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Raised the NHCHAINLENGTH default to 10
2010-06-12
Michael Shirt
s
Raised the NHCHAINLEN
G
TH defau
l
t to 1
0
commit
|
commitdiff
|
tree
2010-06-11
Mic
h
a
el
S
hirts
F
i
x
ed various logic probl
e
ms preventing
proper energy
.
.
.
commit
|
commitdiff
|
tree
2010-02-07
Michael Shirts
added a secon
d
ary
c
heck for
e
r
ror if
t
h
e
error is so
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Mi
c
hael Shirts
M
erge
b
ranch
'
master'
of
git@git
.
groma
c
s
.
org:
g
rom
a
cs
commit
|
commitdiff
|
tree
2010-02-03
Michael Shirts
Fix
f
or memory
error affecting par
a
llel s
i
mulation
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Mi
c
hael Shirts
A fix to c
o
m
pute_bonds_lambda
-
the
val
u
e o
f
nr_n
o
nperturbed
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Mich
a
el
S
hirts
R
e
visin
g
the iteration of NPT for single precision
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Mic
h
ael Sh
i
rts
Final fix for parallel
checkpointi
n
g with
N
ose-hoover
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Mi
c
hael Shirts
Contin
u
ing fixes
f
or checkp
o
inting
i
n p
a
rallel (also
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael Shi
r
t
s
M
e
rge branch 'master' of git@
g
it
.
groma
c
s
.
org:g
r
omacs
commit
|
commitdiff
|
tree
2010-01-22
M
i
chael Shirts
A variety
o
f changes to correctl
y
do chec
k
pointi
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Michael
S
h
irts
Re
m
o
ved warning cause
d
by
th
r
owing away 'c
o
nst' definition
.
commit
|
commitdiff
|
tree
2010-01-18
Micha
e
l
Shirts
Fixes for
entr
y
to a
n
d
r
eading ex
t
en
d
ed system variable
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-17
Michael Shirts
Ad
d
ing
back in change
s
tha
t
mysteriou
s
ly disap
p
eared
.
commit
|
commitdiff
|
tree
2010-01-17
Michael Shi
r
t
s
Revis
i
o
n
s to harmonize veloc
i
ty
v
erlet with Berk's
.
.
.
commit
|
commitdiff
|
tree
2010-01-11
Michael Shirts
Fixed typo in changing name of n
n
h
chains to nhc
h
ainlength
.
commit
|
commitdiff
|
tree
2010-01-11
Mich
a
el
S
hirt
s
removed
a
depe
n
d
ency on a
file
t
h
at did not exist
.
commit
|
commitdiff
|
tree
2010-01-11
M
ichael Shirts
change
s
t
h
e
nnhchains name to
n
hchai
n
length
commit
|
commitdiff
|
tree
2010-01-11
Mic
h
ael
S
hirts
Merge b
r
anch
'ma
s
ter' of g
i
t://
g
it
.
gro
m
ac
s
.
o
r
g/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Michael Shirts
Merge br
a
n
c
h 'mas
t
er' of git://g
i
t
.
gromacs
.
org/gromacs
commit
|
commitdiff
|
tree
2010-01-07
Michael Shirts
Merge
b
ranch 'master'
o
f g
i
t:
/
/git
.
gromacs
.
o
r
g/gromacs
commit
|
commitdiff
|
tree
2010-01-04
Michae
l
Shirts
Comment
e
d o
u
t som
e
c
heck
i
ng
c
ode u
s
eful for the
future
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
Removed some legacy "
#
i
f
0" code
.
commit
|
commitdiff
|
tree
2010-01-04
Mi
c
hael Shirts
Merge branch 'master
'
of git@git
.
g
ro
m
ac
s
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2010-01-04
Michael S
h
irts
Imp
r
oved output in mdebin
.
c
commit
|
commitdiff
|
tree
2010-01-04
Mi
c
hael
Shirts
N
o
longer need to
s
pecify fe
p
-la
m
bda eve
r
y time --
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Mi
c
hael Shirts
fixe
s
for han
d
l
i
ng periodicity for dihe
d
r
a
l
restraints
.
commit
|
commitdiff
|
tree
2010-01-03
Mi
c
hael Sh
i
rts
r
emoved co
d
e that had be
e
n
#ifdef'ed out
.
commit
|
commitdiff
|
tree
2010-01-03
Micha
e
l Shir
t
s
Fixed the iss
u
es with the restraint
c
a
lculations
.
commit
|
commitdiff
|
tree
2010-01-02
Michael
Shirt
s
R
evision of
han
d
li
n
g
o
f
for
e
i
g
n
la
m
bda b
o
nds
.
commit
|
commitdiff
|
tree
2010-01-01
Michael
Shirts
Fix
f
or
nonbondeds
.
commit
|
commitdiff
|
tree
2010-01-01
Mic
h
a
e
l
S
hirts
More fixes for
the m
u
lti
c
o
mponent l
a
m
b
d
a
.
commit
|
commitdiff
|
tree
2010-01-01
M
ichael
Shirts
Lates
t
r
evision of free energy chang
e
s
.
commit
|
commitdiff
|
tree
2009-12-29
Michae
l
Sh
i
rts
Free e
n
ergy now apparent
l
y working with mul
t
ilambda
.
commit
|
commitdiff
|
tree
2009-12-27
Mic
h
ael Shirts
Merge branch 'master'
o
f git@git
.
gromacs
.
org:g
r
o
m
acs
commit
|
commitdiff
|
tree
2009-12-27
Michael Sh
i
r
t
s
Merge b
r
anch 'ma
s
ter' of git@g
i
t
.
gromac
s
.
o
rg:gromac
s
commit
|
commitdiff
|
tree
2009-12-24
Michael Shirts
Fix for initial energy
.
