
|
tree
2014-04-21
M
i
chae
l
Shirts
Issue
w
ar
n
ings for potential swit
c
h
w/o definin
g
swit
c
h
.
.
.
commit
|
commitdiff
|
tree
2014-02-26
Michael
Shirts
Updating and imp
r
oving A
n
ders
e
n thermost
a
t documentation
commit
|
commitdiff
|
tree
2014-02-06
Michael S
h
irts
E
E
dhdl hea
d
er
should not sp
e
cify o
n
e
l
ambda
commit
|
commitdiff
|
tree
2013-10-17
Mich
a
el
Shirts
Res
t
arting from
checkpoint no longer reinitializes
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Michael Shirts
t
urning off expa
n
ded
e
nsemb
l
e for all integrators
but
.
.
.
commit
|
commitdiff
|
tree
2013-10-16
Michael Shirts
F
i
xes
a problem with pair type 2 inte
r
action
s
with
.
.
.
commit
|
commitdiff
|
tree
2013-09-26
Mic
h
ae
l
Shi
r
ts
l
o
g
i
c
fix
for free energies with mdrun -rerun
commit
|
commitdiff
|
tree
2013-09-16
Michael Shirts
Fixing manual for sc
-
coul description
.
commit
|
commitdiff
|
tree
2013-08-02
Michael Shirts
Fixing proble
m
cau
s
ed by
o
verf
l
ow in expa
n
ded ensemble
.
commit
|
commitdiff
|
tree
2013-06-20
Michael
S
hirt
s
Fixing a
p
roblem when dhdl and replex are not multiples
commit
|
commitdiff
|
tree
2013-05-30
Mic
h
ael Shirts
F
i
xing the cons
t
r
a
int dhdl te
r
m in
s
hake
commit
|
commitdiff
|
tree
2013-05-26
Mic
h
ael Shi
r
ts
F
i
x of memory leak
commit
|
commitdiff
|
tree
2013-05-21
Michael Shirts
Fixed probl
e
m with
b
ond
c
o
nstraint dhdl
being left out
commit
|
commitdiff
|
tree
2013-05-08
Michael Shirts
f
i
x
ing rerun with free ene
r
gy +
.
xtc or
.
g
ro
commit
|
commitdiff
|
tree
2013-04-30
Michael Shirts
Fix
i
ng hand
l
ing
o
f perturb
a
tion
mass changes
.
commit
|
commitdiff
|
tree
2013-04-26
Michae
l
Shirts
Fixi
n
g a
p
roblem with dh/dl 1-4 interactions
commit
|
commitdiff
|
tree
2013-02-25
Michael Shirts
fix imcompatibility
w
ith
t
pr ver
s
<64 with fre
e
en
e
rgy
.
.
.
commit
|
commitdiff
|
tree
2013-02-15
Michae
l
Shi
r
ts
bu
g
fix fo
r
md
-
vv + no
s
e-hoover + (nstcalcenergy > n
s
ttcouple)
commit
|
commitdiff
|
tree
2013-01-18
Michael Shi
r
ts
Adden
d
um for
expanded ensemble
options plus f
o
r
m
a
tting
.
.
.
commit
|
commitdiff
|
tree
2013-01-16
Mi
c
hae
l
Sh
i
rts
f
i
xes issues with pressure control an
d
infrequent evaluation
commit
|
commitdiff
|
tree
2013-01-15
M
icha
e
l Shirts
Continuation of docu
m
entation for ex
p
anded ensemble
.
commit
|
commitdiff
|
tree
2013-01-13
Michael Shirts
F
ixes for md-vv and rer
u
n
commit
|
commitdiff
|
tree
2013-01-01
Michael Shirts
Fixed
a
bug that wi
t
h multiple exc
h
a
n
ges
commit
|
commitdiff
|
tree
2012-12-20
Mi
c
hael Shi
r
ts
Fixe
s
for
andersen temperature
c
o
ntrol
commit
|
commitdiff
|
tree
2012-12-20
Mich
a
el Shirts
Fixes for
e
x
p
anded ensemble an
d
H
R
E
PEX
commit
|
commitdiff
|
tree
2012-12-20
Mich
a
el Shirts
Fix for
t
h
e pre
s
sure in MTT
K
wit
h
constra
i
n
t
s +
dispersion
commit
|
commitdiff
|
tree
2012-12-14
Michael Sh
i
rts
Fix
e
s redmine issue
#107
1
commit
|
commitdiff
|
tree
2012-12-06
M
ichael Shir
t
s
Removing (inaccurate)
virial temp
e
rature calc
.
commit
|
commitdiff
|
tree
2012-11-27
Michael Shir
t
s
Remo
v
es memory allocat
i
on f
r
om free energy
f
o
reig
n
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Michael Shirts
Cl
a
rifica
t
ion of mdp_op
t
,
a
dd
n
st
e
xp
a
n
d
d
ef
a
ults &
.
.
