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Fix cmake Sphinx detection for versions >1.6.4
2012-01-31
David v
a
n der Spoel
Changed
order of parame
t
ers in top file
commit
|
commitdiff
|
tree
2012-01-25
David van der Spo
e
l
Add
e
d two n
e
w bonded
f
unctions
.
commit
|
commitdiff
|
tree
2012-01-22
Davi
d
van der Spoel
M
erge "Print context on r
e
fe
r
ence
data
ch
e
ck
failure
.
"
commit
|
commitdiff
|
tree
2012-01-20
D
avid van der
Sp
o
el
Merge "Fixed timing measureme
n
ts
.
"
i
n
to
release-4-5
.
.
.
commit
|
commitdiff
|
tree
2012-01-17
D
avid van der Spo
e
l
R
e
plac
e
stderr by std
o
u
t in editconf
t
erminal output
.
.
.
commit
|
commitdiff
|
tree
2012-01-04
David van der Spoel
I
n
troduced fatal error in grompp for incorrect
use
.
.
.
commit
|
commitdiff
|
tree
2011-10-18
Davi
d
van de
r
Spo
e
l
Me
r
g
e
"Doxyg
e
n updates for fatalerror module
.
"
commit
|
commitdiff
|
tree
2011-10-18
David van de
r
Spoe
l
M
e
r
ge
"Misc
.
Doxyg
e
n improv
e
m
e
nts
.
"
commit
|
commitdiff
|
tree
2011-09-21
David va
n
der Spoel
C
o
mmente
d
out part of t
h
is
new program that was n
o
t
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
Dav
i
d van d
e
r Sp
o
el
Fixed documentation issue described in redmi
n
e issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-21
D
avi
d
v
a
n der Spoel
F
i
xed d
o
cume
n
tation issue d
e
scribed in redmine issue
.
.
.
commit
|
commitdiff
|
tree
2011-09-19
Davi
d
van der Spoel
Fixed com
p
i
lation issues
commit
|
commitdiff
|
tree
2011-09-19
David van der Spoel
Reso
l
ved gerrit i
s
sue
https://g
e
rrit
.
groma
c
s
.
o
rg/#change,126
commit
|
commitdiff
|
tree
2011-09-13
David
van der
S
poel
Added w
a
rnin
g
l
i
ne
.
commit
|
commitdiff
|
tree
2011-07-20
David van der
S
po
e
l
M
erge branch 'release-4-5-patches' of
g
i
t
@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-07-20
Dav
i
d van der Spoel
Added
i
nitialization
o
f arrays after sren
e
w c
a
ll
.
commit
|
commitdiff
|
tree
2011-07-20
David
v
an de
r
Spoel
Added initialization
of arrays after srenew
ca
l
l
.
commit
|
commitdiff
|
tree
2011-07-02
David van
d
e
r Spoel
Merge br
a
nch 'master' of git@git
.
gr
o
ma
c
s
.
org:gro
m
acs
commit
|
commitdiff
|
tree
2011-07-02
D
a
vid van der
S
poel
Compilation fix
e
s in gmx_density
.
c and histo
g
ram
.
c
p
p
commit
|
commitdiff
|
tree
2011-07-01
Davi
d
van der
Spoel
M
erge bra
n
ch '
r
elease-4
-
5-patches' of git@git
.
g
r
omacs
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
David van
d
er Spoel
M
erge b
r
anch 'r
e
lease-4-5
-
patch
e
s' of git@git
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2011-06-10
David van der
S
po
e
l
A
d
ded g_dos
target
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id
van der Spoel
Furt
h
e
r patches to fluctuation code and
d
e
n
sity
of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van
der Spoe
l
A
d
ded
comp
u
t
ation of
A and U
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id van der Spoel
Up
d
ated,
made default tol
e
r
a
nce for bisector more stringen
t
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vid van der
Spoel
Fix
e
d w
e
i
g
ht functions and a
d
ded -du
m
p opti
o
n (hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
avi
d
va
n
der Spoel
U
pdated
.
