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Use std::vector in nbnxn_search_t
2014-10-28
D
av
i
d van der Spo
e
l
Even more refr
e
shing
quotes
.
commit
|
commitdiff
|
tree
2014-10-14
D
avid
v
an der Spoel
Reorganizing analysis
o
f correlation functions
.
commit
|
commitdiff
|
tree
2014-09-23
Davi
d
va
n
de
r
S
p
o
e
l
Fixe
s
potential bug in n
e
ighborsear
c
hing
.
commit
|
commitdiff
|
tree
2014-09-17
David va
n
der S
p
oel
Merge
r
elease-5-0
into
ma
s
ter
commit
|
commitdiff
|
tree
2014-09-10
D
avid van der Spoel
R
e
m
ove
.
tpa
,
.
tp
b
,
.
tpx,
.
trj files
.
Par
t
of
#
1
500
.
commit
|
commitdiff
|
tree
2014-08-30
David v
a
n
d
e
r Spoel
Fixes is
s
ue with vsiten
and verlet buffers
.
commit
|
commitdiff
|
tree
2014-07-05
David van der Spoel
Fixed inconsistency
in blocka handlin
g
.
commit
|
commitdiff
|
tree
2014-06-29
David
van der Sp
o
el
Fixes
#
1532, SEGV in g_c
u
rrent
.
commit
|
commitdiff
|
tree
2014-06-25
Davi
d
van der Sp
o
el
Adde
d
che
c
k
f
or domain decomposition and shells
.
commit
|
commitdiff
|
tree
2014-06-24
David van d
e
r Spoel
Added check
in grompp for
shells a
n
d
inpu
t
rec is
s
ues
.
commit
|
commitdiff
|
tree
2014-06-22
Dav
i
d v
a
n der Spoel
Implemen
t
e
d f
a
tal error for nstcalcener
g
y!=1 wi
t
h shells
.
commit
|
commitdiff
|
tree
2014-06-13
D
a
vid van de
r
Sp
o
el
Fix
memory-usage error in g_ch
i
commit
|
commitdiff
|
tree
2014-06-11
D
a
vid van d
e
r Spoel
Fi
x
es
bug where -
e
an
d
-
d
t flags d
i
d
not work anymore
.
commit
|
commitdiff
|
tree
2014-06-07
David van
d
er Sp
o
el
Merge "Mer
g
e releas
e
-5-
0
i
n
to master
"
commit
|
commitdiff
|
tree
2014-06-07
Da
v
id van der
S
poel
Me
r
g
e
rele
a
s
e
-5-0 into
m
aster
commit
|
commitdiff
|
tree
2014-06-02
Da
v
id van der
S
p
oel
Fixed
w
r
ong journal
r
e
f
eren
c
e in manua
l
commit
|
commitdiff
|
tree
2014-05-31
Da
v
i
d
v
a
n der
Sp
o
e
l
P
ermit t
r
jconv to read and
write v
e
loc
i
ties
w
ith TNG
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
David van der Spoel
F
ixes a
c
o
m
plic
a
ted bug
in g_
a
naeig
.
commit
|
commitdiff
|
tree
2014-05-15
David van
d
er S
p
oel
Added cmake profiling suppo
r
t
commit
|
commitdiff
|
tree
2014-04-02
David van d
e
r Spoel
R
e
moved pos
s
ib
i
lit
y
of compiling with GSL
.
commit
|
commitdiff
|
tree
2014-03-31
Dav
i
d van der
Spoel
Fixed compilation iss
u
e in
f
grid
.
cpp
d
ue t
o
int/enum
commit
|
commitdiff
|
tree
2014-03-06
David
van der Spoe
l
Six new q
u
o
t
es f
r
om classi
c
litera
t
ure
.
commit
|
commitdiff
|
tree
2014-02-11
David van der Spo
e
l
Fixed a
n
o
ther vmdio
i
ssue
.
commit
|
commitdiff
|
tree
2014-02-10
D
avid van
der Sp
o
el
M
o
ved
conditional cmake code f
o
r vmdio
.
commit
|
commitdiff
|
tree
2014-01-28
David van der Spoe
l
Moved random num
b
er ge
n
erator code
t
o separa
t
e dir
.
commit
|
commitdiff
|
tree
2014-01-18
David van
d
er Spoel
Thi
s
patch move
s
the statis
t
ics librar
y
to its own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
D
avid van der Spoel
This
patch moves p
r
ep
r
ocessing head
e
r
s
to gmxpreproces
s
commit
|
commitdiff
|
tree
2014-01-15
David van d
e
r Spoel
Th
i
s p
a
tch moves the nrama
.