.
commit
|
commitdiff
|
tree
2012-10-12
Michael Sh
i
rts
F
i
xing iss
u
es with
r
ep
l
ic
a
exch
a
nge
commit
|
commitdiff
|
tree
2012-07-31
M
i
ch
a
el Shi
r
ts
Added a check for ef
e
p
t
hat wa
s
missing
.
commit
|
commitdiff
|
tree
2012-07-29
Michael S
h
i
r
ts
F
i
x
in
when to call t
h
e constraints
for anderse
n
.
commit
|
commitdiff
|
tree
2012-06-29
Mic
h
ae
l
Shirts
M
i
nor formatti
n
g and c
o
nsis
t
e
n
c
y
c
hanges to
t
x
tdump
.
c
commit
|
commitdiff
|
tree
2012-06-29
M
ichael Shirts
Correcte
d
c
h
e
ckpo
i
nt
ve
r
sion issues with free ene
r
gy
.
.
.
commit
|
commitdiff
|
tree
2012-06-24
M
i
chael S
h
irts
M
erg
e
"Fix mdp_opt fo
r
matting of ex
p
an
d
ed
e
nsemble
.
.
.
commit
|
commitdiff
|
tree
2012-06-04
Mi
c
h
a
el Shirts
M
e
r
ging in free energy, exp
.
e
nsemble, &
a
nder
s
en t
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
Michael Shirt
s
Fixes problems w
i
th g_m
s
d
and g_energ
y
commit
|
commitdiff
|
tree
2011-09-05
Michael Shirts
Merge
"fixed
in
c
orrect pV t
e
rm
i
n the
e
nergy file"
.
.
.
commit
|
commitdiff
|
tree
2011-07-22
Michae
l
Shirts
n
u
mbe
r
of d
e
grees of freedom can be f
r
actional -- in
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael
S
hirts
Additi
o
nal
fixes to
t
he nst
t
c
o
up
l
e and nstpcouple working
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael
Shirts
A
d
ditional
changes for setting nst
t
couple
commit
|
commitdiff
|
tree
2010-08-19
Mic
h
ael Shirt
s
Fix for readir
.
c so that nstpcouple and ns
t
tc
o
u
p
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Mic
h
ael Shirts
Fixed bug w
i
th
md-v
v
and with v-
r
esc
a
le
commit
|
commitdiff
|
tree
2010-08-19
Michael Shi
r
ts
P
roposed fix for v-resc
a
le a
n
d berends
e
n
for velocity
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
Michael Shirts
Merg
e
bra
n
c
h
'releas
e
-4-
5
-patches' of git@git
.
groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael Shirts
Mer
g
e branch 'release-4-5-patch
e
s'
of git
@
git
.
gr
o
ma
c
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael Shirts
Merge branch '
r
elea
s
e-4
-
5-patches' of
git
@
git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-18
Michael Shirts
Changed the way
e
ner
g
y conse
r
vat
i
on
b
o
oke
e
ping is d
o
ne
.
commit
|
commitdiff
|
tree
2010-08-17
M
i
chael Shirts
Me
r
ge branch 'release-4-5-patches' o
f
git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-08-13
Mi
c
hae
l
Shirts
T
r
ying to get vscale working
w
ith vv
.
commit
|
commitdiff
|
tree
2010-08-09
Michael Shirts
Firs
t
pas
s
at get
t
i
n
g VV / v-r
e
scale f
o
rmula correct
.
commit
|
commitdiff
|
tree
2010-08-07
Mic
h
ael Sh
i
r
t
s
E
l
iminated s
o
me commen
t
ed out code
.
commit
|
commitdiff
|
tree
2010-07-11
Mich
a
el
Sh
i
r
t
s
Fixed i
n
itial display o
f
t
emperature f
o
r md-vv
-
av
e
k
commit
|
commitdiff
|
tree
2010-07-10
Mi
c
hael Shirts
Removed c++
s
tyle
comment
.
commit
|
commitdiff
|
tree
2010-07-10
Michael
S
hirts
Fixe
d
m
i
no
r
formatting co
n
f
lict
.
commit
|
commitdiff
|
tree
2010-07-10
Michae
l
Shi
r
t
s
Fixi
n
g th
e
inclu
d
e file de
f
ini
t
ion f
o
r trotter_update
.
commit
|
commitdiff
|
tree
2010-06-27
Mic
h
ael Shirts
Merge
b
r
anch 'mast
e
r' o
f
g
i
t@git
.
gro
m
acs
.
org:gromac
s
commit
|
commitdiff
|
tree
2010-06-27
M
i
ch
a
e
l
Shir
t
s
Fi
x
ed
g
mx_membed
.
c to agr
e
e with dom
d
.
c
commit
|
commitdiff
|
tree
2010-06-27
Mi
c
hael
S
hir
t
s
R
esto
r
ed
t
he for
b
idding of nstcalcenergy for vv fo
r
.
.
