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Fixed various logic problems preventing proper energy conservation for velocity verlet.
2010-06-11
M
i
ch
a
el Shirts
Fi
x
ed variou
s
logic
p
rob
l
ems
preventing p
r
oper en
e
r
gy
.
.
.
commit
|
commitdiff
|
tree
2010-02-07
M
i
chael Sh
i
rts
added a se
c
o
nda
r
y check for error if t
h
e error is so
.
.
.
commit
|
commitdiff
|
tree
2010-02-03
Michael Shirt
s
Merge branch 'mast
e
r'
of git@g
i
t
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-02-03
Mich
a
e
l
Shirts
Fix for me
m
ory error affecting parallel simulat
i
ons
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Mich
a
el Shi
r
ts
A
f
i
x
t
o co
m
pute_b
o
nds_lam
b
da -
the value of nr_n
o
nper
t
urbed
.
.
.
commit
|
commitdiff
|
tree
2010-01-30
Michael Shirts
Revising
the iteration of NPT for
s
i
ngle
p
recisi
o
n
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael Shirts
Fina
l
f
i
x for
parallel ch
e
ckpointing wi
t
h Nose-hoo
v
er
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael
S
hirts
Continuing
f
ixes for checkpointing
i
n parallel (also
.
.
.
commit
|
commitdiff
|
tree
2010-01-22
Michael
Shirts
Merge branch 'ma
s
ter' o
f
git@
g
it
.
gromacs
.
o
r
g:gro
m
acs
commit
|
commitdiff
|
tree
2010-01-22
Mic
h
a
e
l Shirts
A var
i
ety of changes
to
c
orrectly do chec
k
pointi
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-01-18
Michael
S
hirts
R
e
move
d
warning cau
s
ed by throwing
a
way
'const'
d
e
f
i
n
ition
.
commit
|
commitdiff
|
tree
2010-01-18
Mich
a
e
l
S
h
irts
Fixes for entry to and reading
ext
e
nded s
y
stem
variab
l
e
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-17
Michael Shirts
Adding back in changes th
a
t
mysteriousl
y
disappe
a
red
.
commit
|
commitdiff
|
tree
2010-01-17
Michael Shi
r
ts
Revi
s
ions
t
o harmo
n
ize velo
c
ity ver
l
et with
B
erk'
s
.
.
.
commit
|
commitdiff
|
tree
2010-01-11
Mi
c
hae
l
Shirts
Fi
x
e
d typo
in
c
h
angin
g
name
of nnhcha
i
ns to nhchainl
e
ngth
.
commit
|
commitdiff
|
tree
2010-01-11
M
i
chael Shirts
removed
a
depend
e
n
c
y on a file that did
not exist
.
commit
|
commitdiff
|
tree
2010-01-11
Mic
h
a
e
l Shirts
change
s
the n
n
hchains name to nhchainlength
commit
|
commitdiff
|
tree
2010-01-11
M
i
chael Shirts
Merge b
r
anch 'master' of git://git
.
gr
o
macs
.
org/gr
o
macs
commit
|
commitdiff
|
tree
2010-01-07
Mic
h
ael Shirt
s
Mer
g
e
bran
c
h
'master'
o
f
g
it
:
//git
.
g
rom
a
cs
.
org/
g
romac
s
commit
|
commitdiff
|
tree
2010-01-07
Michael S
h
irts
Merg
e
branch
'master' of git:/
/
g
i
t
.
gromacs
.
org/groma
c
s
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
Com
m
ented out some check
i
ng code u
s
e
ful f
o
r the fu
t
ure
.
.
.
commit
|
commitdiff
|
tree
2010-01-04
M
ich
a
el Shirt
s
Remov
e
d so
m
e
lega
c
y "#
i
f 0" code
.
commit
|
commitdiff
|
tree
2010-01-04
Michael S
h
irts
Merge branch 'maste
r
' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
Improved
o
u
tp
u
t in md
e
bin
.
c
commit
|
commitdiff
|
tree
2010-01-04
Michael Shirts
No longer need
t
o sp
e
cify fep-lambda every time --
.
