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Merge "Misc. Doxygen improvements."
2011-10-18
David van
der Spoel
Merg
e
"Misc
.
Do
x
y
g
en improvements
.
"
commit
|
commitdiff
|
tree
2011-07-20
David
v
an d
e
r S
p
oel
Added
initialization
o
f arrays after srenew cal
l
.
commit
|
commitdiff
|
tree
2011-07-02
D
a
vid van der S
p
oel
Mer
g
e branch
'
mast
e
r' of
g
it@git
.
gromacs
.
or
g
:gromac
s
commit
|
commitdiff
|
tree
2011-07-02
D
a
vi
d
van der
S
poel
Compilation
f
ix
e
s in gmx
_
density
.
c and hi
s
togram
.
cpp
commit
|
commitdiff
|
tree
2011-06-10
David van der Spoel
A
dded g_dos target
.
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d
van der Spo
e
l
F
u
r
ther p
a
tche
s
to flu
c
tuation c
o
de and densit
y
of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
v
id van der S
p
o
e
l
Added computation of
A a
n
d U
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Sp
o
e
l
Updated, made defa
u
lt toleranc
e
for b
i
sect
o
r mor
e
stringent
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
va
n
der Spoel
Fix
e
d
weight f
u
nctions and add
e
d -du
m
p o
p
tion (hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d
van
der
S
poel
Up
d
ated
.
Fix
e
d computation of fr
e
qu
e
ncy
.
commit
|
commitdiff
|
tree
2011-05-31
David van de
r
Spo
e
l
Updated the eqn for computi
n
g D
e
l
ta
.
Now get
r
ou
g
hly
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spo
e
l
M
u
ltiplie
d
the DoS b
y
the timestep (between frames)
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id
v
an d
e
r
S
poel
Updat
e
d
.
Now
c
o
mp
u
tes
diffusion from the VAC
F
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
van der Spo
e
l
Fix
e
d x-axis to be in r
e
ciprocal
c
m
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Furthe
r
updates
.
Sti
l
l
not perfect
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
Ad
d
ed st
u
ff to co
m
pute cP and S
.
N
o
t co
m
ple
t
e yet
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoe
l
Updated to c
o
mput
e
the fluidicity
.
Added refs fo
r
citation
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van der Spoel
Update
d
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
van der
Spoel
New
commit
|
commitdiff
|
tree
2011-05-31
D
avid van de
r
Sp
o
el
Further pa
t
ches
t
o
fluctuation code and densit
y
of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David
va
n
der Spoel
Mer
g
e bra
n
ch 'master' of git@git
.
gromacs
.
org:
g
romacs
commit
|
commitdiff
|
tree
2011-05-31
D
avid van der Spoel
Add
e
d quot
e
.
commit
|
commitdiff
|
tree
2011-05-23
David van de
r
Spoel
Re-implem
e
nted the fl
u
ctuation analysis, b
a
sed on En
t
ha
l
py
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
D
av
i
d va
n
der
S
p
o
el
R
e
-imple
m
e
nted the fluctuatio
n
analysis, based on
E
nthalpy
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
David van der Spoel
Merge branch 'release-
4
-5-patches'
o
f git
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
D
a
vi
d
v
an
d
er Spoel
Added
g_
h
ydorder
.
1
m
a
n
pa
g
e
.
commit
|
commitdiff
|
tree
2011-04-06
Davi
d
van
d
er Spoel
Fixed header for
g
m
x
_conect_in
i
t
commit
|
commitdiff
|
tree
2011-04-06
D
a
vid van der Spoel
Fix
e
d header
f
or gmx_con
e
ct_init
commit
|
commitdiff
|
tree
2011-04-04
David van der Spoel
Merge branch 'release
-
4-5-
p
atch
e
s' of gi
t
@g
i
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-04-04
D
a
v
id van der Spoel
Removed sup
e
rfluous fil
e
.
commit
|
commitdiff
|
tree
2011-04-04
David van der
Spoel
Made n
e
w programs
c
o
m
p
i
le with gcc
-pedantic
.
commit
|
commitdiff
|
tree
2011-04-04
D
avid van
d
er Spoel
New entry
commit
|
commitdiff
|
tree
2011-04-04
D
a
v
id van der Spoel
Ad
d
ed
1
a
nal
y
s
i
s
tool manual
.
commit
|
commitdiff
|
tree
2011-04-04
Davi
d
v
an der Spo
e
l
M
erge branch 'release-4-5-
p
atches'
into orderpa
r
m
commit
|
commitdiff
|
tree
2011-04-04
David van der
S
poel
Lates
t
fixes fro
m
Bjorn Steen Saeth
r
e
commit
|
commitdiff
|
tree
2011-03-24
Da
v
id van der Spoel
Added Bjorn's co
d
e, impleme
n
ted
r
unning averag
e
filtering
.
commit
|
commitdiff
|
tree
2011-03-05
David
van der Spoe
l
Merge br
a
nch 'release-4-5-patches' of git@git
.