[ch
]
to the g
m
xana d
i
r
.
commit
|
commitdiff
|
tree
2014-01-13
David van
der
S
poel
C
leaned up list of GROMACS aut
h
ors
commit
|
commitdiff
|
tree
2014-01-09
David van der Spoel
F
ixed prec
i
sion
in thermal
e
xpans
i
on coef
f
icient
c
alc
.
commit
|
commitdiff
|
tree
2013-12-23
David
v
an der Spoel
Fixed comp
i
lat
i
on issue
d
ue
to
g
cc4
.
8
commit
|
commitdiff
|
tree
2013-12-21
Da
v
id van de
r
Sp
o
el
More No
b
e
l
quote
s
and others
commit
|
commitdiff
|
tree
2013-11-07
David van der Spoel
12 new
q
uotes
commit
|
commitdiff
|
tree
2013-09-30
David
v
a
n der
S
poel
Change name o
f
gmxdump to dum
p
and g
m
xc
h
eck to check
commit
|
commitdiff
|
tree
2013-09-29
D
a
vid va
n
der Spoe
l
Fixes bug in processing virtual_sitesn
in grompp
.
commit
|
commitdiff
|
tree
2013-09-26
David van der Spoel
Made M
W
of t
h
e V
s
i
te
p
arti
c
le ty
p
e
.
commit
|
commitdiff
|
tree
2013-09-21
David van de
r
S
p
oel
Moved
n
gmx
t
o
C
++, renam
e
d it to view
.
commit
|
commitdiff
|
tree
2013-08-30
D
a
vid v
a
n der Spoel
U
pdated g
_
c
lus
t
e
r
commit
|
commitdiff
|
tree
2013-07-24
David van der Spoel
Fixes #1312
u
niniti
a
lized
e
rror in g_en
e
mat
.
commit
|
commitdiff
|
tree
2013-07-17
David van der Spoel
A
dded citation to fre
e
volume paper
.
commit
|
commitdiff
|
tree
2013-06-14
David van der Spoel
New analysi
s
too
l
to comput
e
the free volume
and t
o
t
a
l
.
.
.
commit
|
commitdiff
|
tree
2013-05-30
Dav
i
d v
a
n der Spoel
Fix
e
s #11
9
4 erro
r
reading
4
.
5
.
5 tpr
f
iles
with di
h
res
commit
|
commitdiff
|
tree
2013-05-16
David va
n
d
er Spoel
Fixed two compila
t
ion
issues
.
commit
|
commitdiff
|
tree
2013-05-02
David van der Spoe
l
Fi
x
e
s #1238
g_hydor
d
er does no
t
call set_
p
bc
.
commit
|
commitdiff
|
tree
2013-05-01
David va
n
der Spoe
l
Merge
"
U
p
dated sou
r
ce for Van der Waals r
a
dii
.
"
commit
|
commitdiff
|
tree
2013-04-25
Davi
d
v
an der Spoel
Updated sourc
e
for Van der
W
a
als r
a
dii
.
commit
|
commitdiff
|
tree
2013-04-16
David van der Sp
o
e
l
Merge "cor
r
ected gr
o
mpp rvdw cha
r
ge-group rad
i
i check
.
.
.
commit
|
commitdiff
|
tree
2013-04-13
David van de
r
S
p
oel
Mer
g
e
"added mdrun
c
heck for Ve
r
let+pe
r
turbed atom
s
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
D
a
vid van de
r
Spoel
Mer
g
e
"Add his
t
ogram o
u
t
put f
o
r 'g
m
x gangle'
.
"
commit
|
commitdiff
|
tree
2013-03-07
D
avi
d
van de
r
S
poe
l
Fixes #1183 PBC bug in g_mi
n
dist
commit
|
commitdiff
|
tree
2013-02-15
Dav
i
d v
a
n der Spoel
Merge "Fixed an initializatio
n
issue in gmx
_
dipoles
.
.