F
ixed computation of fre
q
uency
.
commit
|
commitdiff
|
tree
2011-05-31
David va
n
der Spoel
Updated t
h
e eqn for computing
Delta
.
No
w
get
r
oughly
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
Davi
d
v
a
n der S
p
oe
l
Mu
l
tipl
i
ed the D
o
S by the timest
e
p (betwe
e
n frames)
.
commit
|
commitdiff
|
tree
2011-05-31
David va
n
der
Spoe
l
Updated
.
N
o
w computes diffusion from the VACF
.
commit
|
commitdiff
|
tree
2011-05-31
D
avi
d
van der S
p
oel
Fixed x-axis to be in reciprocal cm
.
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d
van der Sp
o
el
Further updates
.
Still not perfec
t
.
commit
|
commitdiff
|
tree
2011-05-31
Da
v
id v
a
n der Sp
o
el
Added stuff t
o
comp
u
te cP and S
.
Not
complete ye
t
.
commit
|
commitdiff
|
tree
2011-05-31
David van de
r
Spoel
Updated to c
o
mput
e
t
h
e fl
u
idicity
.
A
dd
e
d
r
efs
f
or citation
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Spoel
U
p
dated
commit
|
commitdiff
|
tree
2011-05-31
David van de
r
Spoel
N
ew
commit
|
commitdiff
|
tree
2011-05-31
Dav
i
d
van der Spoel
Further pat
c
hes to fl
u
ctua
t
ion co
d
e and
d
ensity of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
David van
d
er Spoel
Merge b
r
anch 'm
a
s
t
er' of gi
t
@git
.
gromacs
.
o
rg:g
r
omac
s
commit
|
commitdiff
|
tree
2011-05-31
David
van der Spoel
Added quote
.
commit
|
commitdiff
|
tree
2011-05-31
David van der
S
poel
Further pat
c
hes to fluctuation code a
n
d
d
e
nsity of
.
.
.
commit
|
commitdiff
|
tree
2011-05-31
D
a
vi
d
van der Spoel
A
dded quote
.
commit
|
commitdiff
|
tree
2011-05-31
David van der Sp
o
el
M
erge branch 'r
e
leas
e
-4-5-patche
s
' of git@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David
v
an der Spo
e
l
Merge br
a
nc
h
'release-4-5
-
patches' of gi
t
@git
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
Dav
i
d van
d
er Spoel
Re-implem
e
nt
e
d the fluctuatio
n
analys
i
s,
b
ased on
E
nthalpy
.
.
.
commit
|
commitdiff
|
tree
2011-05-23
David van der Spoel
Re-imple
m
en
t
ed the fluc
t
uation a
n
aly
s
is, based on
E
nthalp
y
.
.
.
commit
|
commitdiff
|
tree
2011-05-07
David van der Sp
o
el
Added com
p
utatio
n
of A
and U
.
commit
|
commitdiff
|
tree
2011-05-06
D
a
vid van der Spoel
Updated,
made defau
l
t tolerance for bise
c
tor more
s
t
r
in
g
ent
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
David van der Sp
o
el
Fix
e
d
weight functions
a
n
d added
-dump opti
o
n
(hidden
.
.
.
commit
|
commitdiff
|
tree
2011-05-06
David van
d
e
r Spoel
Update
d
.
Fixed comput
a
tion
o
f fre
q
uency
.
commit
|
commitdiff
|
tree
2011-05-06
Dav
i
d
van der Spoel
Mer
g
e branch 'rele
a
se-4-5-pa
t
c
h
es' of gi
t
@gi
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-05-02
David van der S
p
oel
Updated the eqn for com
p
uting Delta
.
Now get roughly
.
.
.
commit
|
commitdiff
|
tree
2011-05-01
Davi
d
van der Spoel
Multiplied the DoS by the
timestep (bet
w
een frames)
.
commit
|
commitdiff
|
tree
2011-04-26
David van der S
p
oel
Updated
.