g
r
om
a
cs
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
David
van der Spo
e
l
Fi
x
ed S
E
GV in eneconv
when
u
s
ing the -e f
l
ag
.
commit
|
commitdiff
|
tree
2011-01-30
David
v
an der Spoel
Fixed
m
o
re PBC
a
n
d indexing stuff
.
commit
|
commitdiff
|
tree
2011-01-30
Dav
i
d
van der
S
poel
Fix
e
d typo
.
commit
|
commitdiff
|
tree
2011-01-30
David v
a
n der
S
p
o
el
M
erge
b
ranch 'relea
s
e-4-5-patches
'
into
o
rderparm
commit
|
commitdiff
|
tree
2011-01-29
D
a
vid
v
a
n der Spo
e
l
M
e
rge
branch 'release-
4
-5-
p
atches' o
f
git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
David van der
Spo
e
l
A
dd
e
d code in g_nmeig to compute the q
u
a
ntum corre
c
tions
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
David va
n
der Spoel
M
e
rge
b
ranch
'
relea
s
e-4-5-patches' of git@
g
it
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
Davi
d
van der Spoel
Fixed bug 678
which was
d
ue to calling g
m
x_fatal w
i
thout
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
David van der Spoel
Fixed bug 678
w
hich
w
as due to calling gmx_fatal
wit
h
out
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
David
van d
e
r
S
poel
Merge branch 'release-4-5-pa
t
ch
e
s
'
of
g
it@git
.
grom
a
cs
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
David van der
S
p
oel
A
d
ded warnin
g
in g_dipoles
commit
|
commitdiff
|
tree
2010-12-23
David
v
an der Spoel
Merge branch 'release
-
4
-5-patch
e
s'
commit
|
commitdiff
|
tree
2010-12-23
Dav
i
d va
n
der Spoel
Fixed b
u
g in st
a
tistics which did not
allow f
i
ttin
g
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
Davi
d
van der Spoel
Merge branch 'release-4-5-pa
t
ches'
commit
|
commitdiff
|
tree
2010-12-11
D
avid va
n
d
er Spoel
M
e
rge branch 're
l
ease-4-5-patc
h
es' of git
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
D
a
vid
van der
Spo
e
l
Mer
g
e branch
'master' o
f
git
.
gromacs
.
org:g
r
omac
s
commit
|
commitdiff
|
tree
2010-12-11
Davi
d
v
a
n der Spoel
M
erge branch 'release-4-5-pa
t
ches'
commit
|
commitdiff
|
tree
2010-12-11
David va
n
der Spoel
Added 1 q
u
ote
.
commit
|
commitdiff
|
tree
2010-12-09
Da
v
id van der Spoel
Merge
branch 'relea
s
e-4-5
-
patches'
commit
|
commitdiff
|
tree
2010-12-09
D
a
vid v
a
n de
r
Spoe
l
Added f
a
tal error for
when peo
p
le use ene
r
gy files
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
D
avid van de
r
Spoel
M
erge branch 'release-4-5-patches'
commit
|
commitdiff
|
tree
2010-11-28
D
a
vid van der Spoel
Fixed bug
z
i
l
la 616 about forma
t
ting in the help
t
e
x
t
.
commit
|
commitdiff
|
tree
2010-11-26
David van der Spoel
Fixed SEGV bug in g_sham
.
commit
|
commitdiff
|
tree
2010-11-18
D
a
vid van
der Spoel
Ma
d
e
p
ri
n
ting
i
n check_multi_init
conditional, d
e
pendin
g
.
.
.
commit
|
commitdiff
|
tree
2010-11-05
Davi
d
van
d
er Spoel
Fixed compilation is
s
ue
.
commit
|
commitdiff
|
tree
2010-11-05
David van
d
er Spoel
Fix
e
d
c
ompilation
i
ssue
.
commit
|
commitdiff
|
tree
2010-11-05
David va
n
der
S
poel
Added flag
t
o g
m
x
_
stats_get_point
commit
|
commitdiff
|
tree
2010-11-02
David va
n
d
er Spo
e
l
Fixed bug
6
08
by thr
o
wing a fa
t
al erro
r
i
n
grompp
.
commit
|
commitdiff
|
tree
2010-10-28
Davi
d
van d
e
r Spoel
M
e
rge br
a
nch 're
l
ea
s
e
-
4-5-patches' of
git
.
gr
o
macs
.
or
g
.
.
.
commit
|
commitdiff
|
tree
2010-10-28
David v
a
n
der S
p
oel
Fixed bug
604
as reques
t
ed
.
commit
|
commitdiff
|
tree
2010-10-08
Davi
d
van der
S
p
o
el
Merge br
a
nch '
r
elease-4-5-patches
'
of
g
it
.
gromacs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
2010-10-07
David va
n
d
e
r Spoel
Fi
x
ed compila
t
i
o
n
i
ssues wi
t
h C99
c
ompa
t
ibility
.
commit
|
commitdiff
|
tree
2010-10-07
Davi
d
van d
e
r Spoel
Fixes and small
additions to
g_wha
m
, due
t
o
Jo
c
h
en
.