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
Merge branch 'master' of git@git
.
gromacs
.
org:groma
c
s
commit
|
commitdiff
|
tree
2009-12-23
M
ich
a
el Shirts
F
ixed pressu
r
e
d
i
sp
e
r
s
ion corre
c
tion
ord
e
r
.
commit
|
commitdiff
|
tree
2009-12-23
Mich
a
el Shirts
Merge
b
ranch
'm
a
ster' of git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
fixed
s
d
(I think)
.
commit
|
commitdiff
|
tree
2009-12-22
M
i
cha
e
l Shirts
fixing order of DISPCORR and PRES
commit
|
commitdiff
|
tree
2009-12-22
M
ichael Shirts
Merge branc
h
'm
a
s
t
er' of git@g
i
t
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-22
Michael
S
hi
r
ts
Form
a
tting changes for c
a
lc_disp
c
orr
commit
|
commitdiff
|
tree
2009-12-20
M
i
c
hael Shirt
s
Merge br
a
nch 'master' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-20
Michael
S
h
i
r
ts
Cleanup after last comm
i
t
.
commit
|
commitdiff
|
tree
2009-12-20
Michael Shirts
Fixed so
m
e
p
roblem
s
with c
a
lculation of di
s
per
s
ion
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Michael Shirts
Merge branch 'master
'
of git
@
g
it
.
g
r
omacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2009-12-20
M
ich
a
el Shirts
Made defa
u
l
t
v
alue
o
f the num
b
er o
f
nose-hoover chai
n
s
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Micha
e
l Shirts
no
w
Nose-Hoover variables a
r
e writte
n
to mdebin onl
y
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Michae
l
Shirts
Fixed an is
s
ue with checkpointi
n
g not
getting th
e
first
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
Merg
e
branch '
m
as
t
er' of git://
g
it
.
gromacs
.
org
/
groma
c
s
commit
|
commitdiff
|
tree
2009-12-19
Michael
S
h
i
rts
C
o
mmitting t
o
merge
commit
|
commitdiff
|
tree
2009-12-19
M
i
chael
S
hirts
commiting to m
e
r
g
e
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Sh
i
rts
chang
e
d outpu
t
o
p
t
i
ons to be more conc
i
s
e in the dispersio
n
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Mich
a
e
l
Shirts
Some bug fi
x
es for the
d
i
spersion
correc
t
ion
.
commit
|
commitdiff
|
tree
2009-12-19
M
ichael Shirts
Changing
t
h
e cpt file number
;
can't quite get it to
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
M
ichael Shir
t
s
Changing the cpt
vers
i
o
n;
c
an't fi
g
ure out h
o
w
to pr
e
serv
e
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shir
t
s
Merge branch 'master' of git@
g
i
t
.
gro
m
acs
.
o
rg:
g
romacs
commit
|
commitdiff
|
tree
2009-12-19
Micha
e
l
Shirts
Making the code thread safe (removing the stat
i
c
i
n
t
s
.
.
.
commit
|
commitdiff
|
tree
2009-12-17
M
i
ch
a
el Shirts
Merg
e
b
r
anch 'master' of git@
g
it
.
groma
c
s
.
org
:
gromacs
commit
|
commitdiff
|
tree
2009-12-17
Mic
h
ael Shirt
s
added ba
c
k in no
s
ehoover_
x
i
to tpr t
o
avoid i
n
compatib
i
liti
e
s
.
commit
|
commitdiff
|
tree
2009-12-17
Mi
c
hael
S
h
i
rts
C
h
anged
e
iVV2 to
e
iVVAK
,
and "md-vv2"
t
o "
m
d-
v
v-avek
.
.
.
commit
|
commitdiff
|
tree
2009-12-05
Michael Shirts
f
ix for r
e
run
printing
commit
|
commitdiff
|
tree
2009-12-05
M
ichael Shirts
made some outp
u
t
f
i
xes
.
commit
|
commitdiff
|
tree
2009-12-05
Michael Shirts
Merge branch 'master' of git@git
.
gromacs
.
org:grom
a
c
s
commit
|
commitdiff
|
tree
2009-12-04
M
i
c
h
ael Shirts
trying to get par
a
llel version corre
c
t
.
commit
|
commitdiff
|
tree
2009-12-04
Michae
l
S
h
ir
t
s
R
e
write of
t
h
e
h
alf-step eki
n
for veloc
i
t
y verlet,
.
.