Now
com
p
utes diff
u
sion from the VACF
.
commit
|
commitdiff
|
tree
2011-04-23
D
avid va
n
der Spoel
Fix
e
d x
-
axis to be i
n
reci
p
r
o
cal cm
.
commit
|
commitdiff
|
tree
2011-04-23
David van de
r
S
p
oel
Furthe
r
updates
.
Stil
l
not per
f
e
ct
.
commit
|
commitdiff
|
tree
2011-04-22
David van der Spo
e
l
A
d
ded stuff to c
o
mpute cP and S
.
Not com
p
lete y
e
t
.
commit
|
commitdiff
|
tree
2011-04-21
David van der Spoe
l
Update
d
to co
m
pute the fluidici
t
y
.
Added
refs f
o
r citation
.
commit
|
commitdiff
|
tree
2011-04-21
Da
v
id va
n
der Spoel
Fir
s
t v
e
rsion
of a Density of States
analysis to
o
l
.
commit
|
commitdiff
|
tree
2011-04-10
David
v
an der Spoel
Me
r
ge
b
ran
c
h 're
l
e
ase-4-5-patche
s
' of gi
t
.
gromacs
.
o
r
g
.
.
.
commit
|
commitdiff
|
tree
2011-04-10
D
avid
van
der Spoel
Added g
_
hydo
r
de
r
.
1 man
p
age
.
commit
|
commitdiff
|
tree
2011-04-06
D
a
vid van
d
er Spoel
Fix
e
d
h
eader for gmx_
c
onect_in
i
t
commit
|
commitdiff
|
tree
2011-04-06
D
avi
d
van d
e
r Spoel
Fi
x
ed h
e
ader for gmx_conect_init
commit
|
commitdiff
|
tree
2011-04-04
Dav
i
d van der
Spoel
M
erge b
r
anch 're
l
ea
s
e-4-5-patches'
of g
i
t
@
g
it
.
gr
o
m
a
cs
.
.
.
commit
|
commitdiff
|
tree
2011-04-04
David
v
an de
r
Spoel
Removed superfluous fi
l
e
.
commit
|
commitdiff
|
tree
2011-04-04
David van de
r
Sp
o
el
Made new
programs compile with
gcc -peda
n
tic
.
commit
|
commitdiff
|
tree
2011-04-04
David v
a
n der
S
p
oel
New en
t
ry
commit
|
commitdiff
|
tree
2011-04-04
David van
der Spoel
A
dded 1 analy
s
is tool
manua
l
.
commit
|
commitdiff
|
tree
2011-04-04
D
avid van der S
p
oel
Merge branch 'r
e
lease-4-5-p
a
tches' into orderparm
commit
|
commitdiff
|
tree
2011-04-04
David va
n
der Spoel
L
a
test
f
ixes from Bjor
n
Steen Saethre
commit
|
commitdiff
|
tree
2011-03-24
Da
v
id van de
r
Spoel
Add
e
d Bjorn's code, imp
l
eme
n
ted run
n
i
ng average filterin
g
.
commit
|
commitdiff
|
tree
2011-03-05
D
avid van
d
er Spoel
Merge
b
ranch 'rel
e
ase-4-5-patches
'
of gi
t
@
g
i
t
.
gromac
s
.
.
.
commit
|
commitdiff
|
tree
2011-03-05
David van
der Spoel
F
i
xed SEGV in
e
necon
v
w
h
en u
s
ing the -e flag
.
commit
|
commitdiff
|
tree
2011-01-30
David van
der Spoel
Fixed more PBC and i
n
d
e
xing stuff
.
commit
|
commitdiff
|
tree
2011-01-30
David van der Spoel
Fixed typo
.
commit
|
commitdiff
|
tree
2011-01-30
David van der Spoel
Merge
b
r
anch
'
release-4-5-patch
e
s
'
into orderparm
commit
|
commitdiff
|
tree
2011-01-29
Dav
i
d van de
r
Spoel
Merge
br
a
nc
h
're
l
ease-4-
5
-patches' of g
i
t
@
g
i
t
.
gromacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-29
David van der Spoel
Added c
o
de in g_nmeig to compute the quan
t
u
m
corrections
.