.
.
commit
|
commitdiff
|
tree
2010-09-28
David van der Spoel
Re-added g_
k
ineti
c
s to src/tools/M
a
kefile
.
am
commit
|
commitdiff
|
tree
2010-09-25
David van der Spo
e
l
Merge
b
r
an
c
h
'release-4
-
5-patches'
commit
|
commitdiff
|
tree
2010-09-25
Dav
i
d v
a
n de
r
Spoel
Add
e
d softw
a
re-related q
u
ote
commit
|
commitdiff
|
tree
2010-09-24
David van der Spoel
Updated to r
e
f
l
ec
t
bug 557
.
commit
|
commitdiff
|
tree
2010-09-20
David van der Spo
e
l
M
erge branch 'releas
e
-4-5-
p
atches'
o
f g
i
t@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2010-09-20
David va
n
der Spo
e
l
Merge branch 'mast
e
r'
of
git@git
.
gromac
s
.
o
r
g:gromacs
commit
|
commitdiff
|
tree
2010-09-20
Da
v
i
d
van der Spoel
Me
r
g
e branc
h
'rel
e
ase-4-
5
-patches'
commit
|
commitdiff
|
tree
2010-09-20
David van der Spoel
F
ixe
d
b
ug http://bu
g
z
i
lla
.
gromacs
.
org/show_bug
.
cgi
.
.
.
commit
|
commitdiff
|
tree
2010-09-17
David va
n
der Spoel
Remo
v
ed gmx_membed from cmak
e
f
i
le
s
as well
.
commit
|
commitdiff
|
tree
2010-09-16
Davi
d
van der Spo
e
l
Mer
g
e bra
n
ch 'relea
s
e-4-5-patches'
commit
|
commitdiff
|
tree
2010-09-16
David van der
Spo
e
l
Correcte
d
name of
o
n
e of the developers listed in header
.
commit
|
commitdiff
|
tree
2010-09-14
D
avid van der Spo
e
l
Mer
g
e
branch 'release-4-5-patches'
commit
|
commitdiff
|
tree
2010-09-14
Davi
d
van der Spo
e
l
Fixed bug 553
b
y checking
whether an atom name i
s
longer
.
.
.
commit
|
commitdiff
|
tree
2010-09-12
David van
d
er
Spo
e
l
Fixed
d
em
o
t
o
work
w
ith
n
ew pdb
2
gmx that r
e
qui
r
es two
.
.
.
commit
|
commitdiff
|
tree
2010-08-30
David van der Spo
e
l
D
isabled compilation of g_membed for the time being
.
commit
|
commitdiff
|
tree
2010-08-30
David
v
an der Spo
e
l
Me
r
ge bra
n
ch
'
release-
4
-
5
-
patche
s
'
commit
|
commitdiff
|
tree
2010-08-30
David van der Spoel
Added one
q
uot
e
.
commit
|
commitdiff
|
tree
2010-08-27
Dav
i
d
v
an der Spoel
Disabled building template because i
t
d
oe
s
not
compile !
commit
|
commitdiff
|
tree
2010-08-25
David van der
S
poel
Fixed co
m
pilation of the
s
e re
s
olved
co
n
f
l
ict
s
as well
.
.
.
commit
|
commitdiff
|
tree
2010-08-25
David van de
r
Spoel
fixed con
f
li
c
t
s
.
commit
|
commitdiff
|
tree
2010-08-25
Dav
i
d van der
Spoel
Merge
branch 'release-4-5-pat
c
h
es'
commit
|
commitdiff
|
tree
2010-08-25
David
van der
S
poel
Made genrestr -constr to pro
d
uce cons
t
r
a
i
nts of type
.
.
.
commit
|
commitdiff
|
tree
2010-08-22
David van der Sp
o
el
Merge branch '
r
el
e
ase-4-5-patches'
commit
|
commitdiff
|
tree
2010-08-22
D
avid v
a
n der Spoel
Fixed b
u
g 417
.
commit
|
commitdiff
|
tree
2010-08-19
D
a
v
id van der Spoe
l
Fix
e
s more m
i
s
e
r
y in func
t
io
n
skipstr, wher
e
poin
t
e
r
s
.
.
.
commit
|
commitdiff
|
tree
2010-08-19
David van der Spoel
Added two missing incl
u
de file
s
.
Fixed horr
i
ble coding
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
Dav
i
d
v
a
n der Spoel
A
d
ded hea
d
er file
to physic
s
.
c
commit
|
commitdiff
|
tree
2010-08-16
David v
a
n de
r
S
po
e
l
Added routines to physics
.
c
for converting
a
string
.
.
.
commit
|
commitdiff
|
tree
2010-08-16
David van
der
Spoel
A
d
de
d
a
file physics
.
c
with routines that convert values
.
.
.
commit
|
commitdiff
|
tree
2010-08-11
David van
der S
p
oel
Added const in header for the s
p
lit function as well
.
commit
|
commitdiff
|
tree
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