.
.
commit
|
commitdiff
|
tree
2010-01-03
Michael Shir
t
s
fi
x
e
s
for handling per
i
od
i
city for
d
i
h
edral
restraints
.
commit
|
commitdiff
|
tree
2010-01-03
M
i
c
hael Shirts
removed code that ha
d
be
e
n
#ifdef'
e
d out
.
commit
|
commitdiff
|
tree
2010-01-03
Mich
a
el Sh
i
r
t
s
Fixed t
h
e issues with th
e
r
e
straint calculat
i
o
ns
.
commit
|
commitdiff
|
tree
2010-01-02
Michael Shirts
Revisi
o
n of handlin
g
of foreign lamb
d
a bonds
.
commit
|
commitdiff
|
tree
2010-01-01
Michae
l
Sh
i
rts
Fix for nonbo
n
deds
.
commit
|
commitdiff
|
tree
2010-01-01
Mic
h
ae
l
Shirt
s
More fixes f
o
r the multicomponent lamb
d
a
.
commit
|
commitdiff
|
tree
2010-01-01
Mic
h
ael Shi
r
ts
Lates
t
revi
s
ion o
f
fr
e
e
e
nergy changes
.
commit
|
commitdiff
|
tree
2009-12-29
Mi
c
hael
Shirt
s
Fre
e
ene
r
gy now appare
n
tly workin
g
with
multilambda
.
commit
|
commitdiff
|
tree
2009-12-27
M
i
chael S
h
irts
M
e
r
g
e branc
h
'master' of
git@git
.
gromacs
.
org:gr
o
macs
commit
|
commitdiff
|
tree
2009-12-27
Michae
l
Shirts
Me
r
ge
b
ranch 'm
a
s
ter'
o
f git@git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2009-12-24
Mich
a
el
Shirts
Fix for initial energy
.
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
Merge
b
ranch 'ma
s
te
r
'
of git@git
.
gr
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirt
s
Fixe
d
pressure dispersion correcti
o
n order
.
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
Merge bra
n
ch 'master
'
o
f
git@git
.
gromacs
.
or
g
:gromacs
commit
|
commitdiff
|
tree
2009-12-23
Michael Shirts
fi
x
ed sd (I think)
.
commit
|
commitdiff
|
tree
2009-12-22
Mich
a
el Shirts
fixing o
r
d
e
r of DIS
P
C
ORR an
d
PR
E
S
commit
|
commitdiff
|
tree
2009-12-22
Michael Shirts
Merge b
r
anch 'mas
t
er' of git
@
git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-22
Michael Sh
i
rt
s
F
o
rmattin
g
changes for ca
l
c_
d
ispcorr
commit
|
commitdiff
|
tree
2009-12-20
Michael
S
h
irts
M
e
rge branch 'mast
e
r' of
git@git
.
gromacs
.
org
:
gr
o
macs
commit
|
commitdiff
|
tree
2009-12-20
Michael Shi
r
t
s
Cleanup afte
r
las
t
c
om
m
it
.
commit
|
commitdiff
|
tree
2009-12-20
M
i
chael
Shirts
Fixed so
m
e problems with calc
u
latio
n
of di
s
p
ersion
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Micha
e
l Shirts
M
erge
b
ra
n
ch 'master' of
g
it@git
.
g
r
omacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-20
M
ichael
S
hirts
Made default va
l
ue of
t
he numb
e
r of nose-hoover ch
a
ins
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Michael
Shirts
now Nose-Ho
o
v
e
r variables are written to md
e
bin o
n
ly
.
.
