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Merge branch 'master' of git://git.gromacs.org/gromacs
2010-01-11
M
ic
h
ael Shirt
s
Merge branch 'ma
s
t
e
r' o
f
git://git
.
gr
o
macs
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Mic
h
ael Shirts
M
e
rge branch 'master' of git
:
//git
.
gromacs
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Michael Shirts
Merge branch
'master' of gi
t
://
g
it
.
gromacs
.
org/gro
m
a
cs
commit
|
commitdiff
|
tree
2010-01-04
Michael
Shirts
Com
m
ented o
u
t s
o
me checking code useful for
t
he future
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
Removed so
m
e legacy
"#if 0" code
.
commit
|
commitdiff
|
tree
2010-01-04
Micha
e
l Shirts
M
erge branch 'master' of git
@
git
.
g
r
omacs
.
o
r
g:g
r
omacs
commit
|
commitdiff
|
tree
2010-01-04
Michae
l
Shirts
Impr
o
ved o
u
tpu
t
in mdebin
.
c
commit
|
commitdiff
|
tree
2010-01-04
M
i
chael Shir
t
s
No
l
o
n
ger need t
o
spec
i
fy f
e
p
-lambda eve
r
y
t
ime --
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Michael Shirts
fixes
f
o
r
h
a
ndling perio
d
icity for dihed
r
al restrain
t
s
.
commit
|
commitdiff
|
tree
2010-01-03
Michael Shirts
removed
c
ode that had been #ifdef'ed o
u
t
.
commit
|
commitdiff
|
tree
2010-01-03
Micha
e
l Sh
i
rts
Fixed the issues
w
ith
the rest
r
aint
c
alculati
o
ns
.
commit
|
commitdiff
|
tree
2010-01-02
Michael Shirts
Revis
i
on of h
a
ndling of
f
oreign lambda bonds
.
commit
|
commitdiff
|
tree
2010-01-01
Michael Sh
i
rts
Fix fo
r
nonb
o
n
d
eds
.
commit
|
commitdiff
|
tree
2010-01-01
M
i
chael Sh
i
rts
More fixe
s
for th
e
mult
i
c
om
p
o
n
ent lam
b
da
.
commit
|
commitdiff
|
tree
2010-01-01
Michael Shirts
Lates
t
revisi
o
n of free en
e
rgy
c
hanges
.
commit
|
commitdiff
|
tree
2009-12-29
M
i
c
hael
S
hirt
s
Free energy now appar
e
ntly
w
or
k
i
ng with multilambda
.
commit
|
commitdiff
|
tree
2009-12-27
Michael Sh
i
rts
Merge br
a
nc
h
'mas
t
er' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-27
Michae
l
S
h
ir
t
s
Merge branch 'mast
e
r
'
of git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-24
Michael S
h
irt
s
Fix
for in
i
tial energy
.
commit
|
commitdiff
|
tree
2009-12-23
Michae
l
Shirts
Merge branch 'ma
s
ter'
o
f git@git
.
gromacs
.
org:grom
a
cs
commit
|
commitdiff
|
tree
2009-12-23
Mic
h
ae
l
Shirts
Fi
x
ed pr
e
ssure d
i
spersi
o
n corr
e
ct
i
on order
.
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
Merge bran
c
h
'master' of git@git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2009-12-23
M
ic
h
ael S
h
irts
fixed sd
(
I thin
k
)
.
commit
|
commitdiff
|
tree
2009-12-22
Michae
l
Shirts
fixing order of DISPCORR a
n
d PRES
commit
|
commitdiff
|
tree
2009-12-22
Michael Shirts
Merge branch 'master' of git@git
.
grom
a
cs
.
o
r
g:gro
m
acs
commit
|
commitdiff
|
tree
2009-12-22
Michael Shirts
Formatting changes for c
a
lc_dispcorr
commit
|
commitdiff
|
tree
2009-12-20
Michael Shirts
Merge branch 'master' of git@git
.
groma
c
s
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-20
Micha
e
l Shirt
s
C
lea
n
up after l
a
st comm
i
t
.
commit
|
commitdiff
|
tree
2009-12-20
Michael
S
hirts
Fixed
some
p
r
oblems with calc
u
l
at
i
on
o
f dis
p
er
s
ion
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
M
ichael Shirts
Merge b
r
anch 'm
a
ster'
o
f git@g
i
t
.
groma
c
s
.
org:gromac
s
commit
|
commitdiff
|
tree
2009-12-20
Michael S
h
irts
Made defau
l
t va
l
ue of the number of nose-hoov
e
r chains
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Michael Shir
t
s
now
N
ose-
H
oover variables are written
to mdeb
i
n only
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Mich
a
el Shirts
Fix
e
d an issue wi
t
h
c
heckpointing not
getting the first
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirt
s
Merge
b
ranch 'master' of
g
it://git
.
gro
m
acs
.
o
rg/gro
m
acs
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
Committing to merge
commit
|
commitdiff
|
tree
2009-12-19
Mich
a
e
l
S
h
i
r
ts
com
m
iting to merge
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shir
t
s
c
hanged output options to be more concise in the d
i
sp
e
r
s
io
n
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael
S
h
irts
Some
b
ug fi
x
es f
o
r the dis
p
er
s
ion correction
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
Cha
n
ging the cpt file
number; can't quit
e
get it to
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirt
s
Changing the cpt ve
r
sion
;
can't
f
i
gur
e
out how to preserve
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Mi
c
h
ael S
h
irt
s
Merge branch 'master' of g
i
t@gi
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-19
Mich
a
e
l S
h
irts
Making the
c
ode
t
h
read safe (
r
em
o
ving the static ints
.