.
commit
|
commitdiff
|
tree
2013-02-13
David van de
r
S
p
oel
Plain te
x
t quotes
.
commit
|
commitdiff
|
tree
2013-01-14
David van der Sp
o
el
Merge
"F
i
xi
n
g
t
rjconv -sub
"
into
release-4-5-patches
commit
|
commitdiff
|
tree
2013-01-14
David v
a
n der Spo
e
l
Merge "Noting that and w
h
y gmxdump -
s
-sys i
s
broken
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Davi
d
van der Spoel
Fixe
s
#9
9
4 confus
i
on in
a
tomp
r
op
.
commit
|
commitdiff
|
tree
2013-01-07
David v
a
n der Spoel
Merge
"
R
e
moved reference t
o
nonexiste
n
t file i
n
g
_helix
.
.
.
commit
|
commitdiff
|
tree
2012-11-27
David va
n
der Spoel
Merge "M
e
rge r
e
l
ease-4-5-patches i
n
to release-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-11-26
David van der Spoel
Fixe
s
#
1
0
3
5 NaN in g_cluster out
p
u
t
.
commit
|
commitdiff
|
tree
2012-11-20
David van
d
e
r Spo
e
l
Fix
e
s bug
in g_hbon
d
that makes
i
t
prod
u
ce fatal erro
r
.
commit
|
commitdiff
|
tree
2012-11-17
David van
d
er Spoel
Me
r
g
e
"Added grompp
warnin
g
"
into relea
s
e-4-6
commit
|
commitdiff
|
tree
2012-11-17
Dav
i
d van der Spoel
Merge "Remove res
t
o
f the xml sup
p
ort" into relea
s
e
-
4-6
commit
|
commitdiff
|
tree
2012-11-16
Da
v
id va
n
d
er Spo
e
l
Mer
g
e "Removes unuse
d
files" int
o
release-4-
6
commit
|
commitdiff
|
tree
2012-11-12
David
v
a
n
der Spoel
Fixes #1
0
20 options in g_enem
a
t
commit
|
commitdiff
|
tree
2012-10-26
David van der S
p
oe
l
M
erge
"
Fixed Pu
l
p Fiction q
u
ote"
into release-4
-
5
-
patches
commit
|
commitdiff
|
tree
2012-10-21
David van der
S
p
oel
Fi
x
ed Bug #593 about memor
y
hol
e
in trjca
t
.
commit
|
commitdiff
|
tree
2012-10-13
David
v
an der Spoel
Mer
g
e "Fi
x
ing is
s
u
e
s
wi
t
h
repl
i
ca exchange" into release-4-6
commit
|
commitdiff
|
tree
2012-10-12
David van
d
er Sp
o
el
Mer
g
e
"[tool
s
] g_sans - add trajectory aver
e
ging"
commit
|
commitdiff
|
tree
2012-10-04
David van der Sp
o
el
Set
r
etur
n
v
alu
e
t
o F
A
L
S
E
(0) in
e
sti
m
ate_dt in libxd
r
f
.
c
commit
|
commitdiff
|
tree
2012-09-15
Da
v
id van der Spoel
M
erge "Adapted NMR rel
a
ted data to
new pdb fo
r
mat
.
.
.
.
commit
|
commitdiff
|
tree
2012-09-07
David
van der Spo
e
l
Adapted NMR rel
a
ted da
t
a to n
e
w pdb
format
.
commit
|
commitdiff
|
tree
2012-09-04
David van der Spoel
M
a
de t
u
to
r
ial
s
lightly less confusing
.
commit
|
commitdiff
|
tree
2012-08-16
David van
d
e
r
Spoel
Optional computatio
n
of
fluct
.
pro
p
s in g_energy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-07-15
David van der Spoel
Merge "Autogenerat
e
gromacs
.
7 from pr
o
grams
.
tx
t
" i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2012-07-05
David van der Spoel
Merge "Improve Pr
o
gramInfo
a
nd use it e
v
e
rywhere
.
"
commit
|
commitdiff
|
tree
2012-06-30
David va
n
der Spoel
Fixed bug in free
e
nergy calcul
a
ti
o
n for Mo
r
se potentials
commit
|
commitdiff
|
tree
2012-06-21
D
a
vid
van der
Sp
o
e
l
Fixes #9
6
1 - Sh
a
ke
r
e
ports wrong
er
r
or
commit
|
commitdiff
|
tree
2012-06-16
David van der Spoel
F
i
xes #882 - l
o
oping bug in trxio
.
c
commit
|
commitdiff
|
tree
2012-05-27
David van der Spo
e
l
Merge "added explici
t
s
q
r
tf to the float ver
s
ion of
.