.
commit
|
commitdiff
|
tree
2009-12-20
Michael Shirts
Fixed
a
n issue with c
h
eckpoint
i
n
g not
getti
n
g
t
h
e first
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
Michael
S
h
i
rts
Merge branch 'master' of git://git
.
gro
m
acs
.
org
/
gromacs
commit
|
commitdiff
|
tree
2009-12-19
Mic
h
ael Sh
i
rts
Committing to merge
commit
|
commitdiff
|
tree
2009-12-19
M
i
chael Shirts
commiting t
o
merge
.
commit
|
commitdiff
|
tree
2009-12-19
Michael Shirts
c
h
anged outpu
t
options to be
mor
e
concise in the d
i
sper
s
ion
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
M
i
chael Shirts
Some bug f
i
xe
s
for the dispersio
n
correction
.
commit
|
commitdiff
|
tree
2009-12-19
M
ichael Shirts
C
h
anging t
h
e c
p
t fi
l
e number; can
'
t qu
i
te get i
t
to
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
M
i
c
hael Shi
r
ts
Changing th
e
c
p
t
v
ersion; c
a
n't fig
u
re out how to prese
r
ve
.
.
.
commit
|
commitdiff
|
tree
2009-12-19
M
ichael Shir
t
s
Merge bra
n
ch
'master'
o
f gi
t
@git
.
grom
a
cs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-19
Mi
c
hae
l
Shirts
Making the code
thread
s
a
fe (removi
n
g the
s
tat
i
c
ints
.
.
.
commit
|
commitdiff
|
tree
2009-12-17
Michael Shirts
Merge
branch 'master' of g
i
t@git
.
gromacs
.
org
:
gromacs
commit
|
commitdiff
|
tree
2009-12-17
Mich
a
el Shirts
add
e
d back i
n
n
o
sehoover_x
i
t
o
t
p
r
t
o av
o
id in
c
o
m
p
a
tibilitie
s
.
commit
|
commitdiff
|
tree
2009-12-17
Michael Sh
i
rts
Ch
a
n
g
ed eiVV2 to eiV
V
AK, and "md-vv2" to
"md-vv
-
a
v
ek
.
.
.
commit
|
commitdiff
|
tree
2009-12-05
Michae
l
Shirts
fix for rerun printing
commit
|
commitdiff
|
tree
2009-12-05
Michael Shirts
m
a
de s
o
m
e outpu
t
fixes
.
commit
|
commitdiff
|
tree
2009-12-05
Mi
c
hael Shi
r
ts
Merge branch 'mast
e
r
'
of git@git
.
g
r
o
macs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-12-04
M
ichael Shirt
s
trying to get parallel ver
s
ion
c
or
r
ect
.
commit
|
commitdiff
|
tree
2009-12-04
M
i
chael Shirts
Rewrite of the half-s
t
ep ekin
f
o
r velo
c
ity verlet,
.
.
.
commit
|
commitdiff
|
tree
2009-11-30
Michael
S
h
ir
t
s
More ch
a
nges to get it workin
g
with
E
kinA
v
eEkin
commit
|
commitdiff
|
tree
2009-11-30
Mich
a
el
S
hirts
More
f
ixes for corr
e
ct
pressure with EkinAveEk
i
n
commit
|
commitdiff
|
tree
2009-11-30
Michael
S
hirts
Committin
g
another fix!
commit
|
commitdiff
|
tree
2009-11-30
Micha
e
l Shirt
s
T
y
p
o
fi
x
.
commit
|
commitdiff
|
tree
2009-11-30
Mic
h
a
e
l Shirts
Fixed t
y
po
-- correct |
to ||
commit
|
commitdiff
|
tree
2009-11-30
Michael
Sh
i
rts
Ano
t
her try f
o
r gettin
g
paral
l
el p
r
essure computation
.
.
.
commit
|
commitdiff
|
tree
2009-11-30
Michae
l
Shirt
s
F
i
x
that
will
he
l
pfully s
o
lve proble
m
s for parallel
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mi
c
h
ael Shirt
s
Fixed
a bug introduced a few
com
m
its
a
go f
o
r iterat
i
ve
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
M
i
chael Shirts
Added s
o
me expla
n
ati
o
n on a cod
e
b
it that may
need
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
M
i
chae
l
Shirts
Added some
min
o
r
typo fixes
.