.
.
commit
|
commitdiff
|
tree
2009-12-17
Michael Shirts
Merge bra
n
ch 'm
a
ster' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-17
Michael
S
hirts
adde
d
bac
k
in nosehoo
v
er_xi to tpr to avoid incompatibilities
.
commit
|
commitdiff
|
tree
2009-12-17
Michael Sh
i
rts
Changed eiVV2 to eiVVAK, and "md-vv2" to "
m
d-v
v
-avek
.
.
.
commit
|
commitdiff
|
tree
2009-12-05
Mi
c
hae
l
Sh
i
rts
fix for rerun prin
t
ing
commit
|
commitdiff
|
tree
2009-12-05
M
i
chael Shirts
made s
o
me
o
utput fixes
.
commit
|
commitdiff
|
tree
2009-12-05
M
ichael
S
h
i
rts
Me
r
g
e
br
a
nch 'master'
o
f git@g
i
t
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2009-12-04
M
ichael Shirts
trying to get pa
r
allel version
c
orrect
.
commit
|
commitdiff
|
tree
2009-12-04
Mi
c
hael S
h
irts
Re
w
rite of the half-step ekin
for v
e
locity verlet,
.
.
.
commit
|
commitdiff
|
tree
2009-11-30
Michael Shirts
More changes
to get it wor
k
ing
wit
h
Ekin
A
veE
k
in
commit
|
commitdiff
|
tree
2009-11-30
M
i
chael Shirts
More fixes for c
o
rrect pressure with
E
kinAveEkin
commit
|
commitdiff
|
tree
2009-11-30
Michael S
h
irts
C
o
mmitting a
n
other fix!
commit
|
commitdiff
|
tree
2009-11-30
Michael
S
h
i
rts
Typo fix
.
commit
|
commitdiff
|
tree
2009-11-30
Mich
a
el Shirts
Fixed typo -- corr
e
ct
|
to
|
|
commit
|
commitdiff
|
tree
2009-11-30
Mich
a
el Shirts
Ano
t
h
e
r try for getting
p
a
rallel press
u
re co
m
putation
.
.
.
commit
|
commitdiff
|
tree
2009-11-30
Michael Shirts
Fix that will helpf
u
lly solve p
r
oblems for
pa
r
allel
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mic
h
ael Shirts
Fixed
a
bug introduced a
few commits
a
go for it
e
rativ
e
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Michael
Sh
i
rts
Added s
o
me ex
p
lan
a
t
ion on a code bit that may need
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Michael Shi
r
ts
Added some minor typo
fixes
.
Sh
o
ul
d
che
c
k
t
o
make
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
M
i
c
h
ael S
h
irts
R
e
version
o
f
last
c
h
e
c
k
in
g
-- didn't help
.
commit
|
commitdiff
|
tree
2009-11-29
Michael Shirts
Fix for s
e
t90
0
npt wi
t
h Ekin
A
ve
commit
|
commitdiff
|
tree
2009-11-29
Mic
h
ael Shirts
Change for parallel
i
zation
of p
r
ess
u
re calculation
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mi
c
hael Shir
t
s
Fix for par
a
lle
l
t
e
m
pe
r
a
tur
e
an
d
p
r
essure on
i
nitial
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mich
a
el Shir
t
s
New a
t
t
empt
t
o
c
orrectly pass paralle
l
i
n
f
o
rmati
o
n
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mi
c
hael Shirt
s
Typo fix
commit
|
commitdiff
|
tree
2009-11-29
Micha
e
l Shirts
Revert
"
A
t
tempt to
g
et pa
r
al
l
e
lization
wor
k
i
ng correctl
y
.
"
commit
|
commitdiff
|
tree
2009-11-29
Micha
e
l
Shirts
At
t
empt to make the pressu
r
e work i
n
p
a
rallel
!
commit
|
commitdiff
|
tree
2009-11-29
Michael Shir
t
s
Atte
m
pt
to g
e
t parallelization working correctly
.
commit
|
commitdiff
|
tree
2009-11-28
Michael S
h
irt
s
Working for checkpoin
t
in
g
in the
s
ame
w
ay as the CVS
.
.