.
.
commit
|
commitdiff
|
tree
2012-05-25
Da
v
id
van der
S
p
oel
Merge "grompp
n
o
w retains th
e
order of bonds converted
.
.
.
commit
|
commitdiff
|
tree
2012-05-03
David van de
r
S
p
oel
Merge
"Removed unused code from src/kernel/
.
"
commit
|
commitdiff
|
tree
2012-04-29
David van der Spoel
M
erge "changed num
b
e
r of iatoms for F_SETTLE from 1
.
.
.
commit
|
commitdiff
|
tree
2012-04-29
David van
d
er Spo
e
l
Merge "
a
d
d
ed suppor
t
f
or grap
h
s no
t
st
a
rting at 0"
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
Dav
i
d van
der Spoe
l
Merge "[tools] g_
s
a
n
s - splited ou
t
fixes and a
d
d
ed
.
.
.
commit
|
commitdiff
|
tree
2012-04-26
D
avid van
der Spoel
Merge "Va
r
ious impr
o
vements
t
o shell code" into release
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
David van der
S
poel
Merge "A
d
d
ed
s
upp
o
rt for dssp2
.
X
with the -
v
er
o
p
tion
.
.
.
commit
|
commitdiff
|
tree
2012-04-16
D
a
vid van
d
er Spoel
Merge "Expand
e
d the h
e
l
p
text regarding t
h
e
-
r2
and
.
.
.
commit
|
commitdiff
|
tree
2012-04-02
Davi
d
van de
r
Sp
o
el
Merge "Improve
d
pdb2gmx error message"
into releas
e
.
.
.
commit
|
commitdiff
|
tree
2012-03-18
David van
d
er Spoel
Merge "F
i
x typo in Clang CFl
a
gs" into release-4-
5
-
p
atch
e
s
commit
|
commitdiff
|
tree
2012-03-18
Davi
d
van der
Sp
o
e
l
Merge "Merge release
-
4-5-patches into relea
s
e-4-6"
.
.
.
commit
|
commitdiff
|
tree
2012-03-17
David
v
an der Spoel
Removed qhop files f
r
om
this
b
r
anch
.
commit
|
commitdiff
|
tree
2012-03-10
David van d
e
r Spoel
Vibration spectra from velocit
y
A
C
F or Nor
m
al modes
.
commit
|
commitdiff
|
tree
2012-03-09
D
avid v
a
n
d
er Spoe
l
Me
r
g
e "Impr
o
ved cryptic error mess
a
ge" into release
.
.
.
commit
|
commitdiff
|
tree
2012-03-08
D
a
vid
v
an der Spoel
Merge "
M
i
nimal support
f
o
r Clang"
in
t
o release
-
4-
5
.
.
.
commit
|
commitdiff
|
tree
2012-02-25
Da
v
i
d
van der Spoel
Merge "Minor f
o
rmat
t
ing fixes t
o
.
mdp option documentation
.
.
.
commit
|
commitdiff
|
tree
2012-02-03
David
v
an
der Spoel
Merge "
I
mproved
the accuracy o
f
the sd1
integ
r
a
t
o
r
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
D
avi
d
v
a
n der Sp
o
el
M
e
r
ge "g_sans - tool
t
o comp
u
te SANS spectr
a
" into
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David va
n
d
er Spoel
Merge
"Fixed
error mess
a
ge
to ide
n
t
i
f
y
the
c
orrect
.
.
.
commit
|
commitdiff
|
tree
2012-02-01
David van
d
er Spoel
Merge "Fixed trjconv -sub" into releas
e
-4-
5
-patch
e
s
commit
|
commitdiff
|
tree
2012-02-01
David van
d
er Spo
e
l
Mer
g
e "Improved error message" into release-4-5
-
patc
h
es
commit
|
commitdiff
|
tree
2012-01-31
Da
v
id van der Spoel
Me
r
ge "Fi
x
I
CC on Wi
n
dows Build" into r
e
leas
e
-
4
-
5-patches
commit
|
commitdiff
|
tree
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