.
commit
|
commitdiff
|
tree
2010-06-27
Michael Shirts
*Starte
d
to
a
dd s
u
pport of nstcalce
n
e
r
gy to
v
v versio
n
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-22
Michael
S
hirts
Harded the shake constraint package
so that
i
t couldn
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Michael Sh
i
rts
M
erge branch 'master' of git@git
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-06-20
M
ichael
S
h
irts
Eliminating the nstcalc
iss
u
e with v
v
--
i
t
should
.
.
.
commit
|
commitdiff
|
tree
2010-06-20
Mi
c
hael Shi
r
ts
a
d
ded m
o
re information in mdp options
.
commit
|
commitdiff
|
tree
2010-06-12
M
i
chael Shi
r
t
s
R
a
i
s
ed the NHCHAINLENGTH
default to
1
0
commit
|
commitdiff
|
tree
2010-06-11
Micha
e
l Sh
i
rts
Fixed various logic proble
m
s preventing proper en
e
rgy
.
.
.
commit
|
commitdiff
|
tree
2010-02-07
Mich
a
el Shirts
a
dded a secondary check fo
r
e
rror if the error is s
o
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Michael Shirts
Merge
b
ranc
h
'ma
s
t
e
r
' of g
i
t@g
i
t
.
gromacs
.
o
r
g:g
r
o
macs
commit
|
commitdiff
|
tree
2010-02-03
Michael Shirts
Fix for m
e
mo
r
y
error affe
c
ting paral
l
el simula
t
ions
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Michael
Shirts
A
f
i
x to compute_bo
n
ds_lambda -
t
he
val
u
e of nr_no
n
p
e
r
turbed
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Michael Shi
r
ts
Rev
i
sin
g
the
i
teration
o
f
NPT for single precision
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Mich
a
el Shirts
Final
fix for par
a
llel c
h
e
ckpoin
t
ing wi
t
h Nose-hoover
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirts
Contin
u
ing fixes
f
o
r
checkpo
i
nting in
parallel
(also
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michae
l
Shirts
Merg
e
br
a
nch 'ma
s
ter' of git@git
.
g
romacs
.
o
r
g:gro
m
acs
commit
|
commitdiff
|
tree
2010-01-22
Mi
c
hael Shir
t
s
A
v
ariet
y
of changes t
o
corr
e
ct
l
y
d
o checkpointing
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Michael Shirts
R
e
moved wa
r
ning caused by
throwing away 'const'
d
efinit
i
o
n
.
commit
|
commitdiff
|
tree
2010-01-18
Michael Shirt
s
Fixes f
o
r entry to and rea
d
i
n
g
extended system
var
i
able
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-17
Michael
Shirts
A
d
ding back in chang
e
s that my
s
teriously dis
a
ppeared
.
commit
|
commitdiff
|
tree
2010-01-17
Mic
h
ael Shirts
R
evisions to harmoniz
e
velocity verlet with Be
r
k's
.
.
.
commit
|
commitdiff
|
tree
2010-01-11
Mi
c
hael Shirts
Fixed t
y
po in ch
a
ng
i
n
g na
m
e of nnhcha
i
ns to nh
c
hainlen
g
th
.
commit
|
commitdiff
|
tree
2010-01-11
M
i
cha
e
l Shirts
r
emo
v
ed a dependen
c
y on
a
f
i
l
e
that
did not exist
.
commit
|
commitdiff
|
tree
2010-01-11
M
ich
a
el Sh
i
rts
changes the nnhc
h
ains nam
e
t
o
nhchainlength
commit
|
commitdiff
|
tree
2010-01-11
Mich
a
e
l
S
hirts
Merge branch 'master' of git://git
.
gromacs
.
o
rg/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Michael Sh
i
rts
Merge bra
n
ch
'
maste
r
' o
f
git
:
//git
.
grom
a
cs
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Michael Shirts
Merge br
a
nch 'master' of
g
i
t
://git
.
gr
o
macs
.
or
g
/gromacs
commit
|
commitdiff
|
tree
2010-01-04
Michael
S
h
irts
Comme
n
ted out some che
c
king c
o
de
use
f
u
l for the futur
e
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
R
emo
v
ed some legacy "
#
if 0"
c
ode
.
commit
|
commitdiff
|
tree
2010-01-04
Michael Shi
r
ts
M
e
r
ge
b
r
anc
h
'm
a
s
t
e
r'
of git@
g
it
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
Improved output
i
n
m
d
e
b
in
.
c
commit
|
commitdiff
|
tree
2010-01-04
Michael Shir
t
s
No lo
n
ge
r
need t
o
specify
fep-lambda ever
y
time --
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Mi
c
hael Shirt
s
fix
e
s
for handli
n
g periodic
i
ty for dihedral res
t
raints
.
commit
|
commitdiff
|
tree
2010-01-03
M
i
chael Shirts
removed code
th
a
t had
been #
i
f
d
ef'ed
out
.
commit
|
commitdiff
|
tree
2010-01-03
Michael Shirts
F
i
xed the is
s
ue
s
w
ith
t
h
e restraint calcu
l
a
tions
.
commit
|
commitdiff
|
tree
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