.
commit
|
commitdiff
|
tree
2009-11-30
Michael Sh
i
r
t
s
More chang
e
s to get it working with EkinAveEkin
commit
|
commitdiff
|
tree
2009-11-30
Michael Shirts
M
o
re fixes for cor
r
ect p
r
essure w
i
t
h Ekin
A
veEkin
commit
|
commitdiff
|
tree
2009-11-30
Michael
S
h
i
rts
Comm
i
tti
n
g anot
h
er fix!
commit
|
commitdiff
|
tree
2009-11-30
Michael Shirts
Typo fix
.
commit
|
commitdiff
|
tree
2009-11-30
Mi
c
hael Shirts
Fixed t
y
p
o
--
c
orrect | to ||
commit
|
commitdiff
|
tree
2009-11-30
Mich
a
el Shirts
An
o
ther try fo
r
getti
n
g
paral
l
el
pressure co
m
putation
.
.
.
commit
|
commitdiff
|
tree
2009-11-30
Michael
S
hirts
Fix tha
t
will helpf
u
lly sol
v
e problems for paral
l
el
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mi
c
hael Shirts
Fixed a b
u
g
intr
o
duced
a
few commits ago f
o
r iterative
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Michael Shirts
Added some explanation on a code bit th
a
t
m
a
y
need
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Michael Shirts
A
d
de
d
some mi
n
or typo fixes
.
Should ch
e
ck to
m
ak
e
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mic
h
ael Shirts
Reversion of last
checking -- didn't help
.
commit
|
commitdiff
|
tree
2009-11-29
Michael Shirts
Fix fo
r
s
e
t900npt with EkinAv
e
commit
|
commitdiff
|
tree
2009-11-29
Mi
c
hael Shirt
s
Change
f
or p
a
r
alleliz
a
t
i
on of press
u
r
e c
a
lculation
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
M
i
chael Shir
t
s
Fix for parallel temperat
u
re and pressure on i
n
itial
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
M
ichael
S
hirts
Ne
w
a
t
t
e
mpt
to cor
r
e
c
t
l
y pass parallel inform
a
tion
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mich
a
el
Shir
t
s
Ty
p
o
f
ix
commit
|
commitdiff
|
tree
2009-11-29
Michael Shirts
Reve
r
t "Attempt to get paralleli
z
ation w
o
rkin
g
correctly
.
"
commit
|
commitdiff
|
tree
2009-11-29
M
i
chael Shirts
Attempt
to
m
ake the pr
e
ssure wor
k
in pa
r
alle
l
!
commit
|
commitdiff
|
tree
2009-11-29
M
i
ch
a
el Shirts
Att
e
mpt to get paralle
l
ization wo
r
k
i
n
g co
r
rectly
.
commit
|
commitdiff
|
tree
2009-11-28
Michael Shirts
Working for
c
h
eckpointing in
the
s
a
m
e
way as the CVS
.
.
.
commit
|
commitdiff
|
tree
2009-11-28
Mic
h
ael Shir
t
s
Checkpoint
s
n
o
w wo
r
k
i
n the
s
ing
l
e
p
r
o
c
essor cas
e
commit
|
commitdiff
|
tree
2009-11-28
Michael Shirts
Majori
t
y of commits f
o
r cor
r
ect check
p
o
i
nting
.
commit
|
commitdiff
|
tree
2009-11-27
M
ichael
Shir
t
s
Mer
g
e branch
'
ma
s
te
r
'
of g
i
t@
g
it
.
groma
c
s
.
org:grom
a
c
s
commit
|
commitdiff
|
tree
2009-11-26
Michael Shirts
Corre
c
t
i
on t
o
use the refer
e
n
c
e pr
e
ssure, not the extern
a
l
.
.
.
commit
|
commitdiff
|
tree
2009-11-26
Michael Shirts
Changed the pV term to the corre
c
t
one, with the referenc
e
.
.
.
commit
|
commitdiff
|
tree
2009-11-23
M
i
chael Shirts
C
o
mmen
t
ing
c
le
a
nu
p
.
commit
|
commitdiff
|
tree
2009-11-23
Micha
e
l Shirts
Ap
p
arently work
s
wi
t
h all the methods
n
ow, b
o
t
h wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2009-11-22
Micha
e
l
Shirt
s
Che
c
k
i
ng in code th
a
t
d
oes
all but NPT average
Ekin
.
commit
|
commitdiff
|
tree
2009-11-21
Mi
c
hael Shirts
Wor
k
ing
:
md (matches
a
ll), NVE,NVT,N
P
T
E
kinAveVel
,
.
.
.
commit
|
commitdiff
|
tree
2009-11-20
Michael Shir
t
s
W
o
r
ki
n
g with velocity verlet /
harm
o
nic bo
n
d
s
with
.
.
.
commit
|
commitdiff
|
tree
2009-11-20
Michael Shirts
Almost working
n
ow! not
vv f
o
r aver
a
ge kinetic energy
.
.
.
commit
|
commitdiff
|
tree
2009-11-19
M
i
chael
S
h
irts
P
a
rtw
a
y t
h
ro
u
gh with
r
ationaliz
a
ti
o
n of different i
n
tegrator
.
.
.
commit
|
commitdiff
|
tree
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