Shou
l
d check to make
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Michael
Shirts
Reversion of last checking -- didn't h
e
lp
.
commit
|
commitdiff
|
tree
2009-11-29
Micha
e
l S
h
irts
Fix for set900np
t
with Ek
i
nAve
commit
|
commitdiff
|
tree
2009-11-29
Mich
a
el Shirts
Change for paral
l
elization
of pre
s
sur
e
calcu
l
a
t
ion
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Michae
l
Sh
i
rts
Fix for p
a
ral
l
el
te
m
perature and pr
e
ssure on initial
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
M
i
c
hael Sh
i
rts
New attempt to correctly pass paral
l
el informati
o
n
.
.
.
commit
|
commitdiff
|
tree
2009-11-29
Mic
h
ael Shirts
Typo
f
ix
commit
|
commitdiff
|
tree
2009-11-29
Mic
h
a
e
l Shirts
Revert "Attempt to get para
l
lelization
w
orking correctly
.
"
commit
|
commitdiff
|
tree
2009-11-29
M
i
chael Shirt
s
At
t
empt t
o
make the pressu
r
e
w
ork in parallel!
commit
|
commitdiff
|
tree
2009-11-29
Michael Shirts
Attempt
t
o get parallel
i
zat
i
on working c
o
rrec
t
ly
.
commit
|
commitdiff
|
tree
2009-11-28
Mic
h
ael S
h
irts
Workin
g
for checkpointing in the same way
as the CVS
.
.
.
commit
|
commitdiff
|
tree
2009-11-28
Michael Shirts
Checkpoint
s
no
w
work in the single proc
e
ssor case
commit
|
commitdiff
|
tree
2009-11-28
Michael Shi
r
ts
Majo
r
it
y
of co
m
mi
t
s for correct checkp
o
i
n
ting
.
commit
|
commitdiff
|
tree
2009-11-27
Mi
c
h
a
el Shirts
Merg
e
branch 'm
a
s
t
e
r
' of git@git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2009-11-26
Michael Shirt
s
Correct
i
on to use the reference
pressure, not
t
h
e ex
t
ernal
.
.
.
commit
|
commitdiff
|
tree
2009-11-26
M
i
chael Shir
t
s
Change
d
the pV term to the
c
orrect one, w
i
t
h
the reference
.
.
.
commit
|
commitdiff
|
tree
2009-11-23
Michae
l
Shi
r
ts
C
o
mmenting cleanup
.
commit
|
commitdiff
|
tree
2009-11-23
M
ichael Shi
r
ts
Apparently works
w
ith all the
methods
n
ow
,
bo
t
h with
.
.
.
commit
|
commitdiff
|
tree
2009-11-22
M
ichael S
h
irts
Checkin
g
i
n code th
a
t does all but NPT av
e
rage Ekin
.
commit
|
commitdiff
|
tree
2009-11-21
M
ichael Sh
i
rts
Work
i
ng: md
(
matches all)
,
NVE,NVT,NP
T
Eki
n
A
ve
V
el,
.
.
.
commit
|
commitdiff
|
tree
2009-11-20
Michael S
h
irts
Wo
r
king with velocity verlet
/ h
a
rmonic b
o
n
d
s wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2009-11-20
Michael Shirts
Almost work
i
ng now! not vv for average
k
in
e
tic energy
.
.
.
commit
|
commitdiff
|
tree
2009-11-19
M
i
chael Shirts
Partway through with rati
o
nalization of different int
e
gr
a
tor
.
.
.
commit
|
commitdiff
|
tree
2009-11-18
Micha
e
l Shirts
F
ix
for kinetic average
e
n
ergy
.
commit
|
commitdiff
|
tree
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