.
commit
|
commitdiff
|
tree
2009-11-28
M
i
chael Shir
t
s
Che
c
k
p
oint
s
now wo
r
k
i
n
the single pr
o
ces
s
o
r case
commit
|
commitdiff
|
tree
2009-11-28
M
i
chael Shir
t
s
M
a
jority of comm
i
ts f
o
r corr
e
c
t
checkpointing
.
commit
|
commitdiff
|
tree
2009-11-27
Mich
a
e
l
Shi
r
t
s
M
e
rge branch 'mas
t
er' of git@g
i
t
.
gromac
s
.
o
r
g:gro
m
acs
commit
|
commitdiff
|
tree
2009-11-26
Mic
h
ael Shirts
C
orrection to use the reference pressure, not the exter
n
al
.
.
.
commit
|
commitdiff
|
tree
2009-11-26
Michael Shirts
Changed the
p
V term to
the correct o
n
e, wit
h
th
e
reference
.
.
.
commit
|
commitdiff
|
tree
2009-11-23
Michael Sh
i
r
ts
Co
m
menting
c
leanup
.
commit
|
commitdiff
|
tree
2009-11-23
M
ichael Shir
t
s
A
pparently wo
r
ks with
a
ll the methods now, both wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2009-11-22
Mic
h
ael
S
hirts
Checking in
code tha
t
does
all but N
P
T average Eki
n
.
commit
|
commitdiff
|
tree
2009-11-21
Micha
e
l Shirts
Working: md (matches all),
N
VE,NVT,NPT EkinA
v
eVel,
.
.
.
commit
|
commitdiff
|
tree
2009-11-20
Michael Shirts
W
o
rking with velocity verlet / harm
o
nic bond
s
with
.
.
.
commit
|
commitdiff
|
tree
2009-11-20
Mic
h
a
el Shirts
Almo
s
t
work
i
ng now! not vv
f
o
r
aver
a
ge kinetic
energ
y
.
.
.
commit
|
commitdiff
|
tree
2009-11-19
M
i
chael Shirts
Partwa
y
through wi
t
h rationalization of different i
n
tegrator
.
.
.
commit
|
commitdiff
|
tree
2009-11-18
M
i
chael Shirts
Fix for kin
e
tic average energy
.
commit
|
commitdiff
|
tree
2009-11-18
Michael Shirts
Memo
r
y bug fix
commit
|
commitdiff
|
tree
2009-11-17
M
ich
a
el Shirts
b
u
g f
i
x for
l
eap
.
commit
|
commitdiff
|
tree
2009-11-17
Michael Shirt
s
F
i
x for
i
n
itial pressu
r
e
f
o
r parallel
.
commit
|
commitdiff
|
tree
2009-11-17
Michae
l
Sh
i
rts
Some
fixes for s
t
a
rting w
i
th cons
t
raints
.
Right now
.
.
.
commit
|
commitdiff
|
tree
2009-11-17
Mic
h
ael
S
hi
r
ts
fix f
o
r
correct
p
ress
u
re in parallel
.
commit
|
commitdiff
|
tree
2009-11-16
Mi
c
ha
e
l Shirts
Bugfixes for refor
m
atting trotter s
e
tup
.
commit
|
commitdiff
|
tree
2009-11-15
Mic
h
ael Shirts
C
h
anged the organization
o
f trot
t
e
r
updates
to make
.
.
.
commit
|
commitdiff
|
tree
2009-11-14
Michael Shirts
Removed old
trotter code
commit
|
commitdiff
|
tree
2009-11-14
Mich
a
e
l Shir
t
s
chang
e
d
s
e
tu
p
of trotte
r
dec
o
mposition to mak
e
i
t
e
asier
.
.
.
commit
|
commitdiff
|
tree
2009-11-05
Michael
S
hirts
Fix
f
or
t
emperatur
e
not being co
m
puted
correctly
commit
|
commitdiff
|
tree
2009-11-05
Michael Shirts
n
e
w
t
r
y
at gett
i
ng
t
he multiprocessor te
m
perature to
.
.
.
commit
|
commitdiff
|
tree
2009-11-05
Mich
a
el
Shirts
Attempt to fix the pro
b
lem with tempera
t
ure comput
a
tion
.
.
.
commit
|
commitdiff
|
tree
2009-11-05
Michael Shirts
F
o
rma
t
changes to fix global
_
s
t
a
t temp
e
r
ature bug
.
.
.
commit
|
commitdiff
|
tree
2009-11-05
Mi
c
h
a
el
Shirts
Co
m
mitt
i
ng ch
a
nges to have the argument
s
to compute_globals
.
.
.
commit
|
commitdiff
|
tree
2009-11-04
M
i
c
ha
e
l Shir
t
s
Made function
s
acc
e
ssed on
l
y i
n
t
h
ei
r
own file stat
i
c
.
commit
|
commitdiff
|
tree
2009-10-25
Micha
e
l
Shirts
F
i
x for prop
e
r M
P
I
p
ressur
e
control
.
commit
|
commitdiff
|
tree
2009-10-25
M
i
chael Shirts
Added a bug fix f
o
r
c
ommunicat
i
on o
f
iterated inte
g
rator
.
.
.
commit
|
commitdiff
|
tree
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