.
.
commit
|
commitdiff
|
tree
2011-01-26
Da
v
id van der Spoel
Merge bra
n
ch
'
release-4-5-patches' of
gi
t
@g
i
t
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
D
a
vid van der Spoel
Fixed bug
6
78 wh
i
c
h was due to calling gmx_fatal
w
ithout
.
.
.
commit
|
commitdiff
|
tree
2011-01-22
David van der Spoel
Fixed
b
ug
678 which
was due to calling gmx_f
a
tal
without
.
.
.
commit
|
commitdiff
|
tree
2010-12-26
Davi
d
va
n
der Spoel
Merge
br
a
nch
'
release-4-5-patche
s
' of git@
g
it
.
g
romacs
.
.
.
commit
|
commitdiff
|
tree
2010-12-25
David van der
S
poel
Ad
d
ed
war
n
ing in
g
_dipoles
commit
|
commitdiff
|
tree
2010-12-23
David van der Sp
o
el
Merge br
a
nch '
r
elease-4-5
-
patches'
commit
|
commitdiff
|
tree
2010-12-23
D
avid van d
e
r Spoel
F
i
xe
d
bug in statist
i
cs w
h
i
c
h did not allow fit
t
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
David
v
a
n
der Spoel
M
e
rge branch 'release-4-5-patches'
commit
|
commitdiff
|
tree
2010-12-11
David van
der Spoel
Merge
branch 're
l
e
ase-4-5-patch
e
s
'
o
f
g
it
.
gromacs
.
org
.
.
.
commit
|
commitdiff
|
tree
2010-12-11
David van
der Spoel
Merge branch 'mas
t
er' of git
.
gromacs
.
org:gromacs
commit
|
commitdiff
|
tree
2010-12-11
David van d
e
r Sp
o
e
l
M
erge branch 'release-4-5-patches
'
commit
|
commitdiff
|
tree
2010-12-11
Dav
i
d
v
a
n de
r
Spoel
Added 1 qu
o
t
e
.
commit
|
commitdiff
|
tree
2010-12-09
Dav
i
d
van
d
er Spoel
Mer
g
e branch '
r
elea
s
e-4-5-patche
s
'
commit
|
commitdiff
|
tree
2010-12-09
David
v
an der Spoe
l
Added
fata
l
error for w
h
en
people use e
n
erg
y
fi
l
es
.
.
.
commit
|
commitdiff
|
tree
2010-11-28
David
van der Spoel
M
erge branch 'rele
a
se-4-5-patches'
commit
|
commitdiff
|
tree
2010-11-28
D
a
vi
d
van
der Spoel
Fixed bugzi
l
l
a
616 about f
o
rmatting in the hel
p
t
e
x
t
.
commit
|
commitdiff
|
tree
2010-11-26
David van d
e
r Spoel
Fixed SEGV b
u
g in g_sham
.
commit
|
commitdiff
|
tree
2010-11-18
David
va
n
der S
p
oel
Ma
d
e
p
rinting i
n
c
heck_multi_in
i
t condition
a
l
,
depending
.
.
.
commit
|
commitdiff
|
tree
2010-11-05
David van der Sp
o
el
Fixed compil
a
tion
issue
.
commit
|
commitdiff
|
tree
2010-11-05
David v
a
n der Spoel
Fixe
d
compilation
iss
u
e
.
commit
|
commitdiff
|
tree
2010-11-05
D
avi
d
van der Spoel
Added
flag
t
o
g
m
x
_st
a
t
s
_
g
e
t_po
i
nt
commit
|
commitdiff
|
tree
2010-11-02
David va
n
der Spoe
l
Fixed bug 608
b
y throwing a fatal error in grompp
.
commit
|
commitdiff
|
tree
2010-10-28
Davi
d
van
d
er Sp
o
el
Me
r
ge br
a
n
c
h 'release-4-5-
p
atches' of git
.
gr
o
macs
.
o
rg
.
.
.
commit
|
commitdiff
